[ERROR] No full-alignment output for file (Illumina)

[dgslos]

Hi,

I'm using the Clair3-Illumina conda package on haploid data and I'm getting these "[ERROR] No full-alignment output for file" errors. Something related to clair3 or my data?

[INFO] CLAIR3 VERSION: v1.0.6
[INFO] BAM FILE PATH: /home/genomics/dslos/06_development/fusarium/01_mapping/./MY0231.BWA.bam
[INFO] REFERENCE FILE PATH: /home/genomics/dslos/06_development/fusarium/ref/polished.fasta
[INFO] MODEL PATH: /opt/miniforge3/envs/clair3-illumina/bin/models/ilmn
[INFO] OUTPUT FOLDER: /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231
[INFO] PLATFORM: ilmn
[INFO] THREADS: 20
[INFO] BED FILE PATH: /home/genomics/dslos/06_development/fusarium/02_delineate_c90/final_stack_positions_fusarium_C90.0_SMAP10_CL40_275.bed
[INFO] VCF FILE PATH: EMPTY
[INFO] CONTIGS: EMPTY
[INFO] CONDA PREFIX: /opt/miniforge3/envs/clair3-illumina
[INFO] SAMTOOLS PATH: samtools
[INFO] PYTHON PATH: python3
[INFO] PYPY PATH: pypy3
[INFO] PARALLEL PATH: parallel
[INFO] WHATSHAP PATH: whatshap
[INFO] LONGPHASE PATH: EMPTY
[INFO] CHUNK SIZE: 5000000
[INFO] FULL ALIGN PROPORTION: 0.3
[INFO] FULL ALIGN REFERENCE PROPORTION: 0.3
[INFO] PHASING PROPORTION: 0.7
[INFO] MINIMUM MQ: 5
[INFO] MINIMUM COVERAGE: 2
[INFO] SNP AF THRESHOLD: 0.08
[INFO] INDEL AF THRESHOLD: 0.08
[INFO] BASE ERROR IN GVCF: 0.001
[INFO] GQ BIN SIZE IN GVCF: 5
[INFO] ENABLE FILEUP ONLY CALLING: False
[INFO] ENABLE FAST MODE CALLING: False
[INFO] ENABLE CALLING SNP CANDIDATES ONLY: False
[INFO] ENABLE PRINTING REFERENCE CALLS: False
[INFO] ENABLE OUTPUT GVCF: False
[INFO] ENABLE HAPLOID PRECISE MODE: False
[INFO] ENABLE HAPLOID SENSITIVE MODE: True
[INFO] ENABLE INCLUDE ALL CTGS CALLING: True
[INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: True
[INFO] ENABLE REMOVING INTERMEDIATE FILES: False
[INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: False
[INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False
[INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False
[INFO] ENABLE HAPLOTAGGING FINAL BAM: False
[INFO] ENABLE LONG INDEL CALLING: False
[INFO] ENABLE C_IMPLEMENT: True

[WARNING] Illumina platform will disable C implement to support short read realignment process!
+ /opt/miniforge3/envs/clair3-illumina/bin/scripts/clair3.sh --bam_fn /home/genomics/dslos/06_development/fusarium/01_mapping/./MY0231.BWA.bam --ref_fn /home/genomics/dslos/06_development/fusarium/ref/polished.fasta --threads 20 --model_path /opt/miniforge3/envs/clair3-illumina/bin/models/ilmn --platform ilmn --output /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231 --bed_fn=/home/genomics/dslos/06_development/fusarium/02_delineate_c90/final_stack_positions_fusarium_C90.0_SMAP10_CL40_275.bed --vcf_fn=EMPTY --ctg_name=EMPTY --sample_name=MY0231 --chunk_num=0 --chunk_size=5000000 --samtools=samtools --python=python3 --pypy=pypy3 --parallel=parallel --whatshap=whatshap --qual=2 --var_pct_full=0.3 --ref_pct_full=0.3 --var_pct_phasing=0.7 --snp_min_af=0.08 --indel_min_af=0.08 --min_mq=5 --min_coverage=2 --min_contig_size=0 --pileup_only=False --gvcf=False --base_err=0.001 --gq_bin_size=5 --fast_mode=False --call_snp_only=False --print_ref_calls=False --haploid_precise=False --haploid_sensitive=True --include_all_ctgs=True --no_phasing_for_fa=True --pileup_model_prefix=pileup --fa_model_prefix=full_alignment --remove_intermediate_dir=False --enable_phasing=False --enable_long_indel=False --keep_iupac_bases=False --use_gpu=False --longphase_for_phasing=False --longphase=EMPTY --use_whatshap_for_intermediate_phasing=True --use_longphase_for_intermediate_phasing=False --use_whatshap_for_final_output_phasing=False --use_longphase_for_final_output_phasing=False --use_whatshap_for_final_output_haplotagging=False

