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halelab / GBS-SNP-CROP

GBS SNP Calling Reference Optional Pipeline
GNU General Public License v2.0
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System can't save *.R1.fa.gz #29

Closed rhasbunz closed 2 years ago

rhasbunz commented 4 years ago

Hi halelab

I am using your pipeline but in Step 4 I have this problem:

Mac-Pro-de-Rodrigo-2:demultiplexed rhasbun$ perl GBS-SNP-CROP-4.pl -vs /usr/local/bin/vsearch -d SE -b BarcodeID.txt -rl 150 -t 10 -cl consout -id 0.93 -db 88 -min 32 -MR GSC.MR

#################################

GBS-SNP-CROP, Step 4, v.4.1

################################# Parsing single-end reads for building the Mock Reference...

vsearch v2.9.1_macos_x86_64, 8.0GB RAM, 4 cores https://github.com/torognes/vsearch

Dereplicating file 456.R1.fa 100%
247436026 nt in 1991403 seqs, min 32, max 139, avg 124 Sorting 100% 1762574 unique sequences, avg cluster 1.1, median 1, max 1569 Writing output file 100%
usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory zcat: can't stat: 456.R1.fa.gz (456.R1.fa.gz.Z): No such file or directory vsearch v2.9.1_macos_x86_64, 8.0GB RAM, 4 cores https://github.com/torognes/vsearch

Unable to read from file (tmp.fa) vsearch v2.9.1_macos_x86_64, 8.0GB RAM, 4 cores https://github.com/torognes/vsearch

Unable to read from file (VsearchIN.fa) Unable to open VsearchOUT.fa file Mac-Pro-de-Rodrigo-2:demultiplexed rhasbun$

Can you help me?

Rodrigo

rhasbunz commented 4 years ago

Auto-resolved:

https://www.enmimaquinafunciona.com/pregunta/5593/zcatgzcat-funciona-en-linux-no-en-osx-en-general-linuxosx-compatibilidad