subprocess error

[gucascau]

Hi all, I am working on a polymorphic genome, and tried to use this software. But after installing everything, I kept getting the following error when using the test data. I am not sure what is the reason. Can anyone help me to solve this problem? Thank you so much.

Traceback (most recent call last):
File "./redundans.py", line 521, in
main()
File "./redundans.py", line 516, in main
o.norearrangements, o.verbose, o.log)
File "./redundans.py", line 315, in redundans
libraries = get_libraries(fastq, lastOutFn, mapq, threads, verbose, log)
File "./redundans.py", line 62, in get_libraries
genomeFrac, stdfracTh, maxcfracTh)
File "/home/xinw/software/redundans/bin/fastq2insert_size.py", line 189, in fastq2insert_size
isstats = get_isize_stats(fq1, fq2, fasta, mapq, threads, limit, verbose, stdfracTh, maxcfracTh)
File "/home/xinw/software/redundans/bin/fastq2insert_size.py", line 111, in get_isize_stats
aligner = _get_snap_proc(fq1, fq2, fasta, threads, verbose, alignerlog)
File "/home/xinw/software/redundans/bin/fastq2sspace.py", line 133, in _get_snap_proc
proc = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=log)
File "/usr/local/lib/python2.7/subprocess.py", line 390, in init
errread, errwrite)
File "/usr/local/lib/python2.7/subprocess.py", line 1024, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

[lpryszcz]

Hi, Can you list the content of output dir ls -lah and write me exact command?

[mzinkgraf]

I am getting the same error. Below are are the command and outputs.
Thanks for your help

redundans zinkgrm$ ./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 '', mode 'w' at 0x10f9811e0>, longreads=[], mapq=10, minLength=200, nocleaning=True, nogapclosing=True, norearrangements=False, noreduction=True, noscaffolding=True, outdir='test/run1', overlap=0.8, reference='', resume=False, threads=4, verbose=True)

##################################################
[Fri Dec 8 09:36:31 2017] Reduction...
#file name genome size contigs heterozygous size [%] heterozygous contigs [%] identity [%] possible joins homozygous size [%] homozygous contigs [%]
test/run1/contigs.fa 163897 245 66377 40.50 221 90.20 94.854 0 97520 59.50 24 9.80

##################################################
[Fri Dec 8 09:36:34 2017] Estimating parameters of libraries...
Aligning 19504 mates per library...
Insert size statistics Mates orientation stats
FastQ files read length median mean stdev FF FR RF RR
Traceback (most recent call last):
File "./redundans.py", line 521, in
main()
File "./redundans.py", line 516, in main
o.norearrangements, o.verbose, o.log)
File "./redundans.py", line 315, in redundans
libraries = get_libraries(fastq, lastOutFn, mapq, threads, verbose, log)
File "./redundans.py", line 62, in get_libraries
genomeFrac, stdfracTh, maxcfracTh)
File "/Users/zinkgrm/Documents/scripts/redundans/bin/fastq2insert_size.py", line 189, in fastq2insert_size
isstats = get_isize_stats(fq1, fq2, fasta, mapq, threads, limit, verbose, stdfracTh, maxcfracTh)
File "/Users/zinkgrm/Documents/scripts/redundans/bin/fastq2insert_size.py", line 111, in get_isize_stats
aligner = _get_snap_proc(fq1, fq2, fasta, threads, verbose, alignerlog)
File "/Users/zinkgrm/Documents/scripts/redundans/bin/fastq2sspace.py", line 133, in _get_snap_proc
proc = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=log)
File "/Users/zinkgrm/anaconda2/lib/python2.7/subprocess.py", line 390, in init
errread, errwrite)
File "/Users/zinkgrm/anaconda2/lib/python2.7/subprocess.py", line 1024, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

redundans zinkgrm$ ls -lah test/run1/
total 1200
drwxr-xr-x 17 zinkgrm staff 578B Dec 8 09:36 .
drwxr-xr-x 14 zinkgrm staff 476B Dec 8 09:36 ..
lrwxr-xr-x 1 zinkgrm staff 58B Dec 8 09:36 contigs.fa -> /Users/zinkgrm/Documents/scripts/redundans/test/contigs.fa
-rw-r--r-- 1 zinkgrm staff 23K Dec 8 09:36 contigs.fa.bck
-rw-r--r-- 1 zinkgrm staff 8.7K Dec 8 09:36 contigs.fa.des
lrwxr-xr-x 1 zinkgrm staff 62B Dec 8 09:36 contigs.fa.fai -> /Users/zinkgrm/Documents/scripts/redundans/test/contigs.fa.fai
-rw-r--r-- 1 zinkgrm staff 475B Dec 8 09:36 contigs.fa.prj
-rw-r--r-- 1 zinkgrm staff 984B Dec 8 09:36 contigs.fa.sds
-rw-r--r-- 1 zinkgrm staff 984B Dec 8 09:36 contigs.fa.ssp
-rw-r--r-- 1 zinkgrm staff 121K Dec 8 09:36 contigs.fa.suf
-rw-r--r-- 1 zinkgrm staff 160K Dec 8 09:36 contigs.fa.tis
-rw-r--r-- 1 zinkgrm staff 98K Dec 8 09:36 contigs.reduced.fa
-rw-r--r-- 1 zinkgrm staff 29K Dec 8 09:36 contigs.reduced.fa.0.05
-rw-r--r-- 1 zinkgrm staff 270B Dec 8 09:36 contigs.reduced.fa.0.05.log
-rw-r--r-- 1 zinkgrm staff 1.7K Dec 8 09:36 contigs.reduced.fa.fai
-rw-r--r-- 1 zinkgrm staff 6.9K Dec 8 09:36 contigs.reduced.fa.hetero.tsv
-rw-r--r-- 1 zinkgrm staff 106K Dec 8 09:36 contigs.reduced.fa.hist.png
redundans zinkgrm$

[lpryszcz]

can you make sure snap-aligner is correctly installed? There should be executable in REDUNDANS_SRC/bin/snap. It there isn't, try to compile it: cd bin/snap && make clean && make

[lpryszcz]

Alternatively, update to the latest version and try again. If it fails, you can run it with -b which will use BWA instead of snap-aligner.

git clone --recursive https://github.com/lpryszcz/redundans.git
cd redundans && bin/.compile.sh