[INFO] Check environment variables
[INFO] --include_all_ctgs enabled
[INFO] Call variant in contigs: contig_50 contig_41 contig_18 contig_42 contig_20 contig_69 contig_12 contig_193 contig_25 contig_16 contig_27 contig_21 contig_49 contig_192 contig_36 contig_90 contig_33 contig_200 contig_194 contig_29 contig_61 contig_161 contig_35 contig_32 contig_190 contig_31
[INFO] Chunk number for each contig: 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
[INFO] 1/7 Call variants using pileup model
[INFO] Delay 0 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_192 (chunk 1/1) : 14
Total time elapsed: 2.02 s
[INFO] Delay 0 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_50 (chunk 1/1) : 32
Total time elapsed: 2.10 s
[INFO] Delay 2 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_193 (chunk 1/1) : 4
Total time elapsed: 2.64 s
[INFO] Delay 3 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_36 (chunk 1/1) : 46
Total time elapsed: 2.79 s
[INFO] Delay 3 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_16 (chunk 1/1) : 99
Total time elapsed: 3.42 s
[INFO] Delay 4 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_42 (chunk 1/1) : 31
Total time elapsed: 2.52 s
[INFO] Delay 4 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_20 (chunk 1/1) : 75
Total time elapsed: 2.74 s
[INFO] Delay 4 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_49 (chunk 1/1) : 143
Total time elapsed: 4.24 s
[INFO] Delay 0 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_90 (chunk 1/1) : 163
Total time elapsed: 5.52 s
[INFO] Delay 3 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_18 (chunk 1/1) : 328
Total time elapsed: 8.65 s
[INFO] Delay 3 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_69 (chunk 1/1) : 267
Total time elapsed: 8.21 s
[INFO] Delay 2 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_12 (chunk 1/1) : 404
Total time elapsed: 9.59 s
[INFO] Delay 0 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_200 (chunk 1/1) : 152
Total time elapsed: 4.97 s
[INFO] Delay 4 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_41 (chunk 1/1) : 387
Total time elapsed: 8.88 s
[INFO] Delay 0 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_21 (chunk 1/1) : 465
Total time elapsed: 16.27 s
[INFO] Delay 1 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_61 (chunk 1/1) : 135
Total time elapsed: 5.16 s
[INFO] Delay 4 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_27 (chunk 1/1) : 547
Total time elapsed: 14.39 s
[INFO] Delay 2 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_190 (chunk 1/1) : 24
Total time elapsed: 2.64 s
[INFO] Delay 0 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_194 (chunk 1/1) : 332
Total time elapsed: 11.39 s
[INFO] Delay 3 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_25 (chunk 1/1) : 759
Total time elapsed: 17.16 s
[INFO] Delay 0 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_35 (chunk 1/1) : 375
Total time elapsed: 11.41 s
[INFO] Delay 1 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_29 (chunk 1/1) : 363
Total time elapsed: 11.71 s
[INFO] Delay 4 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_161 (chunk 1/1) : 285
Total time elapsed: 8.75 s
[INFO] Delay 2 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_33 (chunk 1/1) : 458
Total time elapsed: 18.36 s
[INFO] Delay 1 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_32 (chunk 1/1) : 433
Total time elapsed: 13.14 s
[INFO] Delay 3 seconds before starting variant calling ...
[mpileup] 1 samples in 1 input files
Calling variants ...
Total processed positions in contig_31 (chunk 1/1) : 573
Total time elapsed: 12.08 s

real    0m32.658s
user    6m21.829s
sys     0m31.780s
[INFO] 2/7 No phasing for full alignment calling

