-
Notifications
You must be signed in to change notification settings - Fork 34
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Salmon is failing #224
Comments
Hi, same here.. wondering if you are considering keeping this tool updated? |
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>
.
|
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>.
|
I guess I am having the same problem here. Running:
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? |
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.
The text was updated successfully, but these errors were encountered: