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hyunhwan-jeong / SalmonTE

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances
GNU General Public License v3.0
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salmonTe #33

Closed SalimMegat closed 5 years ago

SalimMegat commented 5 years ago

Hi, I have been using salmonTE foe quite some time and I wanted to apply the tool for large scale analysis. However, I tried to used salmon TE on 695 fastq which he seems to detect (see below) in the folder but after I only count 60 output folders. It seems like it just took some random sample and ran the tool on it. Is there any limit in the number of fastQ that can be processed at the same time ? (snakemake) [smegat@hpc-login1 star_script]$ cat slurm-9206873.out 2019-06-19 19:17:32,171 Starting quantification mode 2019-06-19 19:17:32,172 Collecting FASTQ files... 2019-06-19 19:17:32,173 SalmonTE assumes that '/b/home/medecine/smegat/human_fastq/all_fastq/' is a directory, and SalmonTE will search any FASTQ file in the directory. 2019-06-19 22:26:03,413 The input dataset is considered as a paired-ends dataset. 2019-06-19 22:26:03,571 Collected 695 FASTQ files. 2019-06-19 22:26:03,572 Quantification has been finished. 2019-06-19 22:26:03,573 Running Salmon using Snakemake Job counts: count jobs 1 all 1 collect_abundance 1 collect_mappability 695 run_salmon_gz 698 2019-06-19 22:26:14,456 Job counts: count jobs 1 all 1 collect_abundance 1 collect_mappability 695 run_salmon_gz 698

and here is the output folder.

Capture d’écran 2019-06-20 à 10 21 41

Many thanks,

Salim.

SalimMegat commented 5 years ago

Never mind its still running :(

hyunhwan-jeong commented 5 years ago

No problem! Let me know if you have any question!