ERROR ~ Failed to publish file

[DavideGue]

Description of the bug

I'am running the pipeline on Azure Cloud using Slurm and durum wheat WGS data and a custom RefSeq fasta file. The working directory is located on a blob storage.
The genome indexing task completed succesfully in the work dir ( I can see all index files) but I got an error message and in the directory /svevo/davide_tmp/outdir/reference/bwa one file out of five index files is missing

Command used and terminal output

nextflow run /nf-core-sarek_3.5.0/3_5_0/ -params-file nf-param2.json

executor >  slurm (88)
[c6/0781be] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[-        ] NFC…EPARE_GENOME:BWAMEM2_INDEX -
[-        ] NFC…E_GENOME:DRAGMAP_HASHTABLE -
[68/574f09] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[-        ] NFC…E_GENOME:MSISENSORPRO_SCAN -
[-        ] NFC…PARE_GENOME:SAMTOOLS_FAIDX -
[-        ] NFC…TABIX_BCFTOOLS_ANNOTATIONS -
[-        ] NFC…PREPARE_GENOME:TABIX_DBSNP -
[-        ] NFC…ME:TABIX_GERMLINE_RESOURCE -
[-        ] NFC…RE_GENOME:TABIX_KNOWN_SNPS -
[-        ] NFC…_GENOME:TABIX_KNOWN_INDELS -
[-        ] NFC…K:PREPARE_GENOME:TABIX_PON -
[72/ff7847] NFC…VALS:BUILD_INTERVALS (fai) | 1 of 1 ✔
[1a/2fe29c] NFC…TE_INTERVALS_BED (fai.bed) | 1 of 1 ✔
[2f/77c417] NFC…hr6A_RagTag_2_1-131277541) | 27 of 27 ✔
[64/989ff6] NFC…IX_INTERVAL_COMBINED (fai) | 1 of 1 ✔
[-        ] NFC…RING_DECOMPRESS_TO_FQ_PAIR -
[-        ] NFC…SPRING_DECOMPRESS_TO_R1_FQ -
[-        ] NFC…SPRING_DECOMPRESS_TO_R2_FQ -
[-        ] NFC…NPUT:SAMTOOLS_VIEW_MAP_MAP -
[39/baabf1] NFC…SAREK:FASTQC (TdS2-lane_2) | 4 of 4 ✔
[c2/125407] NFC…:SAREK:FASTP (TdS2-lane_2) | 4 of 4 ✔
[e7/2a8860] NFC…:BWAMEM1_MEM (TdS2-lane_2) | 0 of 48
Plus 41 more processes waiting for tasks…
ERROR ~ Failed to publish file: /svevo/davide_tmp/workdir/c6/0781be4c222f8bf7d83ea0a5007716/bwa; to: /svevo/davide_tmp/outdir/reference/bwa [copy] -- See log file for details

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '.nextflow.log' file for details
-[nf-core/sarek] Pipeline completed with errors-
WARN: Killing running tasks (48)

Cleaning up...

Relevant files

output (3).log

nf-param2.json

System information

Azure cloud

[FriederikeHanssen]

This one here seems related: #712

[DavideGue]

Thank you for your reply. However, after following the suggestions in #712 we still get error message as below:
executor > slurm (88)
[4c/209d40] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…EPARE_GENOME:BWAMEM2_INDEX -
[- ] NFC…E_GENOME:DRAGMAP_HASHTABLE -
[23/3a4ff6] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…E_GENOME:MSISENSORPRO_SCAN -
[- ] NFC…PARE_GENOME:SAMTOOLS_FAIDX -
[- ] NFC…TABIX_BCFTOOLS_ANNOTATIONS -
[- ] NFC…PREPARE_GENOME:TABIX_DBSNP -
[- ] NFC…ME:TABIX_GERMLINE_RESOURCE -
[- ] NFC…RE_GENOME:TABIX_KNOWN_SNPS -
[- ] NFC…_GENOME:TABIX_KNOWN_INDELS -
[- ] NFC…K:PREPARE_GENOME:TABIX_PON -
[44/e6390c] NFC…VALS:BUILD_INTERVALS (fai) | 1 of 1 ✔
[92/ae71d1] NFC…TE_INTERVALS_BED (fai.bed) | 1 of 1 ✔
[2b/111741] NFC…hr6B_RagTag_2_1-225437615) | 27 of 27 ✔
[d8/c48447] NFC…IX_INTERVAL_COMBINED (fai) | 1 of 1 ✔
[- ] NFC…RING_DECOMPRESS_TO_FQ_PAIR -
[- ] NFC…SPRING_DECOMPRESS_TO_R1_FQ -
[- ] NFC…SPRING_DECOMPRESS_TO_R2_FQ -
[- ] NFC…NPUT:SAMTOOLS_VIEW_MAP_MAP -
[34/08b538] NFC…SAREK:FASTQC (TdS2-lane_2) | 4 of 4 ✔
[17/b03d7d] NFC…:SAREK:FASTP (TdS2-lane_2) | 4 of 4 ✔
[8c/550741] NFC…:BWAMEM1_MEM (TdS2-lane_2) | 0 of 48
Plus 41 more processes waiting for tasks…

executor > slurm (88)
[4c/209d40] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…EPARE_GENOME:BWAMEM2_INDEX -
[- ] NFC…E_GENOME:DRAGMAP_HASHTABLE -
[23/3a4ff6] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…E_GENOME:MSISENSORPRO_SCAN -
[- ] NFC…PARE_GENOME:SAMTOOLS_FAIDX -
[- ] NFC…TABIX_BCFTOOLS_ANNOTATIONS -
[- ] NFC…PREPARE_GENOME:TABIX_DBSNP -
[- ] NFC…ME:TABIX_GERMLINE_RESOURCE -
[- ] NFC…RE_GENOME:TABIX_KNOWN_SNPS -
[- ] NFC…_GENOME:TABIX_KNOWN_INDELS -
[- ] NFC…K:PREPARE_GENOME:TABIX_PON -
[44/e6390c] NFC…VALS:BUILD_INTERVALS (fai) | 1 of 1 ✔
[92/ae71d1] NFC…TE_INTERVALS_BED (fai.bed) | 1 of 1 ✔
[2b/111741] NFC…hr6B_RagTag_2_1-225437615) | 27 of 27 ✔
[d8/c48447] NFC…IX_INTERVAL_COMBINED (fai) | 1 of 1 ✔
[- ] NFC…RING_DECOMPRESS_TO_FQ_PAIR -
[- ] NFC…SPRING_DECOMPRESS_TO_R1_FQ -
[- ] NFC…SPRING_DECOMPRESS_TO_R2_FQ -
[- ] NFC…NPUT:SAMTOOLS_VIEW_MAP_MAP -
[34/08b538] NFC…SAREK:FASTQC (TdS2-lane_2) | 4 of 4 ✔
[17/b03d7d] NFC…:SAREK:FASTP (TdS2-lane_2) | 4 of 4 ✔
[8c/550741] NFC…:BWAMEM1_MEM (TdS2-lane_2) | 0 of 48
Plus 41 more processes waiting for tasks…
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1)'

Caused by:
Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1) terminated with an error exit status (1)

Command executed:

INDEX=find -L ./ -name "*.amb" | sed 's/\.amb$//'

bwa mem
-K 100000000 -Y -R "@rg\tID:null.TdS1.lane_1\tPU:lane_1\tSM:Sample1_TdS1\tLB:TdS1\tDS:/svevo/davide_tmp/MG5323_v0.5.splitchromosomes.w60.fasta\tPL:ILLUMINA"
-t 24
$INDEX
0004.TdS1-lane_1_1.fastp.fastq.gz 0004.TdS1-lane_1_2.fastp.fastq.gz
| samtools sort --threads 24 -o TdS1-lane_1.0004.bam -

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM":
bwa: $(echo $(bwa 2>&1) | sed 's/^.Version: //; s/Contact:.$//')
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.samtools //; s/Using.$//')
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
[M::mem_pestat] low and high boundaries for proper pairs: (1, 704)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667822 reads in 690.290 CPU sec, 28.926 real sec
[M::process] read 668024 sequences (100000140 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96666, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 352, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (100, 600)
[M::mem_pestat] mean and std.dev: (350.39, 73.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 700)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667928 reads in 746.042 CPU sec, 31.278 real sec
[M::process] read 667972 sequences (100000116 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96712, 3, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (298, 351, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (94, 604)
[M::mem_pestat] mean and std.dev: (349.00, 75.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 706)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 668024 reads in 685.185 CPU sec, 28.753 real sec
[M::process] read 667978 sequences (100000196 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97590, 6, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (96, 606)
[M::mem_pestat] mean and std.dev: (351.31, 75.03)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 708)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667972 reads in 668.546 CPU sec, 28.021 real sec
[M::process] read 667946 sequences (100000172 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97376, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (302, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (102, 602)
[M::mem_pestat] mean and std.dev: (352.14, 74.40)
[M::mem_pestat] low and high boundaries for proper pairs: (2, 702)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667978 reads in 733.688 CPU sec, 30.737 real sec
[E::aux_parse] Incomplete aux field
samtools sort: truncated file. Aborting

Work dir:
/svevo/davide_tmp/workdir/af/3d0de8f81836310dec69a79e28809e

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- Check '.nextflow.log' file for details

executor > slurm (88)
[4c/209d40] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…EPARE_GENOME:BWAMEM2_INDEX -
[- ] NFC…E_GENOME:DRAGMAP_HASHTABLE -
[23/3a4ff6] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…E_GENOME:MSISENSORPRO_SCAN -
[- ] NFC…PARE_GENOME:SAMTOOLS_FAIDX -
[- ] NFC…TABIX_BCFTOOLS_ANNOTATIONS -
[- ] NFC…PREPARE_GENOME:TABIX_DBSNP -
[- ] NFC…ME:TABIX_GERMLINE_RESOURCE -
[- ] NFC…RE_GENOME:TABIX_KNOWN_SNPS -
[- ] NFC…_GENOME:TABIX_KNOWN_INDELS -
[- ] NFC…K:PREPARE_GENOME:TABIX_PON -
[44/e6390c] NFC…VALS:BUILD_INTERVALS (fai) | 1 of 1 ✔
[92/ae71d1] NFC…TE_INTERVALS_BED (fai.bed) | 1 of 1 ✔
[2b/111741] NFC…hr6B_RagTag_2_1-225437615) | 27 of 27 ✔
[d8/c48447] NFC…IX_INTERVAL_COMBINED (fai) | 1 of 1 ✔
[- ] NFC…RING_DECOMPRESS_TO_FQ_PAIR -
[- ] NFC…SPRING_DECOMPRESS_TO_R1_FQ -
[- ] NFC…SPRING_DECOMPRESS_TO_R2_FQ -
[- ] NFC…NPUT:SAMTOOLS_VIEW_MAP_MAP -
[34/08b538] NFC…SAREK:FASTQC (TdS2-lane_2) | 4 of 4 ✔
[17/b03d7d] NFC…:SAREK:FASTP (TdS2-lane_2) | 4 of 4 ✔
[af/3d0de8] NFC…:BWAMEM1_MEM (TdS1-lane_1) | 1 of 48, failed: 1
Plus 41 more processes waiting for tasks…
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1)'

Caused by:
Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1) terminated with an error exit status (1)

Command executed:

INDEX=find -L ./ -name "*.amb" | sed 's/\.amb$//'

bwa mem
-K 100000000 -Y -R "@rg\tID:null.TdS1.lane_1\tPU:lane_1\tSM:Sample1_TdS1\tLB:TdS1\tDS:/svevo/davide_tmp/MG5323_v0.5.splitchromosomes.w60.fasta\tPL:ILLUMINA"
-t 24
$INDEX
0004.TdS1-lane_1_1.fastp.fastq.gz 0004.TdS1-lane_1_2.fastp.fastq.gz
| samtools sort --threads 24 -o TdS1-lane_1.0004.bam -

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM":
bwa: $(echo $(bwa 2>&1) | sed 's/^.Version: //; s/Contact:.$//')
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.samtools //; s/Using.$//')
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
[M::mem_pestat] low and high boundaries for proper pairs: (1, 704)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667822 reads in 690.290 CPU sec, 28.926 real sec
[M::process] read 668024 sequences (100000140 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96666, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 352, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (100, 600)
[M::mem_pestat] mean and std.dev: (350.39, 73.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 700)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667928 reads in 746.042 CPU sec, 31.278 real sec
[M::process] read 667972 sequences (100000116 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96712, 3, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (298, 351, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (94, 604)
[M::mem_pestat] mean and std.dev: (349.00, 75.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 706)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 668024 reads in 685.185 CPU sec, 28.753 real sec
[M::process] read 667978 sequences (100000196 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97590, 6, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (96, 606)
[M::mem_pestat] mean and std.dev: (351.31, 75.03)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 708)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667972 reads in 668.546 CPU sec, 28.021 real sec
[M::process] read 667946 sequences (100000172 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97376, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (302, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (102, 602)
[M::mem_pestat] mean and std.dev: (352.14, 74.40)
[M::mem_pestat] low and high boundaries for proper pairs: (2, 702)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667978 reads in 733.688 CPU sec, 30.737 real sec
[E::aux_parse] Incomplete aux field
samtools sort: truncated file. Aborting

