Missing pickle file

[mnshgl0110]

Hi,
I am trying to run cutesv on human HG002 genome. But I am getting the missing pickle file error:
FileNotFoundError: [Errno 2] No such file or directory: 'hg002/results/KMT2C_chr13_10688343_10754814.pickle'
cutesv.log
Based on the suggestions here, I have tried conda as well as git install. Further, I also tried different number to threads (from here), but that did not work either.
Any suggestions, how can I make it work?

[Meltpinkg]

Hello, @mnshgl0110

This may caused by the reference used in the read alignment not equaling the reference used in running cuteSV. Please ensure the reference chromosomes in the read alignment and SV calling is the same.
Hope it will help!

Best,
Shuqi

[mulderdt]

Hi, I am getting the same issue since moving from cuteSV 2.0.3 to 2.1.1.

Most samples work fine. I have checked that the reference matches alignment and cuteSV process.

I have seen it fail on chr17.pickle and on chr2.pickle.

It seems to be transient and if I just rerun it it works fine. It doesn't look to be a resources issue.

Thanks,

see error below

ERROR ~ Error executing process > 'cuteSV_single (LR-115_father-F139924)'

Caused by:
Process cuteSV_single (LR-115_father-F139924) terminated with an error exit status (1)

Command executed:

cuteSV --sample LR-115_father-F139924 --threads 4 -md 500 -mi 500 -s 5 -L -1 --genotype F139924_1_lane.bam hg38_no_alt.fa LR-115_father-F139924.vcf .

Command exit status:
1

Command output:
(empty)

Command error:
2025-01-06 01:19:20,555 [INFO] Finished chrUn_KI270751v1-chrX:TRA/BND.
2025-01-06 01:19:20,555 [INFO] Finished chrUn_KI270751v1-chrY:TRA/BND.
2025-01-06 01:19:20,556 [INFO] Finished chrUn_KI270755v1-chrX:TRA/BND.
2025-01-06 01:19:20,557 [INFO] Finished chrUn_KI270756v1-chrY:TRA/BND.
2025-01-06 01:19:20,557 [INFO] Finished chrUn_KI270757v1-chrX:TRA/BND.
2025-01-06 01:19:20,557 [INFO] Finished chrUn_KI270757v1-chrY:TRA/BND.
2025-01-06 01:19:20,580 [INFO] Finished chr4-chrY:TRA/BND.
2025-01-06 01:19:20,638 [INFO] Finished chr3-chrUn_GL000224v1:TRA/BND.
2025-01-06 01:19:20,638 [INFO] Finished chr3-chrUn_GL000226v1:TRA/BND.
2025-01-06 01:19:20,638 [INFO] Finished chr3-chrUn_KI270333v1:TRA/BND.
2025-01-06 01:19:20,638 [INFO] Finished chr3-chrUn_KI270336v1:TRA/BND.
2025-01-06 01:19:20,654 [INFO] Finished chrX-chrY:TRA/BND.
2025-01-06 01:19:20,847 [INFO] Finished chr3-chrUn_KI270337v1:TRA/BND.
2025-01-06 01:19:20,848 [INFO] Finished chr3-chrUn_KI270362v1:TRA/BND.
2025-01-06 01:19:20,848 [INFO] Finished chr3-chrUn_KI270435v1:TRA/BND.
2025-01-06 01:19:20,848 [INFO] Finished chr3-chrUn_KI270438v1:TRA/BND.
2025-01-06 01:19:20,848 [INFO] Finished chr3-chrUn_KI270442v1:TRA/BND.
2025-01-06 01:19:20,848 [INFO] Finished chr3-chrUn_KI270467v1:TRA/BND.
2025-01-06 01:19:20,848 [INFO] Finished chr3-chrUn_KI270510v1:TRA/BND.
2025-01-06 01:19:20,848 [INFO] Finished chr3-chrUn_KI270519v1:TRA/BND.
2025-01-06 01:19:20,848 [INFO] Finished chr3-chrUn_KI270584v1:TRA/BND.
2025-01-06 01:19:20,848 [INFO] Finished chr3-chrUn_KI270589v1:TRA/BND.
2025-01-06 01:19:20,848 [INFO] Finished chr3-chrUn_KI270590v1:TRA/BND.
2025-01-06 01:19:20,848 [INFO] Finished chr3-chrUn_KI270741v1:TRA/BND.
2025-01-06 01:19:20,848 [INFO] Finished chr3-chrUn_KI270742v1:TRA/BND.
2025-01-06 01:19:20,848 [INFO] Finished chr3-chrUn_KI270743v1:TRA/BND.
2025-01-06 01:19:20,849 [INFO] Finished chr3-chrUn_KI270744v1:TRA/BND.
2025-01-06 01:19:20,849 [INFO] Finished chr3-chrUn_KI270745v1:TRA/BND.
2025-01-06 01:19:20,849 [INFO] Finished chr3-chrUn_KI270746v1:TRA/BND.
2025-01-06 01:19:20,849 [INFO] Finished chr3-chrUn_KI270747v1:TRA/BND.
2025-01-06 01:19:20,849 [INFO] Finished chr3-chrUn_KI270748v1:TRA/BND.
2025-01-06 01:19:20,849 [INFO] Finished chr3-chrUn_KI270749v1:TRA/BND.
2025-01-06 01:19:20,849 [INFO] Finished chr3-chrUn_KI270750v1:TRA/BND.
2025-01-06 01:19:20,849 [INFO] Finished chr3-chrUn_KI270751v1:TRA/BND.
2025-01-06 01:19:20,849 [INFO] Finished chr3-chrUn_KI270754v1:TRA/BND.
2025-01-06 01:19:20,849 [INFO] Finished chr3-chrUn_KI270756v1:TRA/BND.
2025-01-06 01:19:21,147 [INFO] Finished chrUn_KI270743v1-chrUn_KI270744v1:TRA/BND.
2025-01-06 01:19:21,147 [INFO] Finished chrUn_KI270743v1-chrX:TRA/BND.
2025-01-06 01:19:21,178 [INFO] Finished chr3-chrUn_KI270757v1:TRA/BND.
2025-01-06 01:19:21,937 [INFO] Finished chr3-chrX:TRA/BND.
2025-01-06 01:19:22,202 [INFO] Finished chr3-chrY:TRA/BND.
2025-01-06 01:19:22,245 [INFO] Writing to your output file.
Traceback (most recent call last):
File "/usr/local/bin/cuteSV", line 1269, in
run(sys.argv[1:])
File "/usr/local/bin/cuteSV", line 1265, in run
main_ctrl(args, argv)
File "/usr/local/bin/cuteSV", line 1232, in main_ctrl
with open("%sresults/%s.pickle"%(temporary_dir,chrom), "rb") as f:
FileNotFoundError: [Errno 2] No such file or directory: './results/chr2.pickle'

