Problem with fatsq-dump

Question

[Utpal]

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.

[GenoMax]

But the command fastq-dump SRR1972917 does not.

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.

[Utpal]

with the command which fastq-dump it returns:

~/.conda/envs/sratoolkit_env/bin/fastq-dump

With fastq-dump I get the following error meg:

2023-03-25T11:59:07 fastq-dump.2.8.0 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -9984 ( X509 - Certificate verification failed, e.g. CRL, CA or signature check failed )
2023-03-25T11:59:07 fastq-dump.2.8.0 sys: mbedtls_ssl_get_verify_result returned 0x8 (  !! The certificate is not correctly signed by the trusted CA  )
2023-03-25T11:59:07 fastq-dump.2.8.0 err: item not found while constructing within virtual database module - the path 'SRR1972917' cannot be opened as database or table
(sratoolkit_env)

Thanks.

[GenoMax]

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.

Try

conda install -c bioconda sra-tools

this should give you the latest SRA tools which v.3.0.3.

[Utpal]

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

It returned:

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:

• defaults/linux-64::glib==2.56.2=hd408876_0
• defaults/linux-64::libssh2==1.8.0=h9cfc8f7_4
• defaults/linux-64::dbus==1.13.2=h714fa37_1
• defaults/linux-64::gstreamer==1.14.0=hb453b48_1
• defaults/linux-64::libcurl==7.61.0=h1ad7b7a_0
• defaults/linux-64::curl==7.61.0=h84994c4_0
• defaults/linux-64::gst-plugins-base==1.14.0=hbbd80ab_1
• defaults/linux-64::alabaster==0.7.11=py37_0
• defaults/linux-64::appdirs==1.4.3=py37h28b3542_0 .......................................................................................... .......................................................................................... .......................................................................................... .......................................................................................... / Killed (base)