ERROR: GBK file conversion failed, tbl2asn parallel script has died #599
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So sounds like a memory issue then? Maybe I misunderstood, but seemed to suggest you could manually run this following command and it executed successfully?: How you have this written is it will use 1 cpu, ie You could try to wrap the command in |
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It was a memory issue at first, but I think I got around that issue (I probably shouldn't have mentioned it, sorry for the confusion) To clarify, The command you pasted technically works, in that there are no errors, but the When trying to complete the pipeline, I changed the If it is useful, I think I have some issues with GLIBC in the environment because |
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Okay, I guess I would try to re-install |
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yes exactly - we use a system installed one not bioconda one. |
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You can "force" remove dependencies with conda with the --force flag (I think): That should just remove the |
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Just tried all of your suggestions with no luck. A couple of questions to try to get around this issue:
Thanks again |
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In its simplest form it would be something like: the tbl2asn folder should contain genome.fsa (genome) and genome.tbl (the annotation). |
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Ah, then it sounds like tbl2asn is working fine because those files were generated... |
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Sorry I wasn't clear - the genome and annotation files are the input. You can essentially run the command I entered manually and it should hopefully yield an interpretable error. Output files will be generated in that same folder, ie the genome.gbf would be the genbank flatfile. But there will be several other submission files generated. |
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Annoyingly works like a charm: So I think the issue is GLIBC because I needed to load the module from my cluster's install to make tbl2asn work. However, when the module is loaded Does tbl2asn need to be run within the |
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I guess if it works interactively but not when you submit job to cluster than sounds like your GLIBC error is related to order in which modules are loaded or something associated with activating that environment. One of the last steps is to write the GBK output files (ie tbl2asn), so after that step the scripts reformat a few things and move files around in the proper places so they can be parsed properly by |
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I don't load any modules from the cluster apart from glibc for this particular step. Agreed, would be awesome if it worked in my hands ;_; I am looking at the predict.py script and it's SO close to finishing. Please correct me if I'm wrong, but this seems like all that my run is missing at the moment: This is probably out of the scope of an issue page, but is it possible for you to let me know which files to move over the results folder so I can utilize your downstream utilities? This is what is in the misc folder (all not listed, just since EVM output): |
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I can tell you where stuff should go -- but the problem is that this same step is at the end of update/annotate scripts as well. I could modify the code so it doesn't completely fail at this step, ie tbl2asn fails but it is kind of an important step as that is what generates all of the data for NCBI submission. I wonder if it is the genome size, if you run |
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Hi @Thatguy027, I reorganized the last few steps there so all files should be in proper place before tbl2asn dies. I also added a step to try to run tbl2asn single threaded as a backup, I'm not sure if this will solve your problem or not. But would be great if you could test and provide some feedback, update with pip: |
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Awesome, I will def test it out. The test run you suggested failed in my hands at the tbl2asn, though with some additional messages: |
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Okay, that is just the wrapper for the test function that is failing -- several layers of python there make the error not very intelligible. So its dying with the same error related to a non-functional |
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Hi @nextgenusfs Ihope you are well, is there any follow up on this error ? I'm also having same issue on the docker and conda version. If which possible is there an older funannotate version that i can use to avoid this error? |
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I cannot replicate this with docker image. |
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Hi @nextgenusfs i also got the same error with funannotate v1.8.13 Here is the code : THis is the log file: [12/01/22 22:09:19]: OS: Ubuntu 20.04, 40 cores, ~ 99 GB RAM. Python: 3.8.13 |
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Did you update |
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Yes i did but i'm still getting the same error Which Funannotate version are you using? if your version is running fine i can maybe install it. |
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Hi @nextgenusfs i just wanted to update you i found a way around the issue. I decided to: Hopefully something similar will work for those have the same error |
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I’m getting the same error (GBK file conversion failed, tbl2asn parallel script has died), but only at the annotate step. Predict worked fine. Mine hangs at "Converting to final Genbank format, good luck!” seemingly indefinitely and spits out the error and quits when I hit enter. I’m running version 1.8.15, installed with conda I’ve already got interproscan-version="5.52-86.0” as mentioned by @kalonji08 command: Log: [EDIT: I tried this in Docker as well and I’m getting the exact same issue. Funannotate predict runs fine. tbl2asn fails at the end of the annotate step] |
Hello again ;_;
I ran into another issue
Thanks in advance!
Are you using the latest release?
v1.8.8
Describe the bug
A little unsure about this
output error:
Tried running the command outside of the funannotate predict workflow and the initial issue was a core dump. I requested more memory and got around the core dump issue
From predict log files:
What command did you issue?
Same as the issue from earlier today, but with
--keep_evmflag:This fails as outlined above, but I can successfully run the line causing the issue outside of the predict workflow:
A couple of things about that line:
--sbt /u/project/kruglyak/thatguy0/conda/envs/funannotate/lib/python3.7/site-packages/funannotate/config/test.sbt.valand.gbffiles in thepredict_misc/tbl2asare both emptyLogfiles
logfiles.zip
OS/Install Information
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