Work dir:
/svevo/davide_tmp/workdir/af/3d0de8f81836310dec69a79e28809e

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details

executor > slurm (88)
[4c/209d40] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…EPARE_GENOME:BWAMEM2_INDEX -
[- ] NFC…E_GENOME:DRAGMAP_HASHTABLE -
[23/3a4ff6] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…E_GENOME:MSISENSORPRO_SCAN -
[- ] NFC…PARE_GENOME:SAMTOOLS_FAIDX -
[- ] NFC…TABIX_BCFTOOLS_ANNOTATIONS -
[- ] NFC…PREPARE_GENOME:TABIX_DBSNP -
[- ] NFC…ME:TABIX_GERMLINE_RESOURCE -
[- ] NFC…RE_GENOME:TABIX_KNOWN_SNPS -
[- ] NFC…_GENOME:TABIX_KNOWN_INDELS -
[- ] NFC…K:PREPARE_GENOME:TABIX_PON -
[44/e6390c] NFC…VALS:BUILD_INTERVALS (fai) | 1 of 1 ✔
[92/ae71d1] NFC…TE_INTERVALS_BED (fai.bed) | 1 of 1 ✔
[2b/111741] NFC…hr6B_RagTag_2_1-225437615) | 27 of 27 ✔
[d8/c48447] NFC…IX_INTERVAL_COMBINED (fai) | 1 of 1 ✔
[- ] NFC…RING_DECOMPRESS_TO_FQ_PAIR -
[- ] NFC…SPRING_DECOMPRESS_TO_R1_FQ -
[- ] NFC…SPRING_DECOMPRESS_TO_R2_FQ -
[- ] NFC…NPUT:SAMTOOLS_VIEW_MAP_MAP -
[34/08b538] NFC…SAREK:FASTQC (TdS2-lane_2) | 4 of 4 ✔
[17/b03d7d] NFC…:SAREK:FASTP (TdS2-lane_2) | 4 of 4 ✔
[af/3d0de8] NFC…:BWAMEM1_MEM (TdS1-lane_1) | 1 of 48, failed: 1
Plus 41 more processes waiting for tasks…
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1)'

Caused by:
Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1) terminated with an error exit status (1)

Command executed:

INDEX=find -L ./ -name "*.amb" | sed 's/\.amb$//'

bwa mem
-K 100000000 -Y -R "@rg\tID:null.TdS1.lane_1\tPU:lane_1\tSM:Sample1_TdS1\tLB:TdS1\tDS:/svevo/davide_tmp/MG5323_v0.5.splitchromosomes.w60.fasta\tPL:ILLUMINA"
-t 24
$INDEX
0004.TdS1-lane_1_1.fastp.fastq.gz 0004.TdS1-lane_1_2.fastp.fastq.gz
| samtools sort --threads 24 -o TdS1-lane_1.0004.bam -

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM":
bwa: $(echo $(bwa 2>&1) | sed 's/^.Version: //; s/Contact:.$//')
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.samtools //; s/Using.$//')
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
[M::mem_pestat] low and high boundaries for proper pairs: (1, 704)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667822 reads in 690.290 CPU sec, 28.926 real sec
[M::process] read 668024 sequences (100000140 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96666, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 352, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (100, 600)
[M::mem_pestat] mean and std.dev: (350.39, 73.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 700)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667928 reads in 746.042 CPU sec, 31.278 real sec
[M::process] read 667972 sequences (100000116 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96712, 3, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (298, 351, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (94, 604)
[M::mem_pestat] mean and std.dev: (349.00, 75.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 706)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 668024 reads in 685.185 CPU sec, 28.753 real sec
[M::process] read 667978 sequences (100000196 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97590, 6, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (96, 606)
[M::mem_pestat] mean and std.dev: (351.31, 75.03)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 708)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667972 reads in 668.546 CPU sec, 28.021 real sec
[M::process] read 667946 sequences (100000172 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97376, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (302, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (102, 602)
[M::mem_pestat] mean and std.dev: (352.14, 74.40)
[M::mem_pestat] low and high boundaries for proper pairs: (2, 702)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667978 reads in 733.688 CPU sec, 30.737 real sec
[E::aux_parse] Incomplete aux field
samtools sort: truncated file. Aborting

Work dir:
/svevo/davide_tmp/workdir/af/3d0de8f81836310dec69a79e28809e

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details

executor > slurm (88)
[4c/209d40] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…EPARE_GENOME:BWAMEM2_INDEX -
[- ] NFC…E_GENOME:DRAGMAP_HASHTABLE -
[23/3a4ff6] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…E_GENOME:MSISENSORPRO_SCAN -
[- ] NFC…PARE_GENOME:SAMTOOLS_FAIDX -
[- ] NFC…TABIX_BCFTOOLS_ANNOTATIONS -
[- ] NFC…PREPARE_GENOME:TABIX_DBSNP -
[- ] NFC…ME:TABIX_GERMLINE_RESOURCE -
[- ] NFC…RE_GENOME:TABIX_KNOWN_SNPS -
[- ] NFC…_GENOME:TABIX_KNOWN_INDELS -
[- ] NFC…K:PREPARE_GENOME:TABIX_PON -
[44/e6390c] NFC…VALS:BUILD_INTERVALS (fai) | 1 of 1 ✔
[92/ae71d1] NFC…TE_INTERVALS_BED (fai.bed) | 1 of 1 ✔
[2b/111741] NFC…hr6B_RagTag_2_1-225437615) | 27 of 27 ✔
[d8/c48447] NFC…IX_INTERVAL_COMBINED (fai) | 1 of 1 ✔
[- ] NFC…RING_DECOMPRESS_TO_FQ_PAIR -
[- ] NFC…SPRING_DECOMPRESS_TO_R1_FQ -
[- ] NFC…SPRING_DECOMPRESS_TO_R2_FQ -
[- ] NFC…NPUT:SAMTOOLS_VIEW_MAP_MAP -
[34/08b538] NFC…SAREK:FASTQC (TdS2-lane_2) | 4 of 4 ✔
[17/b03d7d] NFC…:SAREK:FASTP (TdS2-lane_2) | 4 of 4 ✔
[af/3d0de8] NFC…:BWAMEM1_MEM (TdS1-lane_1) | 1 of 48, failed: 1
Plus 41 more processes waiting for tasks…
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1)'

Caused by:
Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1) terminated with an error exit status (1)

Command executed:

INDEX=find -L ./ -name "*.amb" | sed 's/\.amb$//'

bwa mem
-K 100000000 -Y -R "@rg\tID:null.TdS1.lane_1\tPU:lane_1\tSM:Sample1_TdS1\tLB:TdS1\tDS:/svevo/davide_tmp/MG5323_v0.5.splitchromosomes.w60.fasta\tPL:ILLUMINA"
-t 24
$INDEX
0004.TdS1-lane_1_1.fastp.fastq.gz 0004.TdS1-lane_1_2.fastp.fastq.gz
| samtools sort --threads 24 -o TdS1-lane_1.0004.bam -

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM":
bwa: $(echo $(bwa 2>&1) | sed 's/^.Version: //; s/Contact:.$//')
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.samtools //; s/Using.$//')
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
[M::mem_pestat] low and high boundaries for proper pairs: (1, 704)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667822 reads in 690.290 CPU sec, 28.926 real sec
[M::process] read 668024 sequences (100000140 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96666, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 352, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (100, 600)
[M::mem_pestat] mean and std.dev: (350.39, 73.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 700)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667928 reads in 746.042 CPU sec, 31.278 real sec
[M::process] read 667972 sequences (100000116 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96712, 3, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (298, 351, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (94, 604)
[M::mem_pestat] mean and std.dev: (349.00, 75.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 706)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 668024 reads in 685.185 CPU sec, 28.753 real sec
[M::process] read 667978 sequences (100000196 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97590, 6, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (96, 606)
[M::mem_pestat] mean and std.dev: (351.31, 75.03)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 708)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667972 reads in 668.546 CPU sec, 28.021 real sec
[M::process] read 667946 sequences (100000172 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97376, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (302, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (102, 602)
[M::mem_pestat] mean and std.dev: (352.14, 74.40)
[M::mem_pestat] low and high boundaries for proper pairs: (2, 702)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667978 reads in 733.688 CPU sec, 30.737 real sec
[E::aux_parse] Incomplete aux field
samtools sort: truncated file. Aborting

