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blahah / transrate

Understand your transcriptome assembly
http://hibberdlab.com/transrate
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Salmon is failing #224

Open sagnikbanerjee15 opened 5 years ago

sagnikbanerjee15 commented 5 years ago

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 commented 5 years ago

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

sagnikbanerjee15 commented 5 years ago

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, notifications@github.com 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 https://github.com/blahah/transrate/issues/224#issuecomment-471344693, or mute the thread https://github.com/notifications/unsubscribe-auth/AWXwuSDbae-1KPpt2Sn1mN5WD3k1KlJJks5vVXQYgaJpZM4XL6YH .

MDSharma commented 5 years ago

Yes please!

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

From: Sagnik Banerjee notifications@github.com 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, notifications@github.com 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 https://github.com/blahah/transrate/issues/224#issuecomment-471344693, 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 GitHubhttps://github.com/blahah/transrate/issues/224#issuecomment-471356825, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AHdKOildRmhWIWz05wzR7LK39gtLqZroks5vVXxNgaJpZM4XL6YH.

ghost commented 5 years ago

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!