[INFO] 5/7 Select candidates for full-alignment calling
[INFO] Set variants quality cutoff 15.0
[INFO] Set reference calls quality cutoff 6.0
[INFO] Low quality reference calls to be processed in contig_20: 2
[INFO] Low quality variants to be processed in contig_20: 21
[INFO] Low quality reference calls to be processed in contig_25: 24
[INFO] Low quality variants to be processed in contig_25: 193
[INFO] Low quality reference calls to be processed in contig_41: 8
[INFO] Low quality variants to be processed in contig_41: 97
[INFO] Low quality reference calls to be processed in contig_18: 13
[INFO] Low quality variants to be processed in contig_18: 107
[WARNING] Cannot find any low-quality 0/0, 0/1 or 1/1 variant in pileup output in contig contig_193
[WARNING] Copying pileup.vcf.gz to /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/merge_output.vcf.gz
[INFO] Low quality reference calls to be processed in contig_193: 0
[INFO] Low quality variants to be processed in contig_193: 0
[INFO] Low quality reference calls to be processed in contig_42: 2
[INFO] Low quality variants to be processed in contig_42: 7
[INFO] Low quality reference calls to be processed in contig_27: 8
[INFO] Low quality variants to be processed in contig_27: 159
[INFO] Low quality reference calls to be processed in contig_49: 3
[INFO] Low quality variants to be processed in contig_49: 39
[INFO] Low quality reference calls to be processed in contig_12: 10
[INFO] Low quality variants to be processed in contig_12: 102
[INFO] Low quality reference calls to be processed in contig_16: 2
[INFO] Low quality variants to be processed in contig_16: 24
[INFO] Low quality reference calls to be processed in contig_21: 13
[INFO] Low quality variants to be processed in contig_21: 128
[INFO] Low quality reference calls to be processed in contig_192: 1
[INFO] Low quality variants to be processed in contig_192: 3
[INFO] Low quality reference calls to be processed in contig_200: 3
[INFO] Low quality variants to be processed in contig_200: 35
[INFO] Low quality reference calls to be processed in contig_33: 5
[INFO] Low quality variants to be processed in contig_33: 139
[INFO] Low quality reference calls to be processed in contig_50: 1
[INFO] Low quality variants to be processed in contig_50: 10
[INFO] Low quality reference calls to be processed in contig_90: 3
[INFO] Low quality variants to be processed in contig_90: 42
[INFO] Low quality reference calls to be processed in contig_29: 8
[INFO] Low quality variants to be processed in contig_29: 87
[INFO] Low quality reference calls to be processed in contig_36: 3
[INFO] Low quality variants to be processed in contig_36: 9
[INFO] Low quality reference calls to be processed in contig_194: 4
[INFO] Low quality variants to be processed in contig_194: 103
[INFO] Low quality reference calls to be processed in contig_69: 6
[INFO] Low quality variants to be processed in contig_69: 78
[INFO] Low quality reference calls to be processed in contig_61: 4
[INFO] Low quality variants to be processed in contig_61: 39
[INFO] Low quality reference calls to be processed in contig_35: 9
[INFO] Low quality variants to be processed in contig_35: 111
[INFO] Low quality reference calls to be processed in contig_161: 8
[INFO] Low quality variants to be processed in contig_161: 71
[INFO] Low quality reference calls to be processed in contig_32: 12
[INFO] Low quality variants to be processed in contig_32: 135
[INFO] Low quality reference calls to be processed in contig_190: 1
[INFO] Low quality variants to be processed in contig_190: 7
[INFO] Low quality reference calls to be processed in contig_31: 18
[INFO] Low quality variants to be processed in contig_31: 145