Work dir:
/svevo/davide_tmp/workdir/af/3d0de8f81836310dec69a79e28809e

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details

executor > slurm (88)
[4c/209d40] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…EPARE_GENOME:BWAMEM2_INDEX -
[- ] NFC…E_GENOME:DRAGMAP_HASHTABLE -
[23/3a4ff6] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…E_GENOME:MSISENSORPRO_SCAN -
[- ] NFC…PARE_GENOME:SAMTOOLS_FAIDX -
[- ] NFC…TABIX_BCFTOOLS_ANNOTATIONS -
[- ] NFC…PREPARE_GENOME:TABIX_DBSNP -
[- ] NFC…ME:TABIX_GERMLINE_RESOURCE -
[- ] NFC…RE_GENOME:TABIX_KNOWN_SNPS -
[- ] NFC…_GENOME:TABIX_KNOWN_INDELS -
[- ] NFC…K:PREPARE_GENOME:TABIX_PON -
[44/e6390c] NFC…VALS:BUILD_INTERVALS (fai) | 1 of 1 ✔
[92/ae71d1] NFC…TE_INTERVALS_BED (fai.bed) | 1 of 1 ✔
[2b/111741] NFC…hr6B_RagTag_2_1-225437615) | 27 of 27 ✔
[d8/c48447] NFC…IX_INTERVAL_COMBINED (fai) | 1 of 1 ✔
[- ] NFC…RING_DECOMPRESS_TO_FQ_PAIR -
[- ] NFC…SPRING_DECOMPRESS_TO_R1_FQ -
[- ] NFC…SPRING_DECOMPRESS_TO_R2_FQ -
[- ] NFC…NPUT:SAMTOOLS_VIEW_MAP_MAP -
[34/08b538] NFC…SAREK:FASTQC (TdS2-lane_2) | 4 of 4 ✔
[17/b03d7d] NFC…:SAREK:FASTP (TdS2-lane_2) | 4 of 4 ✔
[70/31fc3e] NFC…:BWAMEM1_MEM (TdS1-lane_1) | 2 of 48, failed: 2
Plus 41 more processes waiting for tasks…

ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1)'

Caused by:
Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1) terminated with an error exit status (1)

Command executed:

INDEX=find -L ./ -name "*.amb" | sed 's/\.amb$//'

bwa mem
-K 100000000 -Y -R "@rg\tID:null.TdS1.lane_1\tPU:lane_1\tSM:Sample1_TdS1\tLB:TdS1\tDS:/svevo/davide_tmp/MG5323_v0.5.splitchromosomes.w60.fasta\tPL:ILLUMINA"
-t 24
$INDEX
0004.TdS1-lane_1_1.fastp.fastq.gz 0004.TdS1-lane_1_2.fastp.fastq.gz
| samtools sort --threads 24 -o TdS1-lane_1.0004.bam -

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM":
bwa: $(echo $(bwa 2>&1) | sed 's/^.Version: //; s/Contact:.$//')
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.samtools //; s/Using.$//')
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
[M::mem_pestat] low and high boundaries for proper pairs: (1, 704)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667822 reads in 690.290 CPU sec, 28.926 real sec
[M::process] read 668024 sequences (100000140 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96666, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 352, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (100, 600)
[M::mem_pestat] mean and std.dev: (350.39, 73.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 700)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667928 reads in 746.042 CPU sec, 31.278 real sec
[M::process] read 667972 sequences (100000116 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96712, 3, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (298, 351, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (94, 604)
[M::mem_pestat] mean and std.dev: (349.00, 75.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 706)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 668024 reads in 685.185 CPU sec, 28.753 real sec
[M::process] read 667978 sequences (100000196 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97590, 6, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (96, 606)
[M::mem_pestat] mean and std.dev: (351.31, 75.03)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 708)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667972 reads in 668.546 CPU sec, 28.021 real sec
[M::process] read 667946 sequences (100000172 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97376, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (302, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (102, 602)
[M::mem_pestat] mean and std.dev: (352.14, 74.40)
[M::mem_pestat] low and high boundaries for proper pairs: (2, 702)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667978 reads in 733.688 CPU sec, 30.737 real sec
[E::aux_parse] Incomplete aux field
samtools sort: truncated file. Aborting

Work dir:
/svevo/davide_tmp/workdir/af/3d0de8f81836310dec69a79e28809e

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details

executor > slurm (88)
[4c/209d40] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…EPARE_GENOME:BWAMEM2_INDEX -
[- ] NFC…E_GENOME:DRAGMAP_HASHTABLE -
[23/3a4ff6] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…E_GENOME:MSISENSORPRO_SCAN -
[- ] NFC…PARE_GENOME:SAMTOOLS_FAIDX -
[- ] NFC…TABIX_BCFTOOLS_ANNOTATIONS -
[- ] NFC…PREPARE_GENOME:TABIX_DBSNP -
[- ] NFC…ME:TABIX_GERMLINE_RESOURCE -
[- ] NFC…RE_GENOME:TABIX_KNOWN_SNPS -
[- ] NFC…_GENOME:TABIX_KNOWN_INDELS -
[- ] NFC…K:PREPARE_GENOME:TABIX_PON -
[44/e6390c] NFC…VALS:BUILD_INTERVALS (fai) | 1 of 1 ✔
[92/ae71d1] NFC…TE_INTERVALS_BED (fai.bed) | 1 of 1 ✔
[2b/111741] NFC…hr6B_RagTag_2_1-225437615) | 27 of 27 ✔
[d8/c48447] NFC…IX_INTERVAL_COMBINED (fai) | 1 of 1 ✔
[- ] NFC…RING_DECOMPRESS_TO_FQ_PAIR -
[- ] NFC…SPRING_DECOMPRESS_TO_R1_FQ -
[- ] NFC…SPRING_DECOMPRESS_TO_R2_FQ -
[- ] NFC…NPUT:SAMTOOLS_VIEW_MAP_MAP -
[34/08b538] NFC…SAREK:FASTQC (TdS2-lane_2) | 4 of 4 ✔
[17/b03d7d] NFC…:SAREK:FASTP (TdS2-lane_2) | 4 of 4 ✔
[70/31fc3e] NFC…:BWAMEM1_MEM (TdS1-lane_1) | 2 of 48, failed: 2
Plus 41 more processes waiting for tasks…
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1)'

Caused by:
Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1) terminated with an error exit status (1)

Command executed:

