Error 'OSError: [Errno 2] No such file or directory' while running test

[alexis groppi]

Dear Leszek,


Sorry for bothering you again  but before running Redundans on my genome assembly, I've checked the installation by running the included test.
I had this error :

ag@rainman:~/redundans$ ./redundans.py -v -i test/*.fq.gz -f test/contigs.fa -o test/run1
Options: Namespace(fasta='test/contigs.fa', fastq=['test/5000_1.fq.gz', 'test/5000_2.fq.gz', 'test/600_1.fq.gz', 'test/600_2.fq.gz', 'test/pacbio.fq.gz'], identity=0.51, iters=2, joins=5, limit=0.2, linkratio=0.7, log=<open file '<stderr>', mode 'w' at 0x7f53191ce270>, longreads=[], mapq=10, minLength=200, nocleaning=True, nogapclosing=True, norearrangements=False, noreduction=True, noscaffolding=True, outdir='test/run1', overlap=0.66, reference='', resume=False, threads=4, verbose=True)

##################################################
[Mon Feb 27 15:44:35 2017] Preparing contigs...
 101 sequences stored.

##################################################
[Mon Feb 27 15:44:35 2017] Reduction...
#file name      genome size     contigs heterozygous size       [%]     heterozygous contigs    [%]     identity [%]possible joins   homozygous size [%]     homozygous contigs      [%]
test/run1/contigs.fa    149715  101     52714   35.21   79      78.22   94.802  0       97001   64.79   22      21.78

##################################################
[Mon Feb 27 15:50:19 2017] Estimating parameters of libraries...
 Aligning 19400 mates per library...
Insert size statistics                          Mates orientation stats
FastQ files     read length     median  mean    stdev   FF      FR      RF      RR
test/5000_1.fq.gz test/5000_2.fq.gz     50      4998    4990.20 721.47  0       4674    0       0
test/600_1.fq.gz test/600_2.fq.gz       100     599     598.63  47.68   0       10000   0       0

##################################################
[Mon Feb 27 15:50:19 2017] Scaffolding...
 iteration 1.1 of 2.2 ...
Traceback (most recent call last):
  File "./redundans.py", line 512, in <module>
    main()
  File "./redundans.py", line 507, in main
    o.norearrangements, o.verbose, o.log)
  File "./redundans.py", line 314, in redundans
    identity, overlap, minLength, resume)
  File "./redundans.py", line 121, in run_scaffolding
    sspacebin, verbose=0, log=log)
  File "/home/ag/redundans/bin/fastq2sspace.py", line 191, in fastq2sspace
    tabFnames = get_tab_files(out, fasta, libnames, libFs, libRs, libIS, libISStDev, libreadlen, cores, mapq, upto, verbose, log)
  File "/home/ag/redundans/bin/fastq2sspace.py", line 144, in get_tab_files
    proc = _get_aligner_proc(f1.name, f2.name, ref, cores, verbose, bwalog)
  File "/home/ag/redundans/bin/fastq2sspace.py", line 117, in _get_snap_proc
    proc = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=log)
  File "/module/apps/python/2.7.3/lib/python2.7/subprocess.py", line 679, in __init__
    errread, errwrite)
  File "/module/apps/python/2.7.3/lib/python2.7/subprocess.py", line 1249, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

I have tried with python 2.7.3 and python 2.7.9 with the same result

What's going wrong ?

Thanks for your help

Alexis

[alexis groppi]

I found this old FAQ (thanks Google cache ;) ) :

Redundans fails with OSError or maf-convert: not found or lastal: can't interpret: TAB.

Make sure you are using the latest version of LAST aligner and that all dependencies are accessible through your PATH environmental variable.

OSError: [Errno 13] Permission denied

# or

OSError: [Errno 2] No such file or directory

# or
[ERROR] maf-convert: not found

I've checked the version of last installed with Redundans :

 ./lastal --version
lastal 719

But the last version of last is 833 (http://last.cbrc.jp/ )

Should I update the version included in Redundans (/redundans/bin/last/) ? to solve this error ?

Thanks

Alexis