Open jayramr opened 1 year ago
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
Hi,
Please help with sorting this issue
I already reinstalled the squire package still same error
And the files are available in the below location
Thanks Jay