Warning: Could not find any reads in "-"

[funnell]

My latest run had a lot of warnings: https://gist.github.com/funnell/e7021ead4517f01c8a3b Is this anything to be worried about?

[timbitz]

Hi Tyler, can you try running this command for me? I can't seem to reproduce your output.

./vast-tools align --expr -o vast -c 6 VASTDB/Hsa/FASTQ/Test_1-75.fq.gz VASTDB/Hsa/FASTQ/Test_2-75.fq.gz

[funnell]

Hi Tim,

I gave it a try. Here is the gist: https://gist.github.com/funnell/735caa6a45777ddf9e32 I still see the same warnings.

[funnell]

Looks like I'm getting a segfault in Trim.pl

$ bash -c "gzip -dc /share/lustre/tfunnell/local/software/vast-tools/VASTDB/Hsa/FASTQ/Test_1-75.fq.gz | /share/lustre/tfunnell/local/software/vast-tools/bin/Trim.pl --stepSize 25 --fasta --paired <( gzip -dc /share/lustre/tfunnell/local/software/vast-tools/VASTDB/Hsa/FASTQ/Test_2-75.fq.gz )" bash: line 1: 6928 Broken pipe gzip -dc /share/lustre/tfunnell/local/software/vast-tools/VASTDB/Hsa/FASTQ/Test_1-75.fq.gz 6929 Segmentation fault | /share/lustre/tfunnell/local/software/vast-tools/bin/Trim.pl --stepSize 25 --fasta --paired <( gzip -dc /share/lustre/tfunnell/local/software/vast-tools/VASTDB/Hsa/FASTQ/Test_2-75.fq.gz )

and

bin/Trim.pl [1] 7132 segmentation fault bin/Trim.pl

[timbitz]

Hi Tyler, this is weird, and I still can't reproduce the error. Can you tell me more about the OS and version of perl you are using?

That command works on every machine we try, and I've never seen a perl seg fault before... so I don't know..

Can you try something? Open a new file tmp.pl and paste this:

#!/usr/bin/env perl
use Digest::MD5 qw(md5_hex md5_base64);
print md5_base64("testing base")."\n";
print md5_hex("testing hex")."\n";

then run perl tmp.pl

[funnell]

I did some testing and just including the line:

use Digest::MD5 qw(md5_hex md5_base64);

will cause a segfault. I suspect there is something weird with my Perl environment. Let me check into it.

[funnell]

Okay this was definitely caused by my perl environment. sorry!