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trinityrnaseq / trinity_community_codebase

Software contributed by Trinity community users to facilitate studies of Trinity-assembled transcriptomes.
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Error at Trinity best transcript set #2

Closed manuelsmendoza closed 5 years ago

manuelsmendoza commented 5 years ago

Hi!

I'm trying to use the Trinity best transcript set guide but i've the following errror. Does anyone know what is happening? 

$ trinity_cdhit_feeder.pl -infile non-rRNA_Trinity.fasta.transdecoder.pep -output Transcriptome.fasta.transdecoder.pep_pass1 -tmp_dir ./tmp -max_children 40 -params -b 180 > cdhit_feeder.log
2019-03-26 19:05:51
Command line arguments were infile: non-rRNA_Trinity.fasta.transdecoder.pep output: Transcriptome.fasta.transdecoder.pep_pass1 tmp_dir: ./tmp max_children: 40 params: -b
could not open ./tmp/job_1_out

Thanks in advance, ~MM.

mathog commented 5 years ago

On 26-Mar-2019 11:12, Manuel Mendoza wrote:

Hi!

I'm trying to use the Trinity best transcript set guide but i've the following errror. Does anyone know what is happening?

$ trinity_cdhit_feeder.pl -infile
non-rRNA_Trinity.fasta.transdecoder.pep -output
Transcriptome.fasta.transdecoder.pep_pass1 -tmp_dir ./tmp
-max_children 40 -params -b 180 > cdhit_feeder.log
2019-03-26 19:05:51
Command line arguments were infile:
non-rRNA_Trinity.fasta.transdecoder.pep output:
Transcriptome.fasta.transdecoder.pep_pass1 tmp_dir: ./tmp
max_children: 40 params: -b
could not open ./tmp/job_1_out

That is my script. The time stamp on my current version is Oct 19 11:28, if yours is older than that let me know and I will upload a new release.

This could be a disk space or directory protection problem. Be sure that the account which is running can read/write in ./tmp. Be sure the disk isn't out of space.

If that isn't it, modify the script and change line 35 to:

$dbglvl=4

clean out ./tmp and run it again. Tell me what it says. Also let me know at least in summary what is in ./tmp.

You may email me directly, the details of this debugging are going to clutter up this list and the only thing that really needs to be posted is the final resolution.

Regards,

David Mathog mathog@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech

mathog commented 5 years ago

On 26-Mar-2019 11:12, Manuel Mendoza wrote:

Hi!

I'm trying to use the Trinity best transcript set guide but i've the following errror.

Also, check that you modified the script properly. The $CDHIT binary path as distributed is for my home system. The script should have caught that though because the -x test should have failed.

BEFORE modification!

cksum trinity_cdhit_feeder.pl 2102552423 4885 trinity_cdhit_feeder.pl wc -l trinity_cdhit_feeder.pl 167 trinity_cdhit_feeder.pl

Regards,

David Mathog mathog@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech

manuelsmendoza commented 5 years ago

Problem solved...

So sorry, it was not related with your script @mathog. It wasn't passing properly the $CDH_BAND variable. Finally, I've solved it by passing directly this command i.e. -params "-b 180".

Thanks so much, ~MM

mathog commented 5 years ago

On 26-Mar-2019 12:14, Manuel Mendoza wrote:

Problem solved...

So sorry, it was not related with your script @mathog. It wasn't passing properly the $CDH_BAND variable. Finally, I've solved it by passing directly this command i.e. -params "-b 180".

In the instructions it currently says:

nice trinity_cdhit_feeder.pl \ -infile Transcriptome.fasta.transdecoder.pep \ -output Transcriptome.fasta.transdecoder.pep_pass1 \ -tmp_dir /tmp/tmpfeed -max_children 40 -params $CDH_BAND

cdhit_feeder.log 2>&1 &

Apparently it should be instead:

nice trinity_cdhit_feeder.pl \ -infile Transcriptome.fasta.transdecoder.pep \ -output Transcriptome.fasta.transdecoder.pep_pass1 \ -tmp_dir /tmp/tmpfeed -max_children 40 -params "$CDH_BAND"

cdhit_feeder.log 2>&1 &

Does the second form work for you?

Regards,

David Mathog mathog@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech

manuelsmendoza commented 5 years ago

It's worked! Thanks!!

shzadiqbal commented 5 years ago

hi i am facing an error while running this pipeline cat keep_these | fastaselecth -sel- -in merge.fasta >Transcriptome_reduced.fasta fastaselecth: fatal error: duplicate entry names in list, alternate header terminators may be needed please help me to solve this. All other previous pipeline ran smoothly till now.