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elzbth / jitterbug

Jitterbug is a bioinformatic software that predicts insertion sites of transposable elements in a sample sequenced by short paired-end reads with respect to an assembled reference.
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subprocess.Popen error #10

Closed maolun closed 7 years ago

maolun commented 7 years ago

I am trying to run jitterbug on Arabidopsis genomes, but an subprocess error occurred that prevents the program from running. It seems that one argument was missing but I can't figure out which one. I wonder if anyone has the same problem and was able to fix it. Thank you.

I have tried python 2.7.9 and 2.7.10 but the same error occurred.

Traceback (most recent call last): File "/home-3/maolun/jitterbug-master/jitterbug.py", line 140, in main(sys.argv[1:]) File "/home-3/maolun/jitterbug-master/jitterbug.py", line 136, in main args.numCPUs, args.bin_size, args.minMAPQ, generate_test_bam, args.pre_filter, args.conf_lib_stats, mem, args.min_cluster_size) File "/home-3/maolun/jitterbug-master/Run_TE_ID_reseq.py", line 248, in run_jitterbug int_bed_reads_select = subprocess.Popen(args) File "/cm/shared/apps/python/2.7.9/lib/python2.7/subprocess.py", line 710, in init errread, errwrite) File "/cm/shared/apps/python/2.7.9/lib/python2.7/subprocess.py", line 1335, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory

Best regards, Mao-Lun

mbosio85 commented 7 years ago

Hi,

in the lines previous to that the args of Popen are defined:

args = ["samtools", "view", "-hb", "-L", bed_file_name, "-o", ins_regions_bam_name, psorted_bamfile_name] 247 # open subprocess 248 int_bed_reads_select = subprocess.Popen(args)

Can you check if the files referring to [bed_file_name and ins_regions_bam_name] exist because it's the likely source of the OSError:[Errno 2] No such file or directory

Mattia

maolun commented 7 years ago

Hi Mattia,

Thanks for the response. It turns out that it has something to do with multiple version of python installed in the cluster I am using at my institute. I have to change the shebang line in jitterbug.py to refer to the correct python version.

Mao-Lun

maolun commented 7 years ago

Update information. I finally figured out what the error is about. It is because the samtools is not available that cause the subprocess.Popen(args) having an error of 'no such file or directory'.

I would suggest maybe adding a line for checking the availability of samtools in the script.

Mao-Lun

mbosio85 commented 7 years ago

Thanks we will add a check for it