Hi, this is my first time reporting an issue, so I apologize if I overlook info, can’t format code correctly in this flavor of markdown, etc. I’ve submitted a bug report via the Galaxy server, but, at the risk of redundancy, wanted to ask for help here to try to get the issue resolved sooner in case someone knows what might be going wrong. I can’t find a previous mention of this particular problem in GalaxyHelp or via Google.
I’m trying to assemble a genome on the Galaxy main server (“version_major”: “18.09”), and have trimmed my reads (SRR5906897, Trimmomatic headcrop 12, slidingwindow 4, 25, minlen 100). When I attempt a de novo assembly via Unicycler, however, it consistently fails with the message:
Error: SPAdes crashed! Please view spades.log for more information.
After issuing the bug report, I received an email with the additional stdout code that appears to have the main issues in the following lines:
libgomp: Thread creation failed: Resource temporarily unavailable == Error == system call for: "['/email@example.com/share/spades-3.12.0-1/bin/spades-hammer', '/pylon5/mc48nsp/xcgalaxy/main/staging/21785278/working/spades_assembly/read_correction/corrected/configs/config.info']" finished abnormally, err code: 1
I’m uncertain whether the crucial issue is the “Resource temporarily unavailable” line or whether
spades-hammer can’t access the
config.info file indicated. I’ve tried re-running the job with " Skip SPAdes error correction step" set to “Yes”, but I appear to receive the same error. I’m assuming this is a legitimate bug that will be hard to resolve on my end, but would appreciate any received wisdom as to the best course of action. Can anyone advise?