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Hi everybody,
I am running trinity v2.0.6 with miseq illumina PE reads (1.4-4M reads) on a 12CPU-24Gb RAM workstation.
Sometimes I get trinity working fine in an home-made pipeline, but often it idles at the first phase, as follows:
I let it run for also a day without any change. When i kill the process, I still see jellyfish run as zombie process.
It is not strictly correlated to the input files, since after reboot, I rerun trinity on the same files and I got it work.
The trinity command is this:
Any suggestion? May it be due to memory?
Should I wait more? On trinity manual, jellyfish should take about one hour (on the samples that I got running, it takes a few minutes, but when it doesn't work, it takes also more than 24h).
Thank you in advance!
I am running trinity v2.0.6 with miseq illumina PE reads (1.4-4M reads) on a 12CPU-24Gb RAM workstation.
Sometimes I get trinity working fine in an home-made pipeline, but often it idles at the first phase, as follows:
Code:
---------------------------------------------------------------------------------- -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- ---------------------------------------------------------------------------------- ------------------------------------------- ----------- Jellyfish -------------------- -- (building a k-mer catalog from reads) -- ------------------------------------------- Tuesday, December 22, 2015: 12:40:46 CMD: /home/gimto/trinityrnaseq-2.0.6/trinity-plugins/jellyfish/bin/jellyfish count -t 6 -m 25 -s 2968824912 --canonical both.fa
It is not strictly correlated to the input files, since after reboot, I rerun trinity on the same files and I got it work.
The trinity command is this:
Code:
Trinity --seqType fq --max_memory 20G --left F1.trimmed.fastq --right R1.trimmed.fastq --CPU 6 --min_contig_length 300 --bypass_java_version_check --verbose --output ./trinity_out_dir
Should I wait more? On trinity manual, jellyfish should take about one hour (on the samples that I got running, it takes a few minutes, but when it doesn't work, it takes also more than 24h).Thank you in advance!
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