Error, the Chrysalis process failed

Bread Pot

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Oct 15, 2015, 2:32:29 AM10/15/15

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Hi everyone

I'm new here,May be it is a simple question, but I have stay in this problem for several hours, so please.....

I have used the Trinity to process an TRANSCRIPTOMIC original FASTQ file, it's a single file.

And my command is "perl Trinity -seqType fq --JM 10G --single /home/onion/20151012start/trinityrnaseq_r20140717/SRR499587.fq --CPU 8"

The Trinity can run several minutes, but stop in here:

Iworm contig assembly time: 77 seconds = 1.28333 minutes.

TIMING CONTIG_BUILDING 77 s.

TIMING PROG_RUNTIME 188 s.

CMD finished (196 seconds)

Thursday, October 15, 2015: 14:10:35 CMD: touch /home/onion/20151012start/trinityrnaseq_r20140717/trinity_out_dir/inchworm.K25.L25.DS.fa.finished

CMD finished (0 seconds)

Thursday, October 15, 2015: 14:10:35 CMD: /home/onion/20151012start/trinityrnaseq_r20140717/Chrysalis/Chrysalis -i single.fa -iworm /home/onion/20151012start/trinityrnaseq_r20140717/trinity_out_dir/inchworm.K25.L25.DS.fa -o /home/onion/20151012start/trinityrnaseq_r20140717/trinity_out_dir/chrysalis -cpu 8 -min_glue 2 -min_iso_ratio 0.05 -glue_factor 0.05 -kmer_size 24 -weldmer_size 48 -min 200 -dist 500 -max_reads 200000 -sort_exec "/usr/bin/sort --parallel=2" -sort_buffer_size 10G -max_mem_reads 10000000 -butterfly /home/onion/20151012start/trinityrnaseq_r20140717/Butterfly/Butterfly.jar 2>&1

sh: 1: /home/onion/20151012start/trinityrnaseq_r20140717/Chrysalis/Chrysalis: not found

time(seconds) unlimited

file(blocks) unlimited

data(kbytes) unlimited

stack(kbytes) 8192

coredump(blocks) 0

memory(kbytes) unlimited

locked memory(kbytes) 64

process 63412

nofiles 1024

vmemory(kbytes) unlimited

locks unlimited

Error, the Chrysalis process failed:

Error, cmd: /home/onion/20151012start/trinityrnaseq_r20140717/Chrysalis/Chrysalis -i single.fa -iworm /home/onion/20151012start/trinityrnaseq_r20140717/trinity_out_dir/inchworm.K25.L25.DS.fa -o /home/onion/20151012start/trinityrnaseq_r20140717/trinity_out_dir/chrysalis -cpu 8 -min_glue 2 -min_iso_ratio 0.05 -glue_factor 0.05 -kmer_size 24 -weldmer_size 48 -min 200 -dist 500 -max_reads 200000 -sort_exec "/usr/bin/sort --parallel=2" -sort_buffer_size 10G -max_mem_reads 10000000 -butterfly /home/onion/20151012start/trinityrnaseq_r20140717/Butterfly/Butterfly.jar 2>&1 died with ret 32512 at Trinity line 1990.

at Trinity line 1525.

main::run_chrysalis('/home/onion/20151012start/trinityrnaseq_r20140717/trinity_out...', 'single.fa', 200, 500, undef, 'single.fa') called at Trinity line 1335

I can't get the answer to solve this problem, please help me...

By the way,I have another PC with 32GB RAM, is it enough for Trinity to analysis my data (original FASATQ size 1.5GB)?and if I want to do some downstream analysis, is 32GB RAM enough too?

Thanks a lot

Bread Pot

Mark Chapman

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Oct 15, 2015, 3:16:24 AM10/15/15

to Bread Pot, trinityrnaseq-users

Hi Breadpot,

Youre using a very old version of trinity so please upgrade. old ones arent supported (and arent as good).

There are several potential reasons for the process failing. One that is often hit is due to space limitations on your server (both total space as well as max number of files) so this is a good place to check first.

Also, If you're trying to run on a computer where you think memory might be a problem then normalise your reads first.

Cheers, good luck,

--Mark

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Bread Pot

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Oct 15, 2015, 4:02:59 AM10/15/15

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Thanks for your help!

I have checked my disk properties, there are 6781 items totalling 17.3GB and free space is 750GB.

AND I will update my Trinity and try again.

Thank you very much.

Mark Chapman於 2015年10月15日星期四 UTC+8下午3時16分24秒寫道：

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Bread Pot

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Oct 15, 2015, 8:00:29 AM10/15/15

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Hi

I have reinstall the new version(2.1.0)and install the software, but I think I met some new problems.

I have tested the sample data, it passed, but when I used my own data,it replys an error information like this:

----------------------------------------------------------------------------------

-------------- Trinity Phase 1: Clustering of RNA-Seq Reads ---------------------

----------------------------------------------------------------------------------

Thursday, October 15, 2015: 19:40:41 CMD: touch single.fa.ok

-------------------------------------------

----------- Jellyfish --------------------

-- (building a k-mer catalog from reads) --

-------------------------------------------

* Running CMD: /home/onion/20151012start/trinityrnaseq-2.1.0/trinity-plugins/jellyfish/bin/jellyfish count -t 8 -m 25 -s 766958445 --canonical single.fa

* Running CMD: /home/onion/20151012start/trinityrnaseq-2.1.0/trinity-plugins/jellyfish/bin/jellyfish dump -L 1 mer_counts.jf > jellyfish.kmers.fa

