Run test and get empty file

[smallwhitelama]

Dear Sir:
I followed setup of amrplusplus/docs/installation.md and ran a simple test.
But I got the empty output files in RunRarefaction and RunResistome folders .
How can I get the correct output?

$ nextflow run main.nf -profile docker --threads 4 --output test
N E X T F L O W ~ version 0.25.1
Launching main.nf [determined_lichterman] - revision: bf5cb509e2
[warm up] executor > local
WARN: The use of first operator is unnecessary when applied to a value channel
WARN: The use of first operator is unnecessary when applied to a value channel
[fa/2403dc] Submitted process > BuildHostIndex (chr21)
[38/51fc63] Submitted process > BuildAMRIndex (megares_database_v1.01)
[5e/9f3628] Submitted process > RunQC (SRR532663)
[fb/cad6a9] Submitted process > QCStats (null)
[8f/9e5b33] Submitted process > AlignReadsToHost (SRR532663)
[23/dc4aac] Submitted process > RemoveHostDNA (SRR532663)
[d3/92f328] Submitted process > BAMToFASTQ (SRR532663)
[a8/4abc88] Submitted process > HostRemovalStats (null)
[47/325dc5] Submitted process > RunKraken (SRR532663)
[bb/c62be8] Submitted process > AlignToAMR (SRR532663)
[32/bf9637] Submitted process > RunSNPFinder (SRR532663)
[93/cec816] Submitted process > RunResistome (SRR532663)
[a0/adfa68] Submitted process > RunRarefaction (SRR532663)
[03/3c6e3c] Submitted process > AMRLongToWide (null)
[a3/316ec4] Submitted process > KrakenLongToWide (null)

[EnriqueDoster]

Hello,

Thanks for trying amrplusplus and hopefully we can get everything working for you. To that end, could you please provide a bit more information about the system you are using to run amrplusplus? Are you using the docker image or are you installing all the required tools to your local system? Can you provide the output from the log file (".nextflow.log") that should in your working directory?

Best,
-Enrique

[smallwhitelama]

Dear Sir:
Thanks for your reply.
I ran amrplusplus in ubuntu16.04 and used to docker image.

nextflow.log

[EnriqueDoster]

Hello, Thanks for passing this on, but I couldn't find any obvious errors. Have you tried to run amrplusplus on your data? Also, does your server have a queuing such as slurm? The jobs were all submitted properly, but weren't actually run and that could happen if your server doesn't let you submit jobs directly. Lastly, have you successfully used docker on your server before? Setting it up can be pretty tricky. Best, -Enrique

…

On Fri, Feb 1, 2019 at 2:52 AM smallwhitelama ***@***.***> wrote: Dear Sir: Thanks for your reply. I ran amrplusplus in ubuntu16.04 and used to docker image. nextflow.log <https://github.com/cdeanj/amrplusplus/files/2820990/nextflow.log> — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ALxtSwIyzyximDSAmBazxHWnu-RvIoCeks5vJA5UgaJpZM4aSSyz> .

[pedres]

Hi,

I am having the same issue. I am running AMRplusplus on a local machine (workstation). I have installed AMRplusplus following the instructions of readme.md file from AMRplusplus folder and then in the same conda environment installed all dependencies. The test run correctly until resistome. Below I paste the error message. I was looking for the nextflow.log in AMRplusplus folder and in the corresponding conda environment but I did not find it.

Thank you very much for your help

Error executing process > 'FAST_AMRplusplus:FASTQ_RESISTOME_WF:runresistome (S1_test)'

Caused by:
Process FAST_AMRplusplus:FASTQ_RESISTOME_WF:runresistome (S1_test) terminated with an error exit status (1)

Command executed:

resistome -ref_fp megares_database_v3.00.fasta -annot_fp megares_annotations_v3.00.csv -sam_fp S1_test.alignment.sam -gene_fp S1_test.AMR.gene.tsv -group_fp S1_test.AMR.group.tsv -mech_fp S1_test.AMR.mechanism.tsv -class_fp S1_test.AMR.class.tsv -type_fp S1_test.AMR.type.tsv -t 10

Command exit status:
1

Command output:
(empty)

Command error:

Program: ResistomeAnalyzer
Contact: Chris Dean cdean11@rams.colostate.edu

Usage: ./resistome [options]

Options:

-ref_fp		STR/FILE	Fasta formatted reference sequence
-annot_fp	STR/FILE	CSV formatted annotation database

rk dir-sam_fp STR/FILE SAM formatted alignment file
/home/-gene_fpo/AMRpluSTR/FILErk/75/efOutput name for gene level resistome
-group_fp STR/FILE Output name for group level resistome
p: vie-mech_fpmplete cSTR/FILEutput byOutput name for mechanism level resistome
-class_fp STR/FILE Output name for class level resistome
-t INT Gene fraction threshold

Work dir:
/home/fulgencio/AMRplusplus/work/75/ef450fc18b936f84c829ed18bd3627