Question: Trinity error with fasta input - solution: use fastq input instead
0
gravatar for jimcypser
9 months ago by
jimcypser0
jimcypser0 wrote:

I'm trying to use Trinity to do a de novo assembly from short reads. However the output file "Assembled Transcripts" is empty, and includes an accopanying error message "A data display parameter is in the error state: fai_file".

The output log file seems to be implying incomplete conversion of FASTQ to FASTA, though I don't know why that should be so, since I ran the conversion already using FASTQ-to-FASTA tool.

Any ideas what I'm doing wrong?

Actual log file content follows:

CMD: java -Xmx64m -XX:ParallelGCThreads=6 -jar /opt/packages/trinity/2.2.0/util/support_scripts/ExitTester.jar 0 Picked up _JAVA_OPTIONS: -Dsun.zip.disableMemoryMapping=true Thursday, December 14, 2017: 20:24:44 CMD: java -Xmx64m -XX:ParallelGCThreads=6 -jar /opt/packages/trinity/2.2.0/util/support_scripts/ExitTester.jar 1 Picked up _JAVA_OPTIONS: -Dsun.zip.disableMemoryMapping=true Thursday, December 14, 2017: 20:24:44 CMD: mkdir -p /local/2066002/trinity_out_dir Thursday, December 14, 2017: 20:24:44 CMD: mkdir -p /local/2066002/trinity_out_dir/chrysalis


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

Converting input files. (in parallel)Thursday, December 14, 2017: 20:24:44 CMD: cat /pylon5/mc48nsp/xcgalaxy/main_staging//17813697/inputs/dataset_22774423.dat | /opt/packages/trinity/2.2.0/trinity-plugins/fastool/fastool --append /1 --to-fasta >> left.fa 2> /pylon5/mc48nsp/xcgalaxy/main_staging//17813697/inputs/dataset_22774423.dat.readcount Thursday, December 14, 2017: 20:24:44 CMD: cat /pylon5/mc48nsp/xcgalaxy/main_staging//17813697/inputs/dataset_22774423.dat | /opt/packages/trinity/2.2.0/trinity-plugins/fastool/fastool --append /2 --to-fasta >> right.fa 2> /pylon5/mc48nsp/xcgalaxy/main_staging//17813697/inputs/dataset_22774423.dat.readcount Thread 2 terminated abnormally: Error, counts of reads in FQ: 207480 (as per cat /pylon5/mc48nsp/xcgalaxy/main_staging//17813697/inputs/dataset_22774423.dat | wc -l) doesn't match fastool's report of FA records: 414960 at /opt/packages/trinity/2.2.0/Trinity line 3087 thread 2. main::ensure_complete_FQtoFA_conversion('cat /pylon5/mc48nsp/xcgalaxy/main_staging//17813697/inputs/da...', '/pylon5/mc48nsp/xcgalaxy/main_staging//17813697/inputs/datase...') called at /opt/packages/trinity/2.2.0/Trinity line 2116 thread 2 main::prep_seqs('ARRAY(0x2620418)', 'fq', 'right', undef) called at /opt/packages/trinity/2.2.0/Trinity line 1317 thread 2 eval {...} called at /opt/packages/trinity/2.2.0/Trinity line 1317 thread 2 Thread 1 terminated abnormally: Error, counts of reads in FQ: 207480 (as per cat /pylon5/mc48nsp/xcgalaxy/main_staging//17813697/inputs/dataset_22774423.dat | wc -l) doesn't match fastool's report of FA records: 414960 at /opt/packages/trinity/2.2.0/Trinity line 3087 thread 1. main::ensure_complete_FQtoFA_conversion('cat /pylon5/mc48nsp/xcgalaxy/main_staging//17813697/inputs/da...', '/pylon5/mc48nsp/xcgalaxy/main_staging//17813697/inputs/datase...') called at /opt/packages/trinity/2.2.0/Trinity line 2116 thread 1 main::prep_seqs('ARRAY(0x2453a40)', 'fq', 'left', undef) called at /opt/packages/trinity/2.2.0/Trinity line 1314 thread 1 eval {...} called at /opt/packages/trinity/2.2.0/Trinity line 1314 thread 1 Trinity run failed. Must investigate error above.

trinity fastq fasta input assembly • 351 views
ADD COMMENTlink modified 9 months ago by Jennifer Hillman Jackson25k • written 9 months ago by jimcypser0
0
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The Galaxy version of Trinity accepts fastq input but not fasta.

It is not clear what you input. If fasta, then try the original fastq instead. If the input was fastq, let us know and we can troubleshoot more.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 9 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 106 users visited in the last hour