* Running CMD: /home/onion/20151012start/trinityrnaseq-2.1.0/trinity-plugins/jellyfish/bin/jellyfish histo -t 8 -o jellyfish.kmers.fa.histo mer_counts.jf

----------------------------------------------

--------------- Inchworm ---------------------

-- (Linear contig construction from k-mers) --

----------------------------------------------

* Running CMD: /home/onion/20151012start/trinityrnaseq-2.1.0/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1 --DS --num_threads 6 --PARALLEL_IWORM > /home/onion/20151012start/trinityrnaseq-2.1.0/trinity_out_dir/inchworm.K25.L25.DS.fa.tmp

* Running CMD: mv /home/onion/20151012start/trinityrnaseq-2.1.0/trinity_out_dir/inchworm.K25.L25.DS.fa.tmp /home/onion/20151012start/trinityrnaseq-2.1.0/trinity_out_dir/inchworm.K25.L25.DS.fa

Thursday, October 15, 2015: 19:40:44 CMD: touch /home/onion/20151012start/trinityrnaseq-2.1.0/trinity_out_dir/inchworm.K25.L25.DS.fa.finished

ERROR, no butterfly assemblies reported. at Trinity line 1258.

And then, I checked the line 1258,it said:" die "ERROR, no butterfly assemblies reported." unless $TRINITY_COMPLETE_FLAG;"

But I don't know what is "TRINITY_COMPLETE_FLAG"......

So,could you please help me to solve this problem? thank you very much!

Best regards

Bread Pot

Mark Chapman於 2015年10月15日星期四 UTC+8下午3時16分24秒寫道：

Hi Breadpot,
Youre using a very old version of trinity so please upgrade. old ones arent supported (and arent as good).
There are several potential reasons for the process failing. One that is often hit is due to space limitations on your server (both total space as well as max number of files) so this is a good place to check first.
Also, If you're trying to run on a computer where you think memory might be a problem then normalise your reads first.
Cheers, good luck,
--Mark

On 15 October 2015 at 07:32, Bread Pot <icegea...@gmail.com> wrote:

Hi everyone

I'm new here,May be it is a simple question, but I have stay in this problem for several hours, so please.....

I have used the Trinity to process an TRANSCRIPTOMIC original FASTQ file, it's a single file.

And my command is "perl Trinity -seqType fq --JM 10G --single /home/onion/20151012start/trinityrnaseq_r20140717/SRR499587.fq --CPU 8"

The Trinity can run several minutes, but it stop in here:

To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-users+unsub...@googlegroups.com.

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Brian Haas

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Oct 15, 2015, 8:21:07 AM10/15/15

to Bread Pot, trinityrnaseq-users

Hi,

This can happen if you're running an RNA-Seq data set through that contains so few reads that it wasn't able to generate any assembled contigs.

What type of data set are you trying to run? (number of reads, PE, length?)

best,

~brian

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--
Dr. Mark A. Chapman
M.Ch...@soton.ac.uk
+44 (0)2380 594396
------------------------------------
Centre for Biological Sciences
University of Southampton
Life Sciences Building 85
Highfield Campus
Southampton
SO17 1BJ

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Bread Pot

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Oct 15, 2015, 9:43:02 AM10/15/15

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Thanks for your help!

I have download these data from NCBI:

TRANSCRIPTOMIC :http://www.ncbi.nlm.nih.gov/sra/SRX148757[accn]

About the data probably is: number of reads~5500000 PE~100 length ~74

My purpose is to find Gene expressive quantity, exactly get every gene's name and its expressive quantity.

I'm just learning bioinformatics for a few days and met some troubles,So I really appreciate your help.

sincerely,

Bread Pot

Brian Haas於 2015年10月15日星期四 UTC+8下午8時21分07秒寫道：

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--
Dr. Mark A. Chapman
M.Ch...@soton.ac.uk
+44 (0)2380 594396
------------------------------------
Centre for Biological Sciences
University of Southampton
Life Sciences Building 85
Highfield Campus
Southampton
SO17 1BJ

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Brian Haas

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Oct 15, 2015, 10:33:30 AM10/15/15

to Bread Pot, trinityrnaseq-users

If you're pulling data from SRA, be sure to convert it to fastq format like so:

https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-FAQ#ques_sra_fq_conversion

Hopefully it works fine after that.

best,

~brian

Bread Pot

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Oct 15, 2015, 12:33:53 PM10/15/15

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It works,thank you Brian!

Thursday, October 15, 2015: 23:36:32 CMD: /home/onion/20151012start/trinityrnaseq-2.1.0/trinity-plugins/parafly/bin/ParaFly -c recursive_trinity.cmds -CPU 8 -v

Number of Commands: 1006

succeeded(1006) 100% completed.

All commands completed successfully. :-)

** Harvesting all assembled transcripts into a single multi-fasta file...

Thursday, October 15, 2015: 23:54:00 CMD: find read_partitions/ -name '*inity.fasta' | /home/onion/20151012start/trinityrnaseq-2.1.0/util/support_scripts/partitioned_trinity_aggregator.pl TRINITY_DN > Trinity.fasta.tmp

###################################################################

Butterfly assemblies are written to /home/onion/20151012start/trinityrnaseq-2.1.0/trinity_out_dir/Trinity.fasta

###################################################################

Brian Haas於 2015年10月15日星期四 UTC+8下午10時33分30秒寫道：

Brian Haas

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Oct 15, 2015, 12:44:05 PM10/15/15

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Excellent!!

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