Local Galaxy: Flye error during consensus, minimap2 stage

, , ,
1

Hi,

I am trying to perform de novo assembly using PacBio CCS reads. The Flye assembly fails at the last stage while starting minimap2. Separately, the galaxy minimap2 tool works great so I’m not sure why the error happens with Flye.

[2023-06-19 14:11:02] INFO: Starting Flye 2.9.1-b1780
[2023-06-19 14:11:02] INFO: >>>STAGE: configure
[2023-06-19 14:11:02] INFO: Configuring run
[2023-06-19 14:11:12] INFO: Total read length: 550827663
[2023-06-19 14:11:12] INFO: Reads N50/N90: 16237 / 2402
[2023-06-19 14:11:12] INFO: Minimum overlap set to 2000
[2023-06-19 14:11:12] INFO: >>>STAGE: assembly
[2023-06-19 14:11:12] INFO: Assembling disjointigs
[2023-06-19 14:11:12] INFO: Reading sequences
[2023-06-19 14:11:18] INFO: Building minimizer index
[2023-06-19 14:11:18] INFO: Pre-calculating index storage
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[2023-06-19 14:11:37] INFO: Filling index
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[2023-06-19 14:14:24] INFO: Extending reads
[2023-06-19 14:16:44] INFO: Overlap-based coverage: 19
[2023-06-19 14:16:44] INFO: Median overlap divergence: 0.00521574
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[2023-06-19 23:05:43] INFO: Assembled 10300 disjointigs
[2023-06-19 23:05:43] INFO: Generating sequence
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[2023-06-19 23:05:53] INFO: Filtering contained disjointigs
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[2023-06-19 23:19:28] INFO: Contained seqs: 8903
[2023-06-19 23:19:29] INFO: >>>STAGE: consensus
[2023-06-19 23:19:29] INFO: Running Minimap2
[2023-06-20 01:15:32] ERROR: Error running minimap2, terminating. See the alignment error log for details: /home/mmqci/galaxy/database/jobs_directory/021/21738/working/out_dir/10-consensus/minimap.stderr

Thank you,
jsalem

2

Hello @jsalem

It looks like the job is running out of resources, or that the job configuration has a problem.

What is the URL of the server where you are working? The paths do not appear to be at UseGalaxy.org.

3

Hi @jennaj ,

I am using a local instance of Galaxy installed on an external hard drive. Where do the resource limitations come from? RAM/memory? I’m hoping there is a way I can fix this…

4

Both in a way, and from your computer. You need to give the job the same resources as it would require if running the tool directly. Galaxy is what sits on top, to organize you files and to offer up diverse tools from many open-source developers that will work together all in the same place.

I added a few tags that link to administration topics. The Docker version of Galaxy is probably the easiest to get running locally but you can decide. More could be going on, maybe the tool dependency configuration has a problem, and this is just not a resource limit problem.

References: