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Crash when running micro-assembly mode on SRR30326616 #54

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evolarjun opened this issue Aug 28, 2024 · 0 comments
Open

Crash when running micro-assembly mode on SRR30326616 #54

evolarjun opened this issue Aug 28, 2024 · 0 comments

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@evolarjun
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SeqSero2 version 1.3.1 crashes in micro-assembly mode on run SRR30326616

$ fasterq-dump --skip-technical --split-files SRR30326616
spots read      : 4,666,195
reads read      : 9,332,390
reads written   : 9,332,390
$ SeqSero2_package.py  --phred_offset 33 -d seqsero2test -t 2 -m a -p 4 -i SRR30326616_1.fastq SRR30326616_2.fastq
building database...
mapping...
check samtools version: 1.13
/netmnt/vast01/pd/prod/PATHOGEN_DETECT/system/2024-08-07.build4289/third-party/SeqSero2/env/bin/SeqSero2_package.py:1205: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
  if LooseVersion(version)<=LooseVersion("1.2"):
[bam_sort_core] merging from 0 files and 4 in-memory blocks...
assembling...
blasting...

Traceback (most recent call last):
  File "/netmnt/vast01/pd/prod/PATHOGEN_DETECT/system/2024-08-07.build4289/third-party/SeqSero2/env/bin/SeqSero2_package.py", line 1657, in <module>
    main()
  File "/netmnt/vast01/pd/prod/PATHOGEN_DETECT/system/2024-08-07.build4289/third-party/SeqSero2/env/bin/SeqSero2_package.py", line 1413, in main
    O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H,Otypes_uniq,H1_cont_stat_list,H2_cont_stat_list=predict_O_and_H_types(Final_list,Final_list_passed,new_fasta) #predict O, fliC and fljB
  File "/netmnt/vast01/pd/prod/PATHOGEN_DETECT/system/2024-08-07.build4289/third-party/SeqSero2/env/bin/SeqSero2_package.py", line 847, in predict_O_and_H_types
    O_choice,O_nodes,special_gene_list,O_nodes_roles,contamination_O,Otypes_uniq=decide_O_type_and_get_special_genes(Final_list,Final_list_passed)#decide the O antigen type and also return special-gene-list for further identification
  File "/netmnt/vast01/pd/prod/PATHOGEN_DETECT/system/2024-08-07.build4289/third-party/SeqSero2/env/bin/SeqSero2_package.py", line 719, in decide_O_type_and_get_special_genes
    highest_O_coverage=max([float(x[0].split("_cov_")[-1].split("_")[0]) for x in final_O if "O-1,3,19_not_in_3,10" not in x[0]])
ValueError: max() arg is an empty sequence
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