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'