Problem with assessing the assembly quality

[Fangqin Zeng]

Hi all,

I just want to use the bowtie_PE_separate_then_join.pl to assess the read content of the assembly and got following error:

CMD: touch /aafc-aac/home/users-data/zengf/RNAseqearly/with_paried_in_sortmerna/trinity_out_dir/Trinity.fasta._ebwt_idx_.start

CMD: bowtie-build -q /aafc-aac/home/users-data/zengf/RNAseqearly/with_paried_in_sortmerna/trinity_out_dir/Trinity.fasta /aafc-aac/home/users-data/zengf/RNAseqearly/with_paried_in_sortmerna/trinity_out_dir/Trinity.fasta

CMD: ln -sf /aafc-aac/home/users-data/zengf/RNAseqearly/with_paried_in_sortmerna/trinity_out_dir/Trinity.fasta target.fa

CMD: samtools faidx /aafc-aac/home/users-data/zengf/RNAseqearly/with_paried_in_sortmerna/trinity_out_dir/Trinity.fasta

Can't exec "samtools": Too many levels of symbolic links at /aafc-aac/home/users-data/mpp/trinityrnaseq-2.2.0/util/bowtie_PE_separate_then_join.pl line 626.

Error, cmd: samtools faidx /aafc-aac/home/users-data/zengf/RNAseqearly/with_paried_in_sortmerna/trinity_out_dir/Trinity.fasta died with ret -1 at /aafc-aac/home/users-data/mpp/trinityrnaseq-2.2.0/util/bowtie_PE_separate_then_join.pl line 628.

main::process_cmd("samtools faidx /aafc-aac/home/users-data/zengf/RNAseqearly/wi"...) called at /aafc-aac/home/users-data/mpp/trinityrnaseq-2.2.0/util/bowtie_PE_separate_then_join.pl line 305

Any suggestions?

Thanks,

Fangqin

[Brian Haas]

Hi Fangqin,

I'm not sure what's happening here.   This script is likely going to get dropped in the next release - it was written in the earlier days, before bowtie2 was developed.

Try just running bowtie2 instead.

best,

~brian

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[Fangqin Zeng]

Hi Brian,

Thanks for your reply. I find the resaon fro this problem. It may be caused by there are different versions of samtools in our server. I try to set a path for this script use the version that I set. Actually the system maybe have other options and don't know how to select. I just gave samtools-0.1.19 the first place to use and then it works.

Fangqin

On Tuesday, 17 May 2016 12:32:42 UTC-6, Brian Haas wrote:

Hi Fangqin,

I'm not sure what's happening here.   This script is likely going to get dropped in the next release - it was written in the earlier days, before bowtie2 was developed.

Try just running bowtie2 instead.

best,

~brian

On Tue, May 17, 2016 at 12:27 PM, Fangqin Zeng <fangqi...@gmail.com> wrote:

Hi all,

I just want to use the bowtie_PE_separate_then_join.pl to assess the read content of the assembly and got following error:

CMD: touch /aafc-aac/home/users-data/zengf/RNAseqearly/with_paried_in_sortmerna/trinity_out_dir/Trinity.fasta._ebwt_idx_.start

CMD: bowtie-build -q /aafc-aac/home/users-data/zengf/RNAseqearly/with_paried_in_sortmerna/trinity_out_dir/Trinity.fasta /aafc-aac/home/users-data/zengf/RNAseqearly/with_paried_in_sortmerna/trinity_out_dir/Trinity.fasta

CMD: ln -sf /aafc-aac/home/users-data/zengf/RNAseqearly/with_paried_in_sortmerna/trinity_out_dir/Trinity.fasta target.fa

CMD: samtools faidx /aafc-aac/home/users-data/zengf/RNAseqearly/with_paried_in_sortmerna/trinity_out_dir/Trinity.fasta

Can't exec "samtools": Too many levels of symbolic links at /aafc-aac/home/users-data/mpp/trinityrnaseq-2.2.0/util/bowtie_PE_separate_then_join.pl line 626.

Error, cmd: samtools faidx /aafc-aac/home/users-data/zengf/RNAseqearly/with_paried_in_sortmerna/trinity_out_dir/Trinity.fasta died with ret -1 at /aafc-aac/home/users-data/mpp/trinityrnaseq-2.2.0/util/bowtie_PE_separate_then_join.pl line 628.

main::process_cmd("samtools faidx /aafc-aac/home/users-data/zengf/RNAseqearly/wi"...) called at /aafc-aac/home/users-data/mpp/trinityrnaseq-2.2.0/util/bowtie_PE_separate_then_join.pl line 305

Any suggestions?

Thanks,

Fangqin

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[Fangqin Zeng]

Hi Brian,

I try to use fasta_tool in trinity/util/fasta_tool to break up my fasta file into different chunks for blast2go analysis. Because it is very slow use our server to do blast analysis. It shows errors:

Undefined subroutine &main::io called at /aafc-aac/home/users-data/mpp/trinityrnaseq-2.2.0/util/fasta_tool line 334

Where can I find this subroutine io?

Thanks,

Fangqin

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[Brian Haas]

Hi Fangqin,

Bob Freeman (CC'd) contributed this.  It looks like it requires the following perl modules:

 use Bio::SeqIO;

 use IO::All;

so, bioperl and IO::All - which is presumably in CPAN.

best,

~b

[Fangqin Zeng]

Hi Bob,

Thanks very much for your reply. I have done with it. The script is very helpful.

Cheers,

Fangqin

On Fri, Jun 24, 2016 at 1:45 PM, Bob Freeman PhD <robert...@g.harvard.edu> wrote:

Greetings, Fangqin (& Brian)!

Yes, this useful script does require some accessory modules from CPAN. IO::All can be installed via this command in your Terminal:

cpan IO::All

And the BioPerl instructions can be found at http://bioperl.org/INSTALL.html

Best,

Bob

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PLEASE NOTE THAT I AM NO LONGER AT FASRC 
I have taken a new position at HBS Research Computing Services
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