INDEX=find -L ./ -name "*.amb" | sed 's/\.amb$//'

bwa mem
-K 100000000 -Y -R "@rg\tID:null.TdS1.lane_1\tPU:lane_1\tSM:Sample1_TdS1\tLB:TdS1\tDS:/svevo/davide_tmp/MG5323_v0.5.splitchromosomes.w60.fasta\tPL:ILLUMINA"
-t 24
$INDEX
0004.TdS1-lane_1_1.fastp.fastq.gz 0004.TdS1-lane_1_2.fastp.fastq.gz
| samtools sort --threads 24 -o TdS1-lane_1.0004.bam -

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM":
bwa: $(echo $(bwa 2>&1) | sed 's/^.Version: //; s/Contact:.$//')
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.samtools //; s/Using.$//')
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
[M::mem_pestat] low and high boundaries for proper pairs: (1, 704)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667822 reads in 690.290 CPU sec, 28.926 real sec
[M::process] read 668024 sequences (100000140 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96666, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 352, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (100, 600)
[M::mem_pestat] mean and std.dev: (350.39, 73.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 700)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667928 reads in 746.042 CPU sec, 31.278 real sec
[M::process] read 667972 sequences (100000116 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96712, 3, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (298, 351, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (94, 604)
[M::mem_pestat] mean and std.dev: (349.00, 75.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 706)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 668024 reads in 685.185 CPU sec, 28.753 real sec
[M::process] read 667978 sequences (100000196 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97590, 6, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (96, 606)
[M::mem_pestat] mean and std.dev: (351.31, 75.03)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 708)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667972 reads in 668.546 CPU sec, 28.021 real sec
[M::process] read 667946 sequences (100000172 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97376, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (302, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (102, 602)
[M::mem_pestat] mean and std.dev: (352.14, 74.40)
[M::mem_pestat] low and high boundaries for proper pairs: (2, 702)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667978 reads in 733.688 CPU sec, 30.737 real sec
[E::aux_parse] Incomplete aux field
samtools sort: truncated file. Aborting

Work dir:
/svevo/davide_tmp/workdir/af/3d0de8f81836310dec69a79e28809e

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details

executor > slurm (88)
[4c/209d40] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…EPARE_GENOME:BWAMEM2_INDEX -
[- ] NFC…E_GENOME:DRAGMAP_HASHTABLE -
[23/3a4ff6] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…E_GENOME:MSISENSORPRO_SCAN -
[- ] NFC…PARE_GENOME:SAMTOOLS_FAIDX -
[- ] NFC…TABIX_BCFTOOLS_ANNOTATIONS -
[- ] NFC…PREPARE_GENOME:TABIX_DBSNP -
[- ] NFC…ME:TABIX_GERMLINE_RESOURCE -
[- ] NFC…RE_GENOME:TABIX_KNOWN_SNPS -
[- ] NFC…_GENOME:TABIX_KNOWN_INDELS -
[- ] NFC…K:PREPARE_GENOME:TABIX_PON -
[44/e6390c] NFC…VALS:BUILD_INTERVALS (fai) | 1 of 1 ✔
[92/ae71d1] NFC…TE_INTERVALS_BED (fai.bed) | 1 of 1 ✔
[2b/111741] NFC…hr6B_RagTag_2_1-225437615) | 27 of 27 ✔
[d8/c48447] NFC…IX_INTERVAL_COMBINED (fai) | 1 of 1 ✔
[- ] NFC…RING_DECOMPRESS_TO_FQ_PAIR -
[- ] NFC…SPRING_DECOMPRESS_TO_R1_FQ -
[- ] NFC…SPRING_DECOMPRESS_TO_R2_FQ -
[- ] NFC…NPUT:SAMTOOLS_VIEW_MAP_MAP -
[34/08b538] NFC…SAREK:FASTQC (TdS2-lane_2) | 4 of 4 ✔
[17/b03d7d] NFC…:SAREK:FASTP (TdS2-lane_2) | 4 of 4 ✔
[98/5d9991] NFC…:BWAMEM1_MEM (TdS1-lane_1) | 3 of 48, failed: 3, retries: 1
Plus 41 more processes waiting for tasks…
[98/5d9991] NOTE: Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1) terminated with an error exit status (137) -- Execution is retried (1)
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1)'

Caused by:
Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1) terminated with an error exit status (1)

Command executed:

INDEX=find -L ./ -name "*.amb" | sed 's/\.amb$//'

bwa mem
-K 100000000 -Y -R "@rg\tID:null.TdS1.lane_1\tPU:lane_1\tSM:Sample1_TdS1\tLB:TdS1\tDS:/svevo/davide_tmp/MG5323_v0.5.splitchromosomes.w60.fasta\tPL:ILLUMINA"
-t 24
$INDEX
0004.TdS1-lane_1_1.fastp.fastq.gz 0004.TdS1-lane_1_2.fastp.fastq.gz
| samtools sort --threads 24 -o TdS1-lane_1.0004.bam -

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM":
bwa: $(echo $(bwa 2>&1) | sed 's/^.Version: //; s/Contact:.$//')
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.samtools //; s/Using.$//')
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
[M::mem_pestat] low and high boundaries for proper pairs: (1, 704)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667822 reads in 690.290 CPU sec, 28.926 real sec
[M::process] read 668024 sequences (100000140 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96666, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 352, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (100, 600)
[M::mem_pestat] mean and std.dev: (350.39, 73.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 700)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667928 reads in 746.042 CPU sec, 31.278 real sec
[M::process] read 667972 sequences (100000116 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96712, 3, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (298, 351, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (94, 604)
[M::mem_pestat] mean and std.dev: (349.00, 75.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 706)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 668024 reads in 685.185 CPU sec, 28.753 real sec
[M::process] read 667978 sequences (100000196 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97590, 6, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (96, 606)
[M::mem_pestat] mean and std.dev: (351.31, 75.03)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 708)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667972 reads in 668.546 CPU sec, 28.021 real sec
[M::process] read 667946 sequences (100000172 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97376, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (302, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (102, 602)
[M::mem_pestat] mean and std.dev: (352.14, 74.40)
[M::mem_pestat] low and high boundaries for proper pairs: (2, 702)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667978 reads in 733.688 CPU sec, 30.737 real sec
[E::aux_parse] Incomplete aux field
samtools sort: truncated file. Aborting

