Entering edit mode
9 weeks ago
Utpal • 0
Hi, I am absolutely new in NGS data analysis and have just started working in centos. I installed sratoolkit with the commands :
conda create –n sratoolkit_env –y conda activate sratoolkit_env conda install –c bioconda sra-tools –y
Then as given in the Biostar Handbook (Bioinformatics Data analysis guide) I tried some commands. The following commands work:
esearch -db sra -query PRJNA257197 esearch -db sra -query PRJNA257197 | efetch -format runinfo > runinfo.csv cat runinfo.csv | cut -f 1 -d ',' | grep SRR | head > runids.txt
But the command
fastq-dump SRR1972917 does not.
I would request your help.
Thanks and regards.
What does it not do? What do you get when you try
which fastq-dump? I just checked that SRR# and it is valid and fastq-dump produces data from it.
with the command which fastq-dump it returns:
With fastq-dump I get the following error meg:
Looks like the developers have an answer for this error: https://github.com/ncbi/sra-tools/issues/139
At least the program seems to be installed correctly. Did you see the file even though you get that error.
this should give you the latest SRA tools which v.3.0.3.
Thank you for your support. I tried the command conda install -c bioconda sra-tools
But, still with the command, fastq-dump it returns:
Usage: fastq-dump [options] <path> [<path>...] fastq-dump [options] <accession>
Use option --help for more information
fastq-dump : 2.8.0
So, it is not upgraded to version 3
Also, I don't see the files expected to be downloaded.
I tried to update conda with the command: conda update -n base conda
Retrieving notices: ...working... done Collecting package metadata (current_repodata.json): done Solving environment: - Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed with repodata from current_repodata.json, will retry with next repodata source. Solving environment: | Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: \ The environment is inconsistent, please check the package plan carefully The following packages are causing the inconsistency: