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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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snakemake error - FileNotFoundError: [Errno 2] No such file or directory: EXPR.csv #32

Closed pillailab closed 5 years ago

pillailab commented 5 years ago

Hello, I am getting the following error which running the quant function SalmonTE.py quant --reference=hs --outpath=~/scratch60/SF3B1/SRP061203/SRX1098126/ --num_threads=8 $fq1 $fq2

I tried changing snakemake version to 5.1.5 but error repeats. I am running using a conda environment, not sure if that it is relevant. thanks ! Manoj

2019-05-17 07:01:02,225 Starting quantification mode 2019-05-17 07:01:02,227 Collecting FASTQ files... 2019-05-17 07:01:02,417 The input dataset is considered as a paired-ends dataset. 2019-05-17 07:01:02,418 Collected 1 FASTQ files. 2019-05-17 07:01:02,418 Quantification has been finished. 2019-05-17 07:01:02,418 Running Salmon using Snakemake NameError in line 24 of /ysm-gpfs/home/mp758/project/Tools/SalmonTE/SalmonTE/snakemake/Snakefile.paired: name 'directory' is not defined File "/ysm-gpfs/home/mp758/project/Tools/SalmonTE/SalmonTE/snakemake/Snakefile.paired", line 24, in 2019-05-17 07:01:04,603 NameError in line 24 of /ysm-gpfs/home/mp758/project/Tools/SalmonTE/SalmonTE/snakemake/Snakefile.paired: name 'directory' is not defined File "/ysm-gpfs/home/mp758/project/Tools/SalmonTE/SalmonTE/snakemake/Snakefile.paired", line 24, in Traceback (most recent call last): File "/ysm-gpfs/home/mp758/project/Tools/SalmonTE/SalmonTE/SalmonTE.py", line 289, in run(args) File "/ysm-gpfs/home/mp758/project/Tools/SalmonTE/SalmonTE/SalmonTE.py", line 240, in run run_salmon(param) File "/ysm-gpfs/home/mp758/project/Tools/SalmonTE/SalmonTE/SalmonTE.py", line 156, in run_salmon with open(os.path.join(param["--outpath"], "EXPR.csv" ), "r") as inp: FileNotFoundError: [Errno 2] No such file or directory: '~/scratch60/SF3B1/SRP061203/SRX1098126/EXPR.csv'

hyunhwan-jeong commented 5 years ago

Hello @pillailab,

It seems that the error is similar to #27. What does $fq1 and $fq2 contain?

Hyun-Hwan Jeong

pillailab commented 5 years ago

Hi @hyunhwaj , Thanks - i did try updating snakemake (to version 5.4) but error still repeats fq1 and fq2 are aliases for fastq files fq1=/home/mp758/scratch60/SF3B1/SRP061203/SRX1098126/fastq/SRX1098126_1.fastq.gz fq2=/home/mp758/scratch60/SF3B1/SRP061203/SRX1098126/fastq/SRX1098126_2.fastq.gz Manoj

hyunhwan-jeong commented 5 years ago

@pillailab

Can you try --outpath=/home/mp758/scratch60/SF3B1/SRP061203/SRX1098126/ instead of --outpath=~/scratch60/SF3B1/SRP061203/SRX1098126/?

Thank you,

Hyun-Hwan Jeong

pillailab commented 5 years ago

@hyunhwaj , That seems to have fixed it and i got the output files. Thank you ! Manoj

hyunhwan-jeong commented 5 years ago

@pillailab, good to hear that! I will try to find the solution for how SalmonTE can handle your initial command line.

Kind Regards,

Hyun-Hwan Jeong