Work dir:
/svevo/davide_tmp/workdir/af/3d0de8f81836310dec69a79e28809e

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details

executor > slurm (88)
[4c/209d40] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…EPARE_GENOME:BWAMEM2_INDEX -
[- ] NFC…E_GENOME:DRAGMAP_HASHTABLE -
[23/3a4ff6] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…E_GENOME:MSISENSORPRO_SCAN -
[- ] NFC…PARE_GENOME:SAMTOOLS_FAIDX -
[- ] NFC…TABIX_BCFTOOLS_ANNOTATIONS -
[- ] NFC…PREPARE_GENOME:TABIX_DBSNP -
[- ] NFC…ME:TABIX_GERMLINE_RESOURCE -
[- ] NFC…RE_GENOME:TABIX_KNOWN_SNPS -
[- ] NFC…_GENOME:TABIX_KNOWN_INDELS -
[- ] NFC…K:PREPARE_GENOME:TABIX_PON -
[44/e6390c] NFC…VALS:BUILD_INTERVALS (fai) | 1 of 1 ✔
[92/ae71d1] NFC…TE_INTERVALS_BED (fai.bed) | 1 of 1 ✔
[2b/111741] NFC…hr6B_RagTag_2_1-225437615) | 27 of 27 ✔
[d8/c48447] NFC…IX_INTERVAL_COMBINED (fai) | 1 of 1 ✔
[- ] NFC…RING_DECOMPRESS_TO_FQ_PAIR -
[- ] NFC…SPRING_DECOMPRESS_TO_R1_FQ -
[- ] NFC…SPRING_DECOMPRESS_TO_R2_FQ -
[- ] NFC…NPUT:SAMTOOLS_VIEW_MAP_MAP -
[34/08b538] NFC…SAREK:FASTQC (TdS2-lane_2) | 4 of 4 ✔
[17/b03d7d] NFC…:SAREK:FASTP (TdS2-lane_2) | 4 of 4 ✔
[98/5d9991] NFC…:BWAMEM1_MEM (TdS1-lane_1) | 3 of 49, failed: 3, retries: 1
Plus 41 more processes waiting for tasks…
[98/5d9991] NOTE: Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1) terminated with an error exit status (137) -- Execution is retried (1)
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1)'

Caused by:
Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1) terminated with an error exit status (1)

Command executed:

INDEX=find -L ./ -name "*.amb" | sed 's/\.amb$//'

bwa mem
-K 100000000 -Y -R "@rg\tID:null.TdS1.lane_1\tPU:lane_1\tSM:Sample1_TdS1\tLB:TdS1\tDS:/svevo/davide_tmp/MG5323_v0.5.splitchromosomes.w60.fasta\tPL:ILLUMINA"
-t 24
$INDEX
0004.TdS1-lane_1_1.fastp.fastq.gz 0004.TdS1-lane_1_2.fastp.fastq.gz
| samtools sort --threads 24 -o TdS1-lane_1.0004.bam -

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM":
bwa: $(echo $(bwa 2>&1) | sed 's/^.Version: //; s/Contact:.$//')
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.samtools //; s/Using.$//')
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
[M::mem_pestat] low and high boundaries for proper pairs: (1, 704)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667822 reads in 690.290 CPU sec, 28.926 real sec
[M::process] read 668024 sequences (100000140 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96666, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 352, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (100, 600)
[M::mem_pestat] mean and std.dev: (350.39, 73.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 700)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667928 reads in 746.042 CPU sec, 31.278 real sec
[M::process] read 667972 sequences (100000116 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96712, 3, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (298, 351, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (94, 604)
[M::mem_pestat] mean and std.dev: (349.00, 75.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 706)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 668024 reads in 685.185 CPU sec, 28.753 real sec
[M::process] read 667978 sequences (100000196 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97590, 6, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (96, 606)
[M::mem_pestat] mean and std.dev: (351.31, 75.03)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 708)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667972 reads in 668.546 CPU sec, 28.021 real sec
[M::process] read 667946 sequences (100000172 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97376, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (302, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (102, 602)
[M::mem_pestat] mean and std.dev: (352.14, 74.40)
[M::mem_pestat] low and high boundaries for proper pairs: (2, 702)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667978 reads in 733.688 CPU sec, 30.737 real sec
[E::aux_parse] Incomplete aux field
samtools sort: truncated file. Aborting

Work dir:
/svevo/davide_tmp/workdir/af/3d0de8f81836310dec69a79e28809e

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details

executor > slurm (88)
[4c/209d40] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…EPARE_GENOME:BWAMEM2_INDEX -
[- ] NFC…E_GENOME:DRAGMAP_HASHTABLE -
[23/3a4ff6] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…E_GENOME:MSISENSORPRO_SCAN -
[- ] NFC…PARE_GENOME:SAMTOOLS_FAIDX -
[- ] NFC…TABIX_BCFTOOLS_ANNOTATIONS -
[- ] NFC…PREPARE_GENOME:TABIX_DBSNP -
[- ] NFC…ME:TABIX_GERMLINE_RESOURCE -
[- ] NFC…RE_GENOME:TABIX_KNOWN_SNPS -
[- ] NFC…_GENOME:TABIX_KNOWN_INDELS -
[- ] NFC…K:PREPARE_GENOME:TABIX_PON -
[44/e6390c] NFC…VALS:BUILD_INTERVALS (fai) | 1 of 1 ✔
[92/ae71d1] NFC…TE_INTERVALS_BED (fai.bed) | 1 of 1 ✔
[2b/111741] NFC…hr6B_RagTag_2_1-225437615) | 27 of 27 ✔
[d8/c48447] NFC…IX_INTERVAL_COMBINED (fai) | 1 of 1 ✔
[- ] NFC…RING_DECOMPRESS_TO_FQ_PAIR -
[- ] NFC…SPRING_DECOMPRESS_TO_R1_FQ -
[- ] NFC…SPRING_DECOMPRESS_TO_R2_FQ -
[- ] NFC…NPUT:SAMTOOLS_VIEW_MAP_MAP -
[34/08b538] NFC…SAREK:FASTQC (TdS2-lane_2) | 4 of 4 ✔
[17/b03d7d] NFC…:SAREK:FASTP (TdS2-lane_2) | 4 of 4 ✔
[98/5d9991] NFC…:BWAMEM1_MEM (TdS1-lane_1) | 3 of 49, failed: 3, retries: 1
Plus 41 more processes waiting for tasks…
[98/5d9991] NOTE: Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1) terminated with an error exit status (137) -- Execution is retried (1)
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1)'

Caused by:
Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1) terminated with an error exit status (1)

Command executed:

INDEX=find -L ./ -name "*.amb" | sed 's/\.amb$//'

bwa mem
-K 100000000 -Y -R "@rg\tID:null.TdS1.lane_1\tPU:lane_1\tSM:Sample1_TdS1\tLB:TdS1\tDS:/svevo/davide_tmp/MG5323_v0.5.splitchromosomes.w60.fasta\tPL:ILLUMINA"
-t 24
$INDEX
0004.TdS1-lane_1_1.fastp.fastq.gz 0004.TdS1-lane_1_2.fastp.fastq.gz
| samtools sort --threads 24 -o TdS1-lane_1.0004.bam -

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM":
bwa: $(echo $(bwa 2>&1) | sed 's/^.Version: //; s/Contact:.$//')
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.samtools //; s/Using.$//')
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
[M::mem_pestat] low and high boundaries for proper pairs: (1, 704)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667822 reads in 690.290 CPU sec, 28.926 real sec
[M::process] read 668024 sequences (100000140 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96666, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 352, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (100, 600)
[M::mem_pestat] mean and std.dev: (350.39, 73.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 700)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667928 reads in 746.042 CPU sec, 31.278 real sec
[M::process] read 667972 sequences (100000116 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96712, 3, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (298, 351, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (94, 604)
[M::mem_pestat] mean and std.dev: (349.00, 75.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 706)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 668024 reads in 685.185 CPU sec, 28.753 real sec
[M::process] read 667978 sequences (100000196 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97590, 6, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (96, 606)
[M::mem_pestat] mean and std.dev: (351.31, 75.03)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 708)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667972 reads in 668.546 CPU sec, 28.021 real sec
[M::process] read 667946 sequences (100000172 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97376, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (302, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (102, 602)
[M::mem_pestat] mean and std.dev: (352.14, 74.40)
[M::mem_pestat] low and high boundaries for proper pairs: (2, 702)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667978 reads in 733.688 CPU sec, 30.737 real sec
[E::aux_parse] Incomplete aux field
samtools sort: truncated file. Aborting

