Errors in mapping and calling

[uedaMT]

Hi, I got the following errors when running squire Map and Call. It looks like similar problems to #19 , but I am not sure how to fix it. Please would you let me know how to solve these problems?

• Map error. Traceback (most recent call last): File "/data02/home/usr/.pyenv/versions/miniconda3-latest/envs/squire/bin/squire", line 11, in load_entry_point('SQuIRE', 'console_scripts', 'squire')() File "/data02/home/usr/bio/SQuIRE/squire/cli.py", line 156, in main subargs.func(args = subargs) File "/data02/home/usr/bio/SQuIRE/squire/Map.py", line 387, in main align_paired(read1,read2,pthreads,trim3,index,outfile,gtf,gzip,prefix, read_length,extra_fapath) File "/data02/home/usr/bio/SQuIRE/squire/Map.py", line 138, in align_paired sp.check_call(["/bin/sh", "-c", sortcommand]) File "/data02/home/usr/.pyenv/versions/miniconda3-latest/envs/squire/lib/python2.7/subprocess.py", line 190, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/bin/sh', '-c', 'samtools sort -@ 1 squire_map/01A_R1_trim.fastqAligned.out.bam squire_map/01A_R1_trim.fastq']' returned non-zero exit status 1

I got the above error, but I confirmed I could get bam file by squire map. So I tried squire call and got the following error.

• Call error Traceback (most recent call last): File "/data02/home/usr/.pyenv/versions/miniconda3-latest/envs/squire/bin/squire", line 11, in load_entry_point('SQuIRE', 'console_scripts', 'squire')() File "/data02/home/usr/bio/SQuIRE/squire/cli.py", line 156, in main subargs.func(args = subargs) File "/data02/home/usr/bio/SQuIRE/squire/Call.py", line 270, in main group1_list=get_groupfiles(group1,gene_files,subF_files,TE_files,subfamily,count_folder) File "/data02/home/usr/bio/SQuIRE/squire/Call.py", line 88, in get_groupfiles TE_files.append(find_file(count_folder,"_TEcounts.txt",sample,1,True)) File "/data02/home/usr/bio/SQuIRE/squire/Call.py", line 43, in find_file raise Exception("No " + pattern + " file")

[MaxwellShih]

Hello @mahoko Not sure whether you have got any solutions. I basically followed @mariuswalter's instruction: https://github.com/wyang17/SQuIRE/issues/19#issuecomment-466719707 Use a text editor such as vim to edit the code of squire/Count.py Hope this helps.

[uedaMT]

My apologies for the delayed response! I followed the instruction #19, but could not fix the problem… So I removed squire and re-installed it. Not sure why, but it worked! Thank you for developing this nice tool!

[netwchao]

Hello，I got the following errors when running squire Call. How can I fix this error：