Can't open mappingstat file for writing : STEP10 -> MAPPING READS: 10.mapsamples.pl

[LeeNicha]

Hi I got an error, it shows below:

[0 seconds]: STEP10 -> MAPPING READS: 10.mapsamples.pl Reading mapping file from /home_bif/onnicha/enterobacter_project/metagenome/ecInfants/data/00.ecInfants.samples Metagenomes found: 262 Mapping with Bowtie2 (Langmead and Salzberg 2012, Nat Methods 9(4), 357-9) Can't open mappingstat file for writing Died at /home_sbi_cold/onnicha/anaconda2/envs/squeezemeta/bin/restart.pl line 585.

I used SqueezeMeta version 1.3.0 Thank you in advanced.

[jtamames]

Hello Did you check that you have disk space available? 262 metagenomes must need a lot of space. Also, are they metagenomes or 16S amplicons? Please attach the syslog file found in the project directory

Best, Javier

[LeeNicha]

Thank you for your reply. I have around 5 TB left and it's metagenome data. I've fixed it by adding $mappingstat = "$resultpath/10.$projectname.mappingstat"; in SqueezeMeta_conf.pl and it worked!!

However, I got a new error as shown below

Output in /home_bif/onnicha/enterobacter_project/metagenome/ecInfants/intermediate/10.ecInfants.mapcount sort: write failed: /tmp/sort5suIKT: No space left on device Stopping in STEP10 -> 10.mapsamples.pl. File /home_bif/onnicha/enterobacter_project/metagenome/ecInfants/intermediate/10.ecInfants.mapcount is empty!

I've checked the space and it has 4.9 TB left. Please look at the syslog file

syslog.txt

[fpusan]

Hi!

According to the syslog you sent, the program seems to have finished abnormally in step 2.

[0 seconds]: STEP2 -> 02.rnas.pl
Running barrnap for Bacteria: /home_sbi_cold/onnicha/anaconda2/envs/SqueezeMeta/SqueezeMeta/bin/barrnap --quiet --threads 18 --kingdom bac --reject 0.1 /home_bif/onnicha/enterobacter_project/metagenome/ecInfants/intermediate/02.ecInfants.maskedrna.fasta --dbdir /home_bif2/onnicha/squeezemeta_db/db > /home_bif/onnicha/enterobacter_project/metagenome/ecInfants/temp/bac.gff
Running barrnap for Archaea: /home_sbi_cold/onnicha/anaconda2/envs/SqueezeMeta/SqueezeMeta/bin/barrnap --quiet --threads 18 --kingdom arc --reject 0.1 /home_bif/onnicha/enterobacter_project/metagenome/ecInfants/intermediate/02.ecInfants.maskedrna.fasta --dbdir /home_bif2/onnicha/squeezemeta_db/db > /home_bif/onnicha/enterobacter_project/metagenome/ecInfants/temp/arc.gff
Running barrnap for Eukaryote: /home_sbi_cold/onnicha/anaconda2/envs/SqueezeMeta/SqueezeMeta/bin/barrnap --quiet --threads 18 --kingdom euk --reject 0.1 /home_bif/onnicha/enterobacter_project/metagenome/ecInfants/intermediate/02.ecInfants.maskedrna.fasta --dbdir /home_bif2/onnicha/squeezemeta_db/db > /home_bif/onnicha/enterobacter_project/metagenome/ecInfants/temp/euk.gff
Running barrnap for Mitochondrial: /home_sbi_cold/onnicha/anaconda2/envs/SqueezeMeta/SqueezeMeta/bin/barrnap --quiet --threads 18 --kingdom mito --reject 0.1 /home_bif/onnicha/enterobacter_project/metagenome/ecInfants/intermediate/02.ecInfants.maskedrna.fasta --dbdir /home_bif2/onnicha/squeezemeta_db/db > /home_bif/onnicha/enterobacter_project/metagenome/ecInfants/temp/mito.gff
Running RDP classifier: java -jar /home_sbi_cold/onnicha/anaconda2/envs/SqueezeMeta/SqueezeMeta/bin/classifier.jar classify /home_bif/onnicha/enterobacter_project/metagenome/ecInfants/temp/16S.fasta -o /home_bif/onnicha/enterobacter_project/metagenome/ecInfants/temp/16S.out -f filterbyconf
Stopping in STEP2 -> 02.rnas.pl. Program finished abnormally

However in your latest message you say that the program failed at step 10. Did you attach the right syslog file?

It seems that the sort command is running directly over /tmp. So maybe your data partition has a lot of free space but the partition in which /tmp is mounted does not. Can you check? Let us know, we should be able to fix it if that's the case.

[LeeNicha]

That's the correct file. If you scroll down, you will see this message [[0 seconds]: STEP10 -> 10.mapsamples.pl Getting raw reads for P10441_S2: cp /home_bif/onnicha/enterobacter_project/metagenome/ecInfants/data/raw_fastq/P10441_S2_trimmed_1.fastq.gz /home_bif/onnicha/enterobacter_project/metagenome/ecInfants/temp/ecInfants.P10441_S2.current_1.gz; cp /home_bif/onnicha/enterobacter_project/metagenome/ecInfants/data/raw_fastq/P10441_S2_trimmed_2.fastq.gz /home_bif/onnicha/enterobacter_project/metagenome/ecInfants/temp/ecInfants.P10441_S2.current_2.gz; Aligning with bowtie2: cp /home_bif/onnicha/enterobacter_project/metagenome/ecInfants/data/raw_fastq/P10441_S2_trimmed_1.fastq.gz /home_bif/onnicha/enterobacter_project/metagenome/ecInfants/temp/ecInfants.P10441_S2.current_1.gz; cp /home_bif/onnicha/enterobacter_project/metagenome/ecInfants/data/raw_fastq/P10441_S2_trimmed_2.fastq.gz /home_bif/onnicha/enterobacter_project/metagenome/ecInfants/temp/ecInfants.P10441_S2.current_2.gz; Stopping in STEP10 -> 10.mapsamples.pl. Program finished abnormally](url)

[fpusan]

Ok, so did you check the available free space in the partition where /tmp is mounted?

[LeeNicha]

I've checked the space of /tmp directory. It's 100G, which it might not enough. So I exported the temporary directory in /home_bif/ , which space has 4.9 TB left. Now it worked.

Thank you for helping. :)

[jtamames]

Great to hear! Closing issue

[andreiprodan]

Hi! I have the same problem, my SqueezeMeta run crashed at the end of step 10 with the same error "sort: write failed: /tmp/sort5suIKT: No space left on device.". I restarted after updating to v1.3.1 but I'm concerned it will crash again at the same step. I have 5 TB of space but only 40 GB on the partition where /tmp is.

How can i export or move the /tmp directory to the partition where I have enough space? Or make it so that the sort command uses a different folder than /tmp?

[jtamames]

Hello Just copy the full project to the new location and restart. Best,

[LeeNicha]

Hi, @andreiprodan These are command that I used to export tmp directory mkdir tmp_dir export TMPDIR='/home/user/tmp_dir' export JOBLIB_TEMP_FOLDER='/home/user/tmp_dir'

[andreiprodan]

@LeeNicha, thanks!