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bfosso / MetaShot

MetaShot (Metagenomics Shotgun) is a complete pipeline designed for the taxonomic classification of the human microbiota members. In MetaShot, third party tools and new developed Python and Bash scripts are integrated to analyze paired-end (PE) Illumina sequences, offering an automated procedure covering all the analysis steps from raw data management to taxonomic profiling. It is designed to analyze both DNA-Seq and RNA-Seq data.
GNU General Public License v3.0
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find_microbiome.py failed when running process on cluster node #9

Closed lmanchon closed 5 years ago

lmanchon commented 5 years ago

running on node-02 at mardi 19 février 2019, 21:05:37 (UTC+0100)

276458 running correctly formatted read_list file fastq control QC.1.trimmed.fastq QC.2.trimmed.fastq START 19/02/2019 21:33:16 Traceback (most recent call last): File "/home/MetaShot/find_microbiome.py", line 220, in process_status = pid_status( proc_id ) File "/home/MetaShot/find_microbiome.py", line 126, in pid_status status = psutil.Process( process_pid ).status( ) File "/home/PSUTIL/lib/python/psutil-5.5.0-py2.7-linux-x86_64.egg/psutil/init.py", line 773, in status return self._proc.status() File "/home/PSUTIL/lib/python/psutil-5.5.0-py2.7-linux-x86_64.egg/psutil/_pslinux.py", line 1525, in wrapper raise NoSuchProcess(self.pid, self._name) psutil.NoSuchProcess: psutil.NoSuchProcess process no longer exists (pid=35159) Feb 19 21:58:40 ..... started STAR run Feb 19 21:58:43 ..... loading genome Feb 19 22:07:59 ..... started STAR run Feb 19 22:07:59 ..... loading genome Feb 19 22:07:59 ..... started mapping Feb 19 22:12:50 ..... finished successfully correctly formatted read_list file Mapping on the genome sam parsing HOST MAPPING IS DONE Feb 19 22:12:53 ..... started STAR run Feb 19 22:12:53 ..... loading genome the indicated /home/MetaShot/trimmed_data_1/R1_micro_candidates.fastq fastq file doesn't exist This script works in two different steps: (1) it maps the sequencing data against the Bacterial division; (2) it extract the mapped pairs and tries to map them on the human reference; Options: -i paired-end file list: a line containing the R1, the R2 files [MANDATORY] -p Number of threads/processors available [MANDATORY] -r reference path [MANDATORY] -s script path path [MANDATORY] -h print this help. Usage: python division_analyser -i read_list

the process is still running or frozen on the node.

bfosso commented 5 years ago

Actually Metashot is not designed to work on cluster. Consequently it is not able to map the process across different nodes.

lmanchon commented 5 years ago

that's what I thought when I looked at the error returns from psutil