real    0m0.693s
user    0m4.550s
sys     0m1.888s

[INFO] 6/7 Call low-quality variants using full-alignment model
[INFO] Delay 0 seconds before starting variant calling ...
[WARNING] Skip full-alignment variant calling for empty full-alignment regions
[INFO] Delay 0 seconds before starting variant calling ...
samtools view: writing to standard output failed[mpileup] fail to read the header of -
: Broken pipe
samtools view: error closing standard output: -1
Calling variants ...
Total processed positions in contig_12 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_12//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_12.0_1.vcf
Total time elapsed: 0.00 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_12.0_1.vcf, remove empty file
[INFO] Delay 0 seconds before starting variant calling ...
Calling variants ...
samtools view: writing to standard output failed: Broken pipe
[mpileup] fail to read the header of -
samtools view: error closing standard output: -1
Total processed positions in contig_18 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_18//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_18.0_1.vcf
Total time elapsed: 0.20 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_18.0_1.vcf, remove empty file
[INFO] Delay 0 seconds before starting variant calling ...
Calling variants ...
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
[mpileup] fail to read the header of -
Total processed positions in contig_29 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_29//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_29.0_1.vcf
Total time elapsed: 1.61 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_29.0_1.vcf, remove empty file
[INFO] Delay 0 seconds before starting variant calling ...
Calling variants ...
[mpileup] fail to read the header of -
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Total processed positions in contig_32 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_32//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_32.0_1.vcf
Total time elapsed: 2.65 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_32.0_1.vcf, remove empty file
[INFO] Delay 1 seconds before starting variant calling ...
Calling variants ...
samtools view: writing to standard output failed: Broken pipe
[mpileup] fail to read the header of -
samtools view: error closing standard output: -1
Total processed positions in contig_200 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_200//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_200.0_1.vcf
Total time elapsed: 2.75 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_200.0_1.vcf, remove empty file
[INFO] Delay 4 seconds before starting variant calling ...
[mpileup] fail to read the header of -
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Calling variants ...
Total processed positions in contig_192 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_192//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_192.0_1.vcf
Total time elapsed: 0.00 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_192.0_1.vcf, remove empty file
[INFO] Delay 4 seconds before starting variant calling ...
samtools view: [mpileup] fail to read the header of -
writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Calling variants ...
Total processed positions in contig_21 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_21//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_21.0_1.vcf
Total time elapsed: 0.00 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_21.0_1.vcf, remove empty file
[INFO] Delay 1 seconds before starting variant calling ...
Calling variants ...
samtools view: [mpileup] fail to read the header of -
writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Total processed positions in contig_27 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_27//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_27.0_1.vcf
Total time elapsed: 3.37 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_27.0_1.vcf, remove empty file
[INFO] Delay 1 seconds before starting variant calling ...
Calling variants ...
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
[mpileup] fail to read the header of -
Total processed positions in contig_31 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_31//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_31.0_1.vcf
Total time elapsed: 4.22 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_31.0_1.vcf, remove empty file
[INFO] Delay 2 seconds before starting variant calling ...
Calling variants ...
samtools view: writing to standard output failed: Broken pipe
[mpileup] fail to read the header of -
samtools view: error closing standard output: -1
Total processed positions in contig_20 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_20//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_20.0_1.vcf
Total time elapsed: 4.51 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_20.0_1.vcf, remove empty file
[INFO] Delay 2 seconds before starting variant calling ...
Calling variants ...
samtools view: [mpileup] fail to read the header of -
writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Total processed positions in contig_161 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_161//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_161.0_1.vcf
Total time elapsed: 5.10 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_161.0_1.vcf, remove empty file
[INFO] Delay 2 seconds before starting variant calling ...
samtools view: [mpileup] fail to read the header of -
writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Calling variants ...
Total processed positions in contig_42 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_42//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_42.0_1.vcf
Total time elapsed: 0.00 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_42.0_1.vcf, remove empty file
[INFO] Delay 3 seconds before starting variant calling ...
Calling variants ...
[mpileup] fail to read the header of -
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Total processed positions in contig_190 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_190//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_190.0_1.vcf
Total time elapsed: 5.91 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_190.0_1.vcf, remove empty file
[INFO] Delay 4 seconds before starting variant calling ...
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
[mpileup] fail to read the header of -
Calling variants ...
Total processed positions in contig_41 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_41//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_41.0_1.vcf
Total time elapsed: 0.00 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_41.0_1.vcf, remove empty file
[INFO] Delay 3 seconds before starting variant calling ...
Calling variants ...
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
[mpileup] fail to read the header of -
Total processed positions in contig_16 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_16//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_16.0_1.vcf
Total time elapsed: 6.90 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_16.0_1.vcf, remove empty file
[INFO] Delay 3 seconds before starting variant calling ...
Calling variants ...
samtools view: writing to standard output failed[mpileup] fail to read the header of -
: Broken pipe
samtools view: error closing standard output: -1
Total processed positions in contig_194 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_194//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_194.0_1.vcf
Total time elapsed: 7.97 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_194.0_1.vcf, remove empty file
[INFO] Delay 3 seconds before starting variant calling ...
Calling variants ...
samtools view: writing to standard output failed[mpileup] fail to read the header of -
: Broken pipe
samtools view: error closing standard output: -1
Total processed positions in contig_25 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_25//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_25.0_1.vcf
Total time elapsed: 8.58 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_25.0_1.vcf, remove empty file
[INFO] Delay 1 seconds before starting variant calling ...
Calling variants ...
[mpileup] fail to read the header of -
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Total processed positions in contig_33 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_33//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_33.0_1.vcf
Total time elapsed: 8.81 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_33.0_1.vcf, remove empty file
[INFO] Delay 2 seconds before starting variant calling ...
Calling variants ...
[mpileup] fail to read the header of -
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Total processed positions in contig_35 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_35//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_35.0_1.vcf
Total time elapsed: 7.88 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_35.0_1.vcf, remove empty file
[INFO] Delay 3 seconds before starting variant calling ...
Calling variants ...
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
[mpileup] fail to read the header of -
Total processed positions in contig_36 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_36//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_36.0_1.vcf
Total time elapsed: 7.69 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_36.0_1.vcf, remove empty file
[INFO] Delay 1 seconds before starting variant calling ...
Calling variants ...
samtools view: writing to standard output failed: Broken pipe
[mpileup] fail to read the header of -
samtools view: error closing standard output: -1
Total processed positions in contig_50 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_50//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_50.0_1.vcf
Total time elapsed: 7.57 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_50.0_1.vcf, remove empty file
[INFO] Delay 2 seconds before starting variant calling ...
Calling variants ...
samtools view: writing to standard output failed: Broken pipe
[mpileup] fail to read the header of -
samtools view: error closing standard output: -1
Total processed positions in contig_49 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_49//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_49.0_1.vcf
Total time elapsed: 7.96 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_49.0_1.vcf, remove empty file
[INFO] Delay 1 seconds before starting variant calling ...
Calling variants ...
[mpileup] fail to read the header of -
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Total processed positions in contig_69 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_69//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_69.0_1.vcf
Total time elapsed: 8.35 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_69.0_1.vcf, remove empty file
[INFO] Delay 3 seconds before starting variant calling ...
Calling variants ...
[mpileup] fail to read the header of -
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Total processed positions in contig_61 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_61//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_61.0_1.vcf
Total time elapsed: 8.01 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_61.0_1.vcf, remove empty file
[INFO] Delay 2 seconds before starting variant calling ...
Calling variants ...
samtools view: [mpileup] fail to read the header of -
writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Total processed positions in contig_90 (chunk 1/1) : 0
[ERROR] No full-alignment output for file contig_90//home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_90.0_1.vcf
Total time elapsed: 8.31 s
[INFO] No vcf output for file /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment_contig_90.0_1.vcf, remove empty file

real    0m22.977s
user    1m20.538s
sys     0m16.302s
[WARNING] No vcf file found with prefix:/home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/tmp/full_alignment_output/full_alignment, output empty vcf file
[WARNING] Copying pileup.vcf.gz to /home/genomics/dslos/06_development/fusarium/03_variant_calling2/MY0231/merge_output.vcf.gz
[INFO] Exit in full-alignment variant calling

[aquaskyline]

Seems you disabled phasing for full alignment [INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: True. Could you please try not disabling it and see if it runs to the end.

[dgslos]

Same error appears. Small detail: it runs to the end in both scenarios, it creates pileup.vcf.gz files, but the full_alignment.vcf.gz files are without any variants called. Because of the warning '[WARNING] Please enable --no_phasing_for_fa if calling variant in non-diploid organisms', no phasing was on since my organisms are haploid.

[aquaskyline]

If that's the case, pileup.vcf.gz is all you can get from Clair3. Looking into your log, it seems the number of variants called are about one to two digits. The low number of variants called with pileup disables full-alignment calling from functioning because full-alignment needs a sufficient number of variants to find the best variant quality cutoff and to phase and haplotag the reads.

[dgslos]

Thanks! Can the error (or maybe better a warning?) message in that case be a bit more self-explanatory? Like the message you wrote now? =)

[JMencius]

Hi @aquaskyline I come across the similar error running the illumina test data provided at the Github page. As far as I comprehend, it is not error but warning due to high-quality pipeup and no work left for full alignment?

OSError: Cannot load library /home/miniconda3/envs/clair3/bin/preprocess/realign/realigner: /home/miniconda3/envs/clair3/bin/preprocess/realign/realigner: cannot open shared object file: No such file or directory
[mpileup] fail to read the header of -
Calling variants ...
Total processed positions in chr20 (chunk 1/1) : 0
[ERROR] No full-alignment output for file ./test/tmp/full_alignment_output/full_alignment_chr20.0_1.vcf
Total time elapsed: 0.00 s
[INFO] No vcf output for file /home/mencius/Downloads/test_ngs/./test/tmp/full_alignment_output/full_alignment_chr20.0_1.vcf, remove empty file

real    0m4.389s
user    0m2.115s
sys     0m1.432s
[WARNING] No vcf file found with prefix:/home/mencius/Downloads/test_ngs/./test/tmp/full_alignment_output/full_alignment, output empty vcf file
[WARNING] Copying pileup.vcf.gz to /home/mencius/Downloads/test_ngs/./test/merge_output.vcf.gz
[INFO] Exit in full-alignment variant calling

real    0m46.090s
user    0m59.090s
sys     0m15.168s