Work dir:
/svevo/davide_tmp/workdir/af/3d0de8f81836310dec69a79e28809e

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details

executor > slurm (88)
[4c/209d40] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…EPARE_GENOME:BWAMEM2_INDEX -
[- ] NFC…E_GENOME:DRAGMAP_HASHTABLE -
[23/3a4ff6] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…E_GENOME:MSISENSORPRO_SCAN -
[- ] NFC…PARE_GENOME:SAMTOOLS_FAIDX -
[- ] NFC…TABIX_BCFTOOLS_ANNOTATIONS -
[- ] NFC…PREPARE_GENOME:TABIX_DBSNP -
[- ] NFC…ME:TABIX_GERMLINE_RESOURCE -
[- ] NFC…RE_GENOME:TABIX_KNOWN_SNPS -
[- ] NFC…_GENOME:TABIX_KNOWN_INDELS -
[- ] NFC…K:PREPARE_GENOME:TABIX_PON -
[44/e6390c] NFC…VALS:BUILD_INTERVALS (fai) | 1 of 1 ✔
[92/ae71d1] NFC…TE_INTERVALS_BED (fai.bed) | 1 of 1 ✔
[2b/111741] NFC…hr6B_RagTag_2_1-225437615) | 27 of 27 ✔
[d8/c48447] NFC…IX_INTERVAL_COMBINED (fai) | 1 of 1 ✔
[- ] NFC…RING_DECOMPRESS_TO_FQ_PAIR -
[- ] NFC…SPRING_DECOMPRESS_TO_R1_FQ -
[- ] NFC…SPRING_DECOMPRESS_TO_R2_FQ -
[- ] NFC…NPUT:SAMTOOLS_VIEW_MAP_MAP -
[34/08b538] NFC…SAREK:FASTQC (TdS2-lane_2) | 4 of 4 ✔
[17/b03d7d] NFC…:SAREK:FASTP (TdS2-lane_2) | 4 of 4 ✔
[98/5d9991] NFC…:BWAMEM1_MEM (TdS1-lane_1) | 3 of 49, failed: 3, retries: 1
Plus 41 more processes waiting for tasks…

ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1)'

Caused by:
Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1) terminated with an error exit status (1)

Command executed:

INDEX=find -L ./ -name "*.amb" | sed 's/\.amb$//'

bwa mem
-K 100000000 -Y -R "@rg\tID:null.TdS1.lane_1\tPU:lane_1\tSM:Sample1_TdS1\tLB:TdS1\tDS:/svevo/davide_tmp/MG5323_v0.5.splitchromosomes.w60.fasta\tPL:ILLUMINA"
-t 24
$INDEX
0004.TdS1-lane_1_1.fastp.fastq.gz 0004.TdS1-lane_1_2.fastp.fastq.gz
| samtools sort --threads 24 -o TdS1-lane_1.0004.bam -

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM":
bwa: $(echo $(bwa 2>&1) | sed 's/^.Version: //; s/Contact:.$//')
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.samtools //; s/Using.$//')
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
[M::mem_pestat] low and high boundaries for proper pairs: (1, 704)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667822 reads in 690.290 CPU sec, 28.926 real sec
[M::process] read 668024 sequences (100000140 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96666, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 352, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (100, 600)
[M::mem_pestat] mean and std.dev: (350.39, 73.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 700)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667928 reads in 746.042 CPU sec, 31.278 real sec
[M::process] read 667972 sequences (100000116 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96712, 3, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (298, 351, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (94, 604)
[M::mem_pestat] mean and std.dev: (349.00, 75.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 706)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 668024 reads in 685.185 CPU sec, 28.753 real sec
[M::process] read 667978 sequences (100000196 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97590, 6, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (96, 606)
[M::mem_pestat] mean and std.dev: (351.31, 75.03)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 708)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667972 reads in 668.546 CPU sec, 28.021 real sec
[M::process] read 667946 sequences (100000172 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97376, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (302, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (102, 602)
[M::mem_pestat] mean and std.dev: (352.14, 74.40)
[M::mem_pestat] low and high boundaries for proper pairs: (2, 702)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667978 reads in 733.688 CPU sec, 30.737 real sec
[E::aux_parse] Incomplete aux field
samtools sort: truncated file. Aborting

Work dir:
/svevo/davide_tmp/workdir/af/3d0de8f81836310dec69a79e28809e

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details

executor > slurm (88)
[4c/209d40] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…EPARE_GENOME:BWAMEM2_INDEX -
[- ] NFC…E_GENOME:DRAGMAP_HASHTABLE -
[23/3a4ff6] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…E_GENOME:MSISENSORPRO_SCAN -
[- ] NFC…PARE_GENOME:SAMTOOLS_FAIDX -
[- ] NFC…TABIX_BCFTOOLS_ANNOTATIONS -
[- ] NFC…PREPARE_GENOME:TABIX_DBSNP -
[- ] NFC…ME:TABIX_GERMLINE_RESOURCE -
[- ] NFC…RE_GENOME:TABIX_KNOWN_SNPS -
[- ] NFC…_GENOME:TABIX_KNOWN_INDELS -
[- ] NFC…K:PREPARE_GENOME:TABIX_PON -
[44/e6390c] NFC…VALS:BUILD_INTERVALS (fai) | 1 of 1 ✔
[92/ae71d1] NFC…TE_INTERVALS_BED (fai.bed) | 1 of 1 ✔
[2b/111741] NFC…hr6B_RagTag_2_1-225437615) | 27 of 27 ✔
[d8/c48447] NFC…IX_INTERVAL_COMBINED (fai) | 1 of 1 ✔
[- ] NFC…RING_DECOMPRESS_TO_FQ_PAIR -
[- ] NFC…SPRING_DECOMPRESS_TO_R1_FQ -
[- ] NFC…SPRING_DECOMPRESS_TO_R2_FQ -
[- ] NFC…NPUT:SAMTOOLS_VIEW_MAP_MAP -
[34/08b538] NFC…SAREK:FASTQC (TdS2-lane_2) | 4 of 4 ✔
[17/b03d7d] NFC…:SAREK:FASTP (TdS2-lane_2) | 4 of 4 ✔
[ba/d84240] NFC…:BWAMEM1_MEM (TdS1-lane_2) | 4 of 49, failed: 4, retries: 2
Plus 41 more processes waiting for tasks…
[ba/d84240] NOTE: Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_2) terminated with an error exit status (143) -- Execution is retried (1)
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1)'

Caused by:
Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1) terminated with an error exit status (1)

Command executed:

