Question: Format convert error while using Trinity Galaxy
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gravatar for utsafar
3.5 years ago by
utsafar20
utsafar20 wrote:

I am using trinity galaxy to assemble an RNA-Seq dataset from saffron.I imported File1 and File2 directly to trinity galaxy. Now I am trying to De novo assemble the dataset, but the assembled transcript file is empty and I received this errors in log file:

Error, cannot convert fastq file to fasta since cannot recognize read orientation as /1 or /2 (instead: 5)Thread 1 terminated abnormally: Error, cmd: /N/dc2/projects/galaxyshared/trinity/third_party_applications/trinityrnaseq-2.1.1/util/..//trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /N/dc2/scratch/trinity/database/files/013/dataset_13499.dat >> left.fa died with ret 768 at /N/dc2/projects/galaxyshared/trinity/third_party_applications/trinityrnaseq-2.1.1/util/insilico_read_normalization.pl line 733. Error, cannot convert fastq file to fasta since cannot recognize read orientation as /1 or /2 (instead: 5)Thread 2 terminated abnormally: Error, cmd: /N/dc2/projects/galaxyshared/trinity/third_party_applications/trinityrnaseq-2.1.1/util/..//trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /N/dc2/scratch/trinity/database/files/013/dataset_13498.dat >> right.fa died with ret 768 at /N/dc2/projects/galaxyshared/trinity/third_party_applications/trinityrnaseq-2.1.1/util/insilico_read_normalization.pl line 733. Error, conversion thread failed at /N/dc2/projects/galaxyshared/trinity/third_party_applications/trinityrnaseq-2.1.1/util/insilico_read_normalization.pl line 334. Error, cmd: /N/dc2/projects/galaxyshared/trinity/third_party_applications/trinityrnaseq-2.1.1/util/insilico_read_normalization.pl --seqType fq --JM 200G --max_cov 50 --CPU 8 --output /N/dc2/scratch/trinity/job_working_directory/008/8256/trinity_out_dir/insilico_read_normalization --left /N/dc2/scratch/trinity/database/files/013/dataset_13499.dat --right /N/dc2/scratch/trinity/database/files/013/dataset_13498.dat --pairs_together --PARALLEL_STATS died with ret 6400 at /N/dc2/projects/galaxyshared/trinity/third_party_applications/trinityrnaseq-2.1.1/Trinity line 2183. TERMINATING COLLECTL, PID = 31363 Ouch!

Why it happens, and how can I pass this step successfully and assemble my data? Thank you

format_convert galaxy trinity • 1.6k views
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by utsafar20

I assume you are using the galaxy mirror at Indiana (based on @Antonio's suggestion in a related thread). Did you download the files from ENA and then upload them without any modifications? If you did then it appears that the files may not have the standard Illumina format fastq identifiers. Galaxy is not able to identify which is read 1 and which is read 2. Will need to take a look at the files. Unless someone else does that before I do.

ADD REPLYlink written 3.5 years ago by genomax75k

I didn't download and upload files. I imported files directly from EBI SRA site. files are almost 9 Gb size and I can't download and upload easily. how can I fix my problem in Trinity galaxy site, with its tools?

ADD REPLYlink written 3.5 years ago by utsafar20
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