cat: "sequence" : No such file or directory
covux
hey,
I ran the run_calls.pl script.
this is
the command:
time perl run_calls.pl --first_kmer 31
--last_kmer 61 --kmer_step 30 --fastaq_index INDEX --auto_cleaning
yes --bc yes --pd no --outdir Test_2 --outvcf NAME --ploidy 1
stampy_hash refname --stampy_bin
/media/STUDENT_FS1/stampy-1.0.31//stampy.py --list_ref_fasta
E.coli_K12_MG1655.fasta --refbindir ref/ --genome_size 5000000
--qthresh 5 --mem_height 21 --mem_width 100 --vcftools_dir
/media/STUDENT_FS1/Program_files/vcftools/ --do_union yes --ref
CoordinatesAndInCalling --workflow independent --logfile vcflog_2.txt
--apply_pop_classifier
after a while i see
this in my terminal:
......
cat:
GTTTTCACTGCCGAAAATGAAAGCCAGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAA:
No such file or directory
cat:
GGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCA:
No such file or directory
cat:
GATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTCCGGCGTATCCGGCGTAGATTC:
No such file or directory
....
just rows upon rows of
sequences.
When i look in my output dir i see
that the "binaries" en "calls" dir are filled
with logs and i read no error messages in the logs files.
the
"vcfs" dir has three files:
SAMPLES: file with a list
of reference and samples.
temp_ref.fa: this file is
empty
tmp_working: this map is empty.
My guess
is that i tell the script the wrong place where to find VCFTools.
so
i also tried the next command line:
time perl run_calls.pl
--first_kmer 31 --last_kmer 61 --kmer_step 30 --fastaq_index INDEX
--auto_cleaning yes --bc yes --pd no --outdir dirname_9 --outvcf NAME
--ploidy 1 stampy_hash refname --stampy_bin /home/johan/bin/stampy.py
--list_ref_fasta E.coli_K12_MG1655.fasta --refbindir ref/
--genome_size 5000000 --qthresh 5 --mem_height 21 --mem_width 100
--vcftools_dir /usr/local/bin/vcftools --do_union yes --ref
CoordinatesAndInCalling --workflow independent --logfile vcflog_9.txt
--apply_pop_classifier
the manual mentions for
--vcftools_dir that the directory should have the following sub
directories: bin,cpp,lib etc.
When i look into my vcftools
dir i don't see the before mentioned maps. ( look image below)
I
use VCFtools version 0.1.15.
is it possible that this version is just not compatible with
the script?
or is something else the cause of this
problem?
Regards,
Covux
