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marbl / metAMOS

A metagenomic and isolate assembly and analysis pipeline built with AMOS
http://marbl.github.io/metAMOS
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Error at Annotate step #209

Closed Ramanandan closed 8 years ago

Ramanandan commented 9 years ago

Dear Dr. Sergey,

For sample (S002990), I executed following commands. Successfully, I got the outputs for annotation, functional annotation and classify.

/bin/sh

../initPipeline -q -1 S002990_r1.fastq -2 S002990_r2.fastq -d S002990_Version1_1 -i 50:150 ../runPipeline -q -v -a spades,velvet-sc,abyss,ray,edena,sga,masurca,soap,soap2,velvet -c FCP -g fraggenescan -p 15 -d S002990_Version1_1 -k 55 -f Preprocess,Assemble,MapReads,FindORFS,Annotate,FunctionalAnnotation,Propagate,FindRepeats,MultiAlign,Classify,Abundance,FindScaffoldORFS -n Scaffold

But for another sample (S00298A), 1) initiPipeline - modified 2 input fastq files and output directory. Rest of them are same as the above command. 2) runpipeline - modified assembly to soap alone instead of spades,velvet-sc,abyss,ray,edena,sga,masurca,soap,soap2,velvet and output directory. Rest of them are same as the above command.

/bin/sh

../initPipeline -q -1 S00298A_r1.fastq -2 S00298A_r2.fastq -d S00298A_Version1_2 -i 50:150 ../runPipeline -q -v -a soap -c FCP -g fraggenescan -p 15 -d S00298A_Version1_2 -k 55 -f Preprocess,Assemble,MapReads,FindORFS,Annotate,FunctionalAnnotation,Propagate,FindRepeats,MultiAlign,Classify,Abundance,FindScaffoldORFS -n Scaffold

I encountered the errors at annotate step. What could have been the reason for this error.

annotate error screenshot 1

annotate error screenshot 2

Ramanandan commented 9 years ago

Can I get some updates on this issue

treangen commented 9 years ago

Hi Ramanandan,

its possible that FCP crashed, you ran out of disk space, and/or the blast DB is missing (unlikely since previous run completed ), or other. Very hard to say without additional information, can you run the last command that failed , NB-BL.py and send the output? Also, I strongly recommend trying again with Kraken (-c kraken) for metagenomic classification .

Ramanandan commented 9 years ago

Dear Dr.Treangen,

I compared the files in ../annotate/out/ between the two samples. For sample S002988, I received the output, but sample S002992 I got errors at annotate step. I have pasted it for your reference. comparing two samples annotate output folder

Do you want to rerun the entire pipeline or just NB-BL.py?

If just to run NB-BL.py, what I give for blastn_results.txt? Usage: python NB-BL.py nb-results blastn-results results-file

Required parameters:

Results of NB classifier with T=0. Results of BLASTN classifier. File to write classification results to. (proba.ctg_1.bl_results.txt) Typical usage: python NB-BL.py proba.ctg_1.nb_results.txt blastn_results.txt proba.ctg_1.bl_results.txt
treangen commented 9 years ago

You only need to rerun the command that failed. you have the full NB-BL.py command provided in the log file/screenshot you previously sent, so you can just copy and paste that command to run. If the command fails again, I'd strongly suggest that you contact the developers of FCP for support (since it worked previously for you, but not on your sample sample S002992) and/or try a different metagenomic classification tool, such as Kraken.

skoren commented 8 years ago

Closed, inactivity