[vast align error]: rm -50.fa.gz Failed in RunDBS_1.pl!

[fenguita]

Dear All

I got this anoying error when I tried to run vast-tools in align mode. Any clues about what's going on?. Something that I am doing is wrong ? . Thanks. Paco

[vast align]: Using VASTDB -> /home/fenguita/work/vast-tools/Hsa [vast align]: Setting output directory to /home/fenguita/work/vast_out [vast align]: Setting tmp directory.. [vast align]: Set tmp directory to /home/fenguita/work/vast_out/tmp! [vast align]: Trimming fastq sequences to 50 nt sequences Use of uninitialized value $root in concatenation (.) or string at /home/fenguita/work/vast-tools/bin/RunDBS_1.pl line 358. [vast trim]: Total processed reads: 118845011 [vast trim]: Total valid fwd reads: 108488609 [vast trim]: Total valid rev reads: 118845011 Use of uninitialized value $root in concatenation (.) or string at /home/fenguita/work/vast-tools/bin/RunDBS_1.pl line 359. Use of uninitialized value $root in concatenation (.) or string at /home/fenguita/work/vast-tools/bin/RunDBS_1.pl line 367. [vast align]: Doing genome subtraction gzip: invalid option -- '0' Try `gzip --help' for more information. Warning: Could not find any reads in "-"

reads processed: 0

reads with at least one reported alignment: 0 (0.00%)

reads that failed to align: 0 (0.00%)

No alignments Use of uninitialized value $root in concatenation (.) or string at /home/fenguita/work/vast-tools/bin/RunDBS_1.pl line 387. [vast align]: Mapping reads to the "splice site-based" (aka "a posteriori") EEJ library and Analyzing... gzip: invalid option -- '0' Try `gzip --help' for more information. Option root requires an argument Warning: Could not find any reads in "-"

reads processed: 0

reads with at least one reported alignment: 0 (0.00%)

reads that failed to align: 0 (0.00%)

No alignments [vast align]: Mapping reads to the "transcript-based" (aka "a priori") SIMPLE EEJ library and Analyzing... gzip: invalid option -- '0' Try `gzip --help' for more information. Option root requires an argument Warning: Could not find any reads in "-"

reads processed: 0

reads with at least one reported alignment: 0 (0.00%)

reads that failed to align: 0 (0.00%)

No alignments [vast align]: Mapping reads to the "transcript-based" (aka "a priori") MULTI EEJ library and Analyzing... gzip: invalid option -- '0' Try `gzip --help' for more information. Option root requires an argument Warning: Could not find any reads in "-"

reads processed: 0

reads with at least one reported alignment: 0 (0.00%)

reads that failed to align: 0 (0.00%)

No alignments [vast align]: Mapping reads to microexon EEJ library and Analyzing... gzip: invalid option -- '0' Try `gzip --help' for more information. Option root requires an argument Warning: Could not find any reads in "-"

reads processed: 0

reads with at least one reported alignment: 0 (0.00%)

reads that failed to align: 0 (0.00%)

No alignments [vast align]: Mapping reads to intron retention library (version 1)... gzip: invalid option -- '0' Try `gzip --help' for more information. Option root requires an argument Warning: Could not find any reads in "-"

reads processed: 0

reads with at least one reported alignment: 0 (0.00%)

reads that failed to align: 0 (0.00%)

No alignments Use of uninitialized value $root in concatenation (.) or string at /home/fenguita/work/vast-tools/bin/RI_summarize.pl line 51. gzip: invalid option -- '0' Try `gzip --help' for more information. Option root requires an argument Warning: Could not find any reads in "-"

reads processed: 0

reads with at least one reported alignment: 0 (0.00%)

reads that failed to align: 0 (0.00%)

No alignments Use of uninitialized value $root in concatenation (.) or string at /home/fenguita/work/vast-tools/bin/RI_summarize_introns.pl line 49. Use of uninitialized value $root in concatenation (.) or string at /home/fenguita/work/vast-tools/bin/RI_summarize_introns.pl line 51. [vast align]: Cleaning -50.fa.gz files! rm: invalid option -- '5' Try 'rm ./-50.fa.gz' to remove the file ‘-50.fa.gz’. Try 'rm --help' for more information. [vast align error]: rm -50.fa.gz Failed in RunDBS_1.pl! at /home/fenguita/work/vast-tools/bin/RunDBS_1.pl line 90.

[mirimia]

What is the name of your fastq file? It looks like a formatting error. (Some constraints are specified in the README). Also, could you provide the exact run command? Thanks

[fenguita]

Hi... thanks for your help. The command line that I used is

/usr/local/vast-tools/vast-tools align A6-Tr-1.txt.gz A6-Tr-2.txt.gz -c 4 -readLen 50 -dbDir /usr/local/vast-tools/

[mirimia]

Hi,

Yes, that's the issue. The fastq files have to be named "fastq", "fq", "fasta" or "fa" at this point. I can make the change to allow txt in the next release.

Also, I would strongly recommend changing the "-" to "_" as indicated in the README.

Thanks Manu

[mirimia]

Just to be sure. I recommend you name your samples, for example:

A6_Tr_1.fq.gz

[fenguita]

Thanks Manu... I got the files renamed and the software is running. I will let you know about the results.