You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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
The text was updated successfully, but these errors were encountered:
SeqSero2 version 1.3.1 crashes in micro-assembly mode on run SRR30326616
The text was updated successfully, but these errors were encountered: