Question: Trinity - problem while assembling fastqsanger reads
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gravatar for cris.kgs
4 months ago by
cris.kgs0
cris.kgs0 wrote:

After concatenating the all the forward reads together and doing the same with the reverse reads, all in fastqsanger format, I tried assembling with trinity, but it gave me this error and an empty fasta file.

Wednesday, December 13, 2017: 21:28:31 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 Wednesday, December 13, 2017: 21:28:31 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 Wednesday, December 13, 2017: 21:28:32 CMD: mkdir -p /local/2059621/trinity_out_dir Wednesday, December 13, 2017: 21:28:32 CMD: mkdir -p /local/2059621/trinity_out_dir/chrysalis


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

Converting input files. (in parallel)Wednesday, December 13, 2017: 21:28:32 CMD: cat /pylon5/mc48nsp/xcgalaxy/main_staging//17802259/inputs/dataset_22757341.dat | /opt/packages/trinity/2.2.0/trinity-plugins/fastool/fastool --append /1 --to-fasta >> left.fa 2> /pylon5/mc48nsp/xcgalaxy/main_staging//17802259/inputs/dataset_22757341.dat.readcount Wednesday, December 13, 2017: 21:28:32 CMD: cat /pylon5/mc48nsp/xcgalaxy/main_staging//17802259/inputs/dataset_22757340.dat | /opt/packages/trinity/2.2.0/trinity-plugins/fastool/fastool --append /2 --to-fasta >> right.fa 2> /pylon5/mc48nsp/xcgalaxy/main_staging//17802259/inputs/dataset_22757340.dat.readcount Thread 2 terminated abnormally: Error, cmd: cat /pylon5/mc48nsp/xcgalaxy/main_staging//17802259/inputs/dataset_22757340.dat | /opt/packages/trinity/2.2.0/trinity-plugins/fastool/fastool --append /2 --to-fasta >> right.fa 2> /pylon5/mc48nsp/xcgalaxy/main_staging//17802259/inputs/dataset_22757340.dat.readcount died with ret 256 at /opt/packages/trinity/2.2.0/Trinity line 2206. Thread 1 terminated abnormally: Error, counts of reads in FQ: 212144040.25 (as per cat /pylon5/mc48nsp/xcgalaxy/main_staging//17802259/inputs/dataset_22757341.dat | wc -l) doesn't match fastool's report of FA records: 212144041 at /opt/packages/trinity/2.2.0/Trinity line 3087 thread 1. main::ensure_complete_FQtoFA_conversion('cat /pylon5/mc48nsp/xcgalaxy/main_staging//17802259/inputs/da...', '/pylon5/mc48nsp/xcgalaxy/main_staging//17802259/inputs/datase...') called at /opt/packages/trinity/2.2.0/Trinity line 2116 thread 1 main::prep_seqs('ARRAY(0x1199418)', '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.

ADD COMMENTlink modified 4 months ago by Jennifer Hillman Jackson24k • written 4 months ago by cris.kgs0
0
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

Trinity in Galaxy accepts fastqsanger formatted dataset inputs. Clicking on the "i" Job Details icon for the dataset, then the stderr link, reports the full error message. The inputs are malformed and were unable to be parsed, resulting in an error.

The problems with the fastq data are also why the transformation from Fastq-to-Fasta failed. You can click on the bug icon for those failed datasets to review the error details (no need submit them). I would expect that other tools using this data as input would also fail or produce odd/partial results. In short, the input must match fastq specification before using Trinity.

Some of the fastq records appear to be partially missing for one of the inputs and the sequence and quality score lengths are not the same in the other. Please be aware the tools that report errors like this only report the first occurrence of a detected problem, and more issues may be present. You will need to review the upstream steps (data sourcing, merging, whatever was done) and correct the dataset's formats before using these in Galaxy.

Hope this helps! Jen, Galaxy team

ADD COMMENTlink written 4 months ago by Jennifer Hillman Jackson24k
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