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Read Assembly and Annotation Pipeline Tool
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Pipeline taxcheck failed with code 1 (Example SRA) #16

Closed Jacob4564 closed 1 year ago

Jacob4564 commented 1 year ago

When running the example SRA file (I'm using google cloud) I get the error, "Pipeline taxcheck failed with code 1."

[2022-09-21 18:08:04] Starting taxcheck pipeline ... [2022-09-21 18:10:05] Retrying taxcheck pipeline with genus_species = Mycoplasma pirum... [2022-09-21 18:12:06] Retrying taxcheck pipeline with genus_species = Mycoplasma... [2022-09-21 18:14:07] Pipeline taxcheck failed with code 1.

Attached are the output files. Any help would be very welcome!

dffc933e00_run (1).log dffc933e00_output (1).tar.gz

EDIT: I also forgot to include that i'm also having trouble running the FASTA of the example SRA as well. This time the SKESA is failing with code 1.

[2022-09-21 18:56:01] Start to download input-2022-04-14.build6021.prod.ani.tgz [2022-09-21 18:56:01] Start to download input-2022-04-14.build6021.prod.tgz [2022-09-21 18:56:31] Error: skesa failed with code 1

Attached are the output files.

34242a7082_run.log 34242a7082_output.tar.gz

thibaudnis commented 1 year ago

Hi - thanks for reporting the issue. It appears that the permissions of the reference data needed to run the annotation have changed. We are investigating.

thibaudnis commented 1 year ago

Can you please try again? This should be fixed. Thanks!

Jacob4564 commented 1 year ago

When working from SRA it appears to work as it is still running and hasn't failed.

However, when trying to work from the FASTA It failed again with the same error but ran for longer than usual

[2022-09-21 21:32:57] Starting skesa ... [2022-09-21 21:32:58] Start to download reference data ... [2022-09-21 21:32:59] Start to download input-2022-04-14.build6021.prod.ani.tgz [2022-09-21 21:32:59] Start to download input-2022-04-14.build6021.prod.tgz [2022-09-21 21:33:28] **Error: skesa failed with code 1

Output files: 57b4191606_output.tar.gz 57b4191606_run.log

p.s. is there a way to view the log as the run progresses?

thibaudnis commented 1 year ago

Crossing fingers for the run off SRA reads... For the other run, from fastq, the issue appears to be in the input file: Error (readsgetter.hpp:286): fastq record must have + in the third line in fastq /gcloud-shared/input0:3.

Jacob4564 commented 1 year ago

All solved thanks so much!

thibaudnis commented 1 year ago

Great!