search

marbl / metAMOS

A metagenomic and isolate assembly and analysis pipeline built with AMOS
http://marbl.github.io/metAMOS
Other
93 stars 45 forks source link

rm: cannot remove `~/all.seq.mates': No such file or directory #264

Closed chen496 closed 7 years ago

chen496 commented 7 years ago

Hi, I have a question that when I run the command without -t eautils, it shows the error following: my file is single and without adapters. if I add the -t option it does not show any problems.

../initPipeline -f -1 51GHLH2.fa -d test2 ../runPipeline -a mira -c fcp -g fraggenescan -y -p 16 -d test2 -v

The PROCESS.log: Picked up _JAVA_OPTIONS: -Xmx512m rm: cannot remove `/nethome/cxw496/software/src/metAMOS-1.5rc3/chen/test2/Preprocess/out/all.seq.mates': No such file or directory

The error:

Starting Task = preprocess.PREPROCESS *** metAMOS running command: java -cp /nethome/cxw496/software/src/metAMOS-1.5rc3/Utilities/java:.:. outputDefaultQuality /nethome/cxw496/software/src/metAMOS-1.5rc3/chen/test2/Preprocess/in/51GHLH2.fa > /nethome/cxw496/software/src/metAMOS-1.5rc3/chen/test2/Preprocess/in/51GHLH2.fa.qual

*** metAMOS running command: rm /nethome/cxw496/software/src/metAMOS-1.5rc3/chen/test2/Preprocess/out/all.seq.mates

Read file corrupted, please fix and restart! Oops, MetAMOS finished with errors! see text in red above for details. Traceback (most recent call last): File "../runPipeline", line 991, in verbose = 1) File "/nethome/cxw496/software/src/metAMOS-1.5rc3/Utilities/ruffus/task.py", line 2965, in pipeline_run raise job_errors RethrownJobError: 

Exception #1
  'exceptions.SystemExit(1)' raised in ...
   Task = def preprocess.Preprocess(...):
   Job  = [[51GHLH2.fa] -> preprocess.success]

Traceback (most recent call last): File "/nethome/cxw496/software/src/metAMOS-1.5rc3/Utilities/ruffus/task.py", line 625, in run_pooled_job_without_exceptions return_value = job_wrapper(param, user_defined_work_func, register_cleanup, touch_files_only) File "/nethome/cxw496/software/src/metAMOS-1.5rc3/Utilities/ruffus/task.py", line 491, in job_wrapper_io_files ret_val = user_defined_work_func(*param) File "/nethome/cxw496/software/src/metAMOS-1.5rc3/src/preprocess.py", line 536, in Preprocess sys.exit(1) SystemExit: 1

Thanks Chen

skoren commented 7 years ago

I think there is a bug in processing unpaired fasta reads, comment out lines 534-536 and it should work.

534 #                   if len(reads) % 2 != 0:
535 #                       print "Read file corrupted, please fix and restart!"
536 #                       sys.exit(1)
chen496 commented 7 years ago

OK, Thank you very much