Stopping in STEP10 -> 10.mapsamples.pl. Program finished abnormally
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I followed some previous recommendations to a similar problem, however it has not worked, it keeps stopping the process in the mapping.
syslog.txt
What error message did you get in your screen / stdout log / stderr log?
Also if your dataset is not very big maybe you can share it with me and I can try running it in my computer and reproduce the error.
And does the error still happen when you run the same command (same extra arguments as your real run, etc) but using the test dataset instead?
As far as I know, the test run well, there is any problem with that, I am not the administator of the server but it works.
I don't mean the test_install.pl script, but a SqueezeMeta run using the test fastq files that we redistribute with the databases.
Can you confirm that this has worked for you?
The issue seems to be similar to #880.
It could also be something related to writing permissions... did you perhaps run out of disk quota?
I think you are right, I just got an email saying that I exceeded my disk quota
Ok! Try running SqueezeMeta with this test dataset and the same options you were adding to your real run. It should run fast and not consume much space. If that works then we can be somewhat confident that SqueezeMeta runs well in your system and the problems are coming from elsewhere (e.g. disk quota)
running "test_install.pl" ?
I don't mean the test_install.pl script, but a SqueezeMeta run using the test fastq files that we redistribute with the databases.
Can you confirm that this has worked for you?
No. When you (or someone else) download the SqueezeMeta databases there is also a test dataset that gets downloaded to the same location. The idea is to run SqueezeMeta on that to make sure everything is working ok.
Ok, but how I can put that to run, thanks for helping me
This test data should be present in the same place as the database.
When running test_install.pl it should say where the database is located.
So if the database is located at /example/path/db then the test data should be in /example/path/test.
There you will find a directory called raw with fastq files, and a couple of samples files formated for SqueezeMeta. From that you can run SqueezeMeta normally.
ok, I see, but i dont know where SqueezeMeta files are located to run it in a script.
Did you find this out?
Otherwise the file /appli/conda-env/bioinfo/squeezemeta-1.6.3/SqueezeMeta/SqueezeMeta_conf.pl has a line indicating where the databases are stored.
Dear fpusan,
I am having the same issue, Stopping in STEP10 -> 10.mapsamples.pl. Program finished abnormally.
Died at /full_path/SqueezeMeta.pl line 969
There is no issue running the test data or other datasets. My disk is not out of space. Here are details of my run:
nohup SqueezeMeta.pl -m coassembly -p coassembly_01 -s sample.txt -f ./ --euk yes -extdb --doublepass no -t 15 &
My dataset includes 8 samples, paired end reads, each fq.gz approx 2.8G. Do you have any idea why the program stopped?
What version of SqueezeMeta?
Can you attach the syslog file here?
Did you run trimming/quality filtering of your reads?
Hi again
So sorry! I was just going to delete the comment. I have found the issue. Files had been moved from that listed in sample.txt. So sorry to bother.
Glad to hear! Closing issue