[Meltpinkg]

Hello, @mulderdt

Sorry for my late reply. I will focus on this question and repair it in this week.

Best,
Shuqi

[Meltpinkg]

Hello, @mulderdt

This seems to be an unstable issue. We updated cuteSV to v2.1.2 and optimized the output log content.
Hope it will help!

Best,
Shuqi

[Lupphes]

Hello, it seems that I have the same issue as was described with version 2.1.2

Traceback (most recent call last):
  File "/scratch.ssd/luppo/job_10621375.pbs-m1/.conda_next/env-bbd419b6a0312844-f62cc41dcb22731dc1d7ae3e0b3842ed/bin/cuteSV", line 1260, in <module>
    run(sys.argv[1:])
  File "/scratch.ssd/luppo/job_10621375.pbs-m1/.conda_next/env-bbd419b6a0312844-f62cc41dcb22731dc1d7ae3e0b3842ed/bin/cuteSV", line 1256, in run
    main_ctrl(args, argv)
  File "/scratch.ssd/luppo/job_10621375.pbs-m1/.conda_next/env-bbd419b6a0312844-f62cc41dcb22731dc1d7ae3e0b3842ed/bin/cuteSV", line 1222, in main_ctrl
    raise FileNotFoundError("[Errno 2] No such directory: %sresults/%s.pickle"%(temporary_dir,chrom))
FileNotFoundError: [Errno 2] No such directory: ./results/NC_091688.1.pickle

#!/usr/bin/env bash -C -e -u -o pipefail
cuteSV         SRR30001036.bam \
    GCF_041296265.fna \
    SRR30001036_sas_cutesv.vcf \
    . \
    --threads 12 \
    --max_cluster_bias_INS 1000 --diff_ratio_merging_INS 0.9 --max_cluster_bias_DEL 1000 --diff_ratio_merging_DEL 0.5 --report_readid --max_split_parts -1 --sample cutesv_report_sample --genotype
cat <<-END_VERSIONS > versions.yml
"NFCORE_EUKAVARIZER:EUKAVARIZER:SV_CALLING_CUTESV:CUTESV":
    cuteSV: $( cuteSV --version 2>&1 | sed 's/cuteSV //g' )
END_VERSIONS

[Meltpinkg]

Hello, @Lupphes

Sorry for my late reply. Since the error appears unstable and transient, I found it hard to reproduce and debug this issue. We have implemented enhanced error detection and handling mechanisms in the latest release of cuteSV, which has been updated on GitHub. If you're still experiencing this problem, you can: (1) execute the updated version of cuteSV from the GitHub repository, (2) check log files for "Finished ... output" lines (where ... is the problematic chromosome). In addition, sharing a minimal dataset that reproduces the error would greatly help our investigation.
We'll continue monitoring this issue and appreciate your feedback.

Best regards,
Shuqi

[superdaa]

Hello, it seems that I have the same issue as was described with version 2.1.2

Traceback (most recent call last): File "/diskNew/changdaD/miniconda3/envs/longread-wgs/bin/cuteSV", line 1260, in <module> run(sys.argv[1:]) ~~~^^^^^^^^^^^^^^ File "/diskNew/changdaD/miniconda3/envs/longread-wgs/bin/cuteSV", line 1256, in run main_ctrl(args, argv) ~~~~~~~~~^^^^^^^^^^^^ File "/diskNew/changdaD/miniconda3/envs/longread-wgs/bin/cuteSV", line 1222, in main_ctrl raise FileNotFoundError("[Errno 2] No such directory: %sresults/%s.pickle"%(temporary_dir,chrom)) FileNotFoundError: [Errno 2] No such directory: work_dir/results/chr7_KI270808v1_alt.pickle

[Meltpinkg]

Hello, @superdaa

It seems like a problem caused by the alt contigs. Could you provide the total running logs or the resource of the input BAM file? It would be more convenient for me to reproduce and locate the issue. Further contact and data sharing can be initiated through my email: sqcao@stu.hit.edu.cn. We'll continue monitoring this issue and appreciate your feedback.

Best regards,
Shuqi

[thom-99]

commenting on this issue,
I had a similar issue when running my pipeline with version 2.1.2
I have tried to downgrade to version 1.0.13 and it runs without errors.

perhaps it can help, cheers.