Hello, I'm trying to run squire Count from the SQuIRE pipeline (https://github.com/wyang17/SQuIRE), but it gives me the following error. Has anyone else encountered this error before and has a solution to fix this issue? Thank you for your help!!
Creating temporary files2022-02-04 03:01:46.965990
Creating unique and multiple alignment bedfiles 2022-02-04 03:01:46.966187
Identifying properly paired reads 2022-02-04 03:01:46.966198
Intersecting bam files with TE bedfile 2022-02-04 03:03:21.196100
Splitting into read1 and read 2 2022-02-04 03:04:29.400540
Combining adjacent TEs with same read alignment 2022-02-04 03:04:50.744557
Getting genomic coordinates of read2022-02-04 03:08:29.343584
Identifying and labeling unique and multi reads2022-02-04 03:09:31.003050
Matching paired-end mates and merging coordinates2022-02-04 03:10:30.134429
join: multi-character tab ‘-o’ Traceback (most recent call last): File "/home/gimena/miniconda3/envs/squire/bin/squire", line 11, in load_entry_point('SQuIRE', 'console_scripts', 'squire')() File "/home/gimena/SQuIRE/squire/cli.py", line 156, in main subargs.func(args = subargs) File "/home/gimena/SQuIRE/squire/Count.py", line 1743, in main match_reads(paired_tempfile1_ulabeled,paired_tempfile2_ulabeled,strandedness,paired_matched_tempfile,paired_unmatched1, paired_unmatched2,debug) #match pairs between paired files File "/home/gimena/SQuIRE/squire/Count.py", line 494, in match_reads sp.check_call(["/bin/sh","-c",joincommand]) File "/home/gimena/miniconda3/envs/squire/lib/python2.7/subprocess.py", line 186, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/bin/sh', '-c', "join -j 12 -t $(printf '\t') -o 1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9,2.10 /home/gimena/simulation/test_squire/test_results2/sample_0/count_folder/sample_0_paired_ulabeled_1.tmpss_HWj_newread_v1 /home/gimena/simulation/test_squire/test_results2/sample_0/count_folder/sample_0_paired_ulabeled_2.tmpSEqE7c_newread_v1 > /home/gimena/simulation/test_squire/test_results2/sample_0/count_folder/sample_0_paired_matched.tmpyDeayp_10k_v1"]' returned non-zero exit status 1
