Salmon is failing

[sagnikbanerjee15]

Hello,

I am using transrate to quantify the quality of de-novo assemblies. This is the command I am running.

nohup /work/LAS/rpwise-lab/sagnik/softwares/transrate/transrate --assembly /work/LAS/rpwise-lab/sagnik/data/maize/AGPv4/transcriptome/transcripts.fa --left /work/LAS/rpwise-lab/sagnik/Gene_Prediction/maize_gene_annotations/data/raw_fastq/SRR5941975_adapter_trimmed_1.fastq --right /work/LAS/rpwise-lab/sagnik/Gene_Prediction/maize_gene_annotations/data/raw_fastq/SRR5941975_adapter_trimmed_2.fastq --threads 16 --output transrate_run_SRR5941975_new_salmon > output_SRR5941975_new_salmon.txt 2> error_SRR5941975_new_salmon.txt

The run fails due to the old version of salmon. I have rerun the command using the new version of salmon (removing deprecated commands) and the run succeeds. I tried to replace salmon with the new version but transrate refused to proceed further. Please help me with this.

Thank you.

[MDSharma]

Hi, same here.. wondering if you are considering keeping this tool updated?

[sagnikbanerjee15]

Hello, I have swapped out snap with bwa and have also made a few changes in the rube code which I can share with you. Thank you.

…

On Sun, 10 Mar 2019, 4:07 pm MD Sharma, ***@***.***> wrote: Hi, same here.. wondering if you are considering keeping this tool updated? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#224 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AWXwuSDbae-1KPpt2Sn1mN5WD3k1KlJJks5vVXQYgaJpZM4XL6YH> .

[MDSharma]

Yes please! Best Regards, MD Sharma(sent via a mobile device.. please blame the AI driven autocorrect algorithm for any errors)

________________________________ From: Sagnik Banerjee <[email protected]> Sent: Sunday, March 10, 2019 9:42:37 PM To: blahah/transrate Cc: Sharma, M D; Comment Subject: Re: [blahah/transrate] Salmon is failing (#224) Hello, I have swapped out snap with bwa and have also made a few changes in the rube code which I can share with you. Thank you.

On Sun, 10 Mar 2019, 4:07 pm MD Sharma, ***@***.***> wrote: Hi, same here.. wondering if you are considering keeping this tool updated? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#224 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AWXwuSDbae-1KPpt2Sn1mN5WD3k1KlJJks5vVXQYgaJpZM4XL6YH> .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub<#224 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AHdKOildRmhWIWz05wzR7LK39gtLqZroks5vVXxNgaJpZM4XL6YH>.

[ghost]

I guess I am having the same problem here.

Running:

transrate --assembly Pd_1_Trinity_4x.fasta --left Pd_1_Trimmomatic_R1.fastq --right Pd_1_Trimmomatic_R2.fastq --threads 30

Ends with a Salmon error:

Exception : [The provided alignment file: "../transrate_results/Pd_1_Trinity_4x/Pd_1_Trimmomatic_R1.fastq.Pd_1_Trimmomatic_R2.fastq.Pd_1_Trinity_4x.bam" does not exist!
]

Is this the same error that you are getting?
Can you please share your fix?
Thanks!