Error while running call

[jayramr]

Hi,

Please help with sorting this issue

I already reinstalled the squire package still same error

squire Call -1 LDN-M* -2 LDN-S* -A mutant -B sibs -i data/analysis/squire_count/ -o data/analysis/squire_call/locus -p 24 -v
Script start time is:2022-12-14 13:35:55.982279

Script Arguments
=================
count_folder=data/analysis/squire_count/
projectname=SQuIRE
output_format=html
pthreads=24
call_folder=data/analysis/squire_call/locus
condition2=sibs
table_only=False
group1=LDN-M1_ACAGTG_L003_R1_001.fastq.gz
func=<function main at 0x1555534c46e0>
group2=LDN-S1_CTTGTA_L003_R1_001.fastq.gz
subfamily=False
verbosity=True
condition1=mutant

Traceback (most recent call last):
  File "/scratch/gencore/conda3/envs/squire/bin/squire", line 10, in <module>
    sys.exit(main())
  File "/scratch/gencore/conda3/envs/squire/lib/python2.7/site-packages/squire/cli.py", line 156, in main
    subargs.func(args = subargs)
  File "/scratch/gencore/conda3/envs/squire/lib/python2.7/site-packages/squire/Call.py", line 271, in main
    group1_list=get_groupfiles(group1,gene_files,subF_files,TE_files,subfamily,count_folder)
  File "/scratch/gencore/conda3/envs/squire/lib/python2.7/site-packages/squire/Call.py", line 88, in get_groupfiles
    TE_files.append(find_file(count_folder,"_TEcounts.txt",sample,1,True))
  File "/scratch/gencore/conda3/envs/squire/lib/python2.7/site-packages/squire/Call.py", line 43, in find_file
    raise Exception("No " + pattern + " file")
Exception: No _TEcounts.txt file

And the files are available in the below location

ls -l data/analysis/squire_count/*_TEcounts.txt

Thanks Jay

[mengying0714]

I have the same question, Have you solved it?

[jayramr]

No i never tried after that.