INDEX=find -L ./ -name "*.amb" | sed 's/\.amb$//'

bwa mem
-K 100000000 -Y -R "@rg\tID:null.TdS1.lane_1\tPU:lane_1\tSM:Sample1_TdS1\tLB:TdS1\tDS:/svevo/davide_tmp/MG5323_v0.5.splitchromosomes.w60.fasta\tPL:ILLUMINA"
-t 24
$INDEX
0004.TdS1-lane_1_1.fastp.fastq.gz 0004.TdS1-lane_1_2.fastp.fastq.gz
| samtools sort --threads 24 -o TdS1-lane_1.0004.bam -

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM":
bwa: $(echo $(bwa 2>&1) | sed 's/^.Version: //; s/Contact:.$//')
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.samtools //; s/Using.$//')
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
[M::mem_pestat] low and high boundaries for proper pairs: (1, 704)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667822 reads in 690.290 CPU sec, 28.926 real sec
[M::process] read 668024 sequences (100000140 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96666, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 352, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (100, 600)
[M::mem_pestat] mean and std.dev: (350.39, 73.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 700)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667928 reads in 746.042 CPU sec, 31.278 real sec
[M::process] read 667972 sequences (100000116 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96712, 3, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (298, 351, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (94, 604)
[M::mem_pestat] mean and std.dev: (349.00, 75.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 706)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 668024 reads in 685.185 CPU sec, 28.753 real sec
[M::process] read 667978 sequences (100000196 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97590, 6, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (96, 606)
[M::mem_pestat] mean and std.dev: (351.31, 75.03)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 708)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667972 reads in 668.546 CPU sec, 28.021 real sec
[M::process] read 667946 sequences (100000172 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97376, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (302, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (102, 602)
[M::mem_pestat] mean and std.dev: (352.14, 74.40)
[M::mem_pestat] low and high boundaries for proper pairs: (2, 702)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667978 reads in 733.688 CPU sec, 30.737 real sec
[E::aux_parse] Incomplete aux field
samtools sort: truncated file. Aborting

Work dir:
/svevo/davide_tmp/workdir/af/3d0de8f81836310dec69a79e28809e

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details

executor > slurm (88)
[4c/209d40] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…EPARE_GENOME:BWAMEM2_INDEX -
[- ] NFC…E_GENOME:DRAGMAP_HASHTABLE -
[23/3a4ff6] NFC…plitchromosomes.w60.fasta) | 1 of 1 ✔
[- ] NFC…E_GENOME:MSISENSORPRO_SCAN -
[- ] NFC…PARE_GENOME:SAMTOOLS_FAIDX -
[- ] NFC…TABIX_BCFTOOLS_ANNOTATIONS -
[- ] NFC…PREPARE_GENOME:TABIX_DBSNP -
[- ] NFC…ME:TABIX_GERMLINE_RESOURCE -
[- ] NFC…RE_GENOME:TABIX_KNOWN_SNPS -
[- ] NFC…_GENOME:TABIX_KNOWN_INDELS -
[- ] NFC…K:PREPARE_GENOME:TABIX_PON -
[44/e6390c] NFC…VALS:BUILD_INTERVALS (fai) | 1 of 1 ✔
[92/ae71d1] NFC…TE_INTERVALS_BED (fai.bed) | 1 of 1 ✔
[2b/111741] NFC…hr6B_RagTag_2_1-225437615) | 27 of 27 ✔
[d8/c48447] NFC…IX_INTERVAL_COMBINED (fai) | 1 of 1 ✔
[- ] NFC…RING_DECOMPRESS_TO_FQ_PAIR -
[- ] NFC…SPRING_DECOMPRESS_TO_R1_FQ -
[- ] NFC…SPRING_DECOMPRESS_TO_R2_FQ -
[- ] NFC…NPUT:SAMTOOLS_VIEW_MAP_MAP -
[34/08b538] NFC…SAREK:FASTQC (TdS2-lane_2) | 4 of 4 ✔
[17/b03d7d] NFC…:SAREK:FASTP (TdS2-lane_2) | 4 of 4 ✔
[ba/d84240] NFC…:BWAMEM1_MEM (TdS1-lane_2) | 4 of 50, failed: 4, retries: 2
Plus 41 more processes waiting for tasks…
[ba/d84240] NOTE: Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_2) terminated with an error exit status (143) -- Execution is retried (1)
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1)'

Caused by:
Process NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (TdS1-lane_1) terminated with an error exit status (1)

Command executed:

INDEX=find -L ./ -name "*.amb" | sed 's/\.amb$//'

bwa mem
-K 100000000 -Y -R "@rg\tID:null.TdS1.lane_1\tPU:lane_1\tSM:Sample1_TdS1\tLB:TdS1\tDS:/svevo/davide_tmp/MG5323_v0.5.splitchromosomes.w60.fasta\tPL:ILLUMINA"
-t 24
$INDEX
0004.TdS1-lane_1_1.fastp.fastq.gz 0004.TdS1-lane_1_2.fastp.fastq.gz
| samtools sort --threads 24 -o TdS1-lane_1.0004.bam -

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM":
bwa: $(echo $(bwa 2>&1) | sed 's/^.Version: //; s/Contact:.$//')
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.samtools //; s/Using.$//')
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
[M::mem_pestat] low and high boundaries for proper pairs: (1, 704)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667822 reads in 690.290 CPU sec, 28.926 real sec
[M::process] read 668024 sequences (100000140 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96666, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 352, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (100, 600)
[M::mem_pestat] mean and std.dev: (350.39, 73.89)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 700)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667928 reads in 746.042 CPU sec, 31.278 real sec
[M::process] read 667972 sequences (100000116 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 96712, 3, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (298, 351, 400)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (94, 604)
[M::mem_pestat] mean and std.dev: (349.00, 75.13)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 706)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 668024 reads in 685.185 CPU sec, 28.753 real sec
[M::process] read 667978 sequences (100000196 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97590, 6, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (300, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (96, 606)
[M::mem_pestat] mean and std.dev: (351.31, 75.03)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 708)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667972 reads in 668.546 CPU sec, 28.021 real sec
[M::process] read 667946 sequences (100000172 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 97376, 1, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (302, 354, 402)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (102, 602)
[M::mem_pestat] mean and std.dev: (352.14, 74.40)
[M::mem_pestat] low and high boundaries for proper pairs: (2, 702)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 667978 reads in 733.688 CPU sec, 30.737 real sec
[E::aux_parse] Incomplete aux field
samtools sort: truncated file. Aborting

Work dir:
/svevo/davide_tmp/workdir/af/3d0de8f81836310dec69a79e28809e

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details
slurmstepd: error: *** JOB 4443 ON crea-research-hpc-1 CANCELLED AT 2025-06-09T11:46:46 ***

[asp8200]

I think the error [E::aux_parse] Incomplete aux field is coming from samtools. I see other people out there got that error from samtools, so you might want to take a look at how they solved it.

Since the output from bwa is being pipped into samtools, the problem might not be samtools but bwa. One possible approach to debugging this might be to go to the workfolder and try to setup things (input-files) in order to run the bwa-command manually and check the validity of the resulting SAM-file.