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Microbial-Ecology-Group / AMRplusplus

AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resistance genes, or resistome.
https://www.meglab.org/
GNU General Public License v3.0
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Multiqc problem/error #31

Closed cbryansantos closed 5 months ago

cbryansantos commented 11 months ago

I'm trying to install nextflow but when I execute the comand "nextflow run main_AMR++.nf -profile conda" , this happens:

ERROR ~ Error executing process > 'FAST_AMRplusplus:FASTQ_QC_WF:multiqc (Running multiQC)'

Caused by: Process FAST_AMRplusplus:FASTQ_QC_WF:multiqc (Running multiQC) terminated with an error exit status (1)

Command executed:

cp multiqc/ . multiqc -v data --interactive -f --cl-config "max_table_rows: 3000" mv multiqc_data/multiqc_general_stats.txt .

Command exit status: 1

Command output: (empty)

Command error:

/// MultiQC 🔍 | v1.18 (4642b16)

[2023-12-14 13:40:42,960] multiqc [DEBUG ] This is MultiQC v1.18 (4642b16) [2023-12-14 13:40:42,962] multiqc [DEBUG ] Loading config settings from: multiqc_config.yaml [2023-12-14 13:40:42,963] multiqc [DEBUG ] New config: {'title': 'AMR++ Bioinformatic pipeline', 'subtitle': 'A pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resistance genes, or resistome.', 'report_header_info': [{'Contact E-mail': 'meglab.metagenomics@gmail.com'}, {'Application Type': 'AMR++'}, {'Project Type': 'FastQC analysis'}], 'custom_logo_url': 'https://www.nextflow.io', 'custom_logo_title': 'Center for Genomic Regulation'} [2023-12-14 13:40:42,963] multiqc [DEBUG ] Found command line config: {'max_table_rows': 3000} [2023-12-14 13:40:42,963] multiqc [DEBUG ] New config: {'max_table_rows': 3000} [2023-12-14 13:40:42,963] multiqc [DEBUG ] Command used: /home/alunos/AMRplusplus/envs/AMR++_env-f6a872478a3709bc95dfc426aba819e3/bin/multiqc -v data1 data2 data3 --interactive -f --cl-config max_table_rows: 3000 [2023-12-14 13:40:43,261] multiqc [DEBUG ] Latest MultiQC version is v1.17 [2023-12-14 13:40:43,262] multiqc [DEBUG ] Working dir : /home/alunos/AMRplusplus/work/ba/e8077a574beebf1ae9ed49c8640509 [2023-12-14 13:40:43,262] multiqc [DEBUG ] Template : default [2023-12-14 13:40:43,262] multiqc [DEBUG ] Running Python 3.9.15 | packaged by conda-forge | (main, Nov 22 2022, 08:45:29) [GCC 10.4.0] [2023-12-14 13:40:43,262] multiqc [INFO ] Report title: AMR++ Bioinformatic pipeline [2023-12-14 13:40:43,262] multiqc [DEBUG ] Analysing modules: custom_content, ccs, ngsderive, purple, conpair, lima, peddy, somalier, methylQA, mosdepth, phantompeakqualtools, qualimap, preseq, hifiasm, quast, qorts, rna_seqc, rockhopper, rsem, rseqc, busco, bustools, goleft_indexcov, gffcompare, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, mirtop, sambamba, gopeaks, homer, hops, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, fgbio, dragen, dragen_fastqc, dedup, pbmarkdup, damageprofiler, mapdamage, biobambam2, jcvi, mtnucratio, picard, vep, bakta, prokka, qc3C, nanostat, samblaster, samtools, sexdeterrmine, seqera_cli, eigenstratdatabasetools, bamtools, jellyfish, vcftools, longranger, stacks, varscan2, snippy, umitools, truvari, bbmap, bismark, biscuit, diamond, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, cellranger, snpsplit, odgi, pangolin, nextclade, freyja, humid, kat, leehom, librarian, adapterRemoval, bbduk, clipandmerge, cutadapt, flexbar, sourmash, kaiju, bracken, kraken, malt, motus, trimmomatic, sickle, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, filtlong, prinseqplusplus, pychopper, porechop, pycoqc, minionