gistfile1.txt

$ ./vast-tools align --expr -o vast -c 6 VASTDB/Hsa/FASTQ/Test_1-75.fq.gz VASTDB/Hsa/FASTQ/Test_2-75.fq.gz                                                                  [18/1922]
Enter passphrase for key '/home/tfunnell/.ssh/id_rsa':
[vast align]: Setting output directory to vast
[vast align]: Setting tmp directory..
[vast align]: Set tmp directory to /share/lustre/tfunnell/local/software/vast-tools/vast/tmp!
[vast align]: Mapping reads against mRNA sequences
[vast align]: Calculating cRPKMs
# reads processed: 100000
# reads with at least one reported alignment: 59694 (59.69%)
# reads that failed to align: 39462 (39.46%)
# reads with alignments suppressed due to -m: 844 (0.84%)
Reported 59694 alignments to 1 output stream(s)
[vast align]: Trimming fastq sequences to 50 nt sequences
[vast align]: Doing genome substraction
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 "splice site-based" (aka "a posteriori") EEJ library and Analyzing...
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...
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...
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...
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...
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
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]: Cleaning Test_1-75-50.fq.gz files!
[vast align]: Cleaning up Test_1-75-50-e.fq.gz!
[vast align]: Completed Mon Jul 21 17:05:29 2014

Ok can you pull the most recent and try again?... I just want to make sure the problem isnt an intermediate commit.