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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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10.mapsamples.pl. Program finished abnormally #810

Closed AntonioPuriel closed 2 months ago

AntonioPuriel commented 3 months ago

[21 seconds]: STEP10 -> 10.mapsamples.pl Creating Bowtie reference: python3 /appli/conda-env/bioinfo/squeezemeta-1.6.2/SqueezeMeta/bin/bowtie2/bowtie2-build --quiet /home3/datawork/apurielh/MetagenOIL/runpool090715_2/Project_MetagenOIL.489/Run_pool.7385/metagenomic715_1/results/01.metagenomic715_1.fasta /home3/datawork/apurielh/MetagenOIL/runpool090715_2/Project_MetagenOIL.489/Run_pool.7385/metagenomic715_1/data/metagenomic715_1.bowtie Getting raw reads for HC_T0: cp /home3/datawork/apurielh/MetagenOIL/runpool090715_2/Project_MetagenOIL.489/Run_pool.7385/metagenomic715_1/data/raw_fastq/HC_T0_ATCACG_L002_R1.fastq.gz /home3/datawork/apurielh/MetagenOIL/runpool090715_2/Project_MetagenOIL.489/Run_pool.7385/metagenomic715_1/temp/metagenomic715_1.HC_T0.current_1.gz; cp /home3/datawork/apurielh/MetagenOIL/runpool090715_2/Project_MetagenOIL.489/Run_pool.7385/metagenomic715_1/data/raw_fastq/HC_T0_ATCACG_L002_R2.fastq.gz /home3/datawork/apurielh/MetagenOIL/runpool090715_2/Project_MetagenOIL.489/Run_pool.7385/metagenomic715_1/temp/metagenomic715_1.HC_T0.current_2.gz; Calling sqm_counter: Sample HC_T0, BAM /home3/datawork/apurielh/MetagenOIL/runpool090715_2/Project_MetagenOIL.489/Run_pool.7385/metagenomic715_1/data/bam/metagenomic715_1.HC_T0.bam, Number of reads 186304900, GFF /home3/datawork/apurielh/MetagenOIL/runpool090715_2/Project_MetagenOIL.489/Run_pool.7385/metagenomic715_1/results/03.metagenomic7151.gff Stopping in STEP10 -> 10.mapsamples.pl. Program finished abnormally [syslog.txt](https://github.com/jtamames/SqueezeMeta/files/14556723/syslog_.txt)

jtamames commented 3 months ago

Hello (a greeting is always appreciated)

As you already know, your metagenome is huge. You have more than 10 M contigs, and your RAM is not that much (500 Gb at best). That´s why you had to restart so many times. If you check #448, you will see that version 1.6.3 uses less memory than 1.6.2, the one that you are running. So my advice is that you update your SqueezeMeta to 1.6.3 and see if it works for you. Alternatively, reducing the number of threads can also help. Best,

fpusan commented 2 months ago

Closing due to lack of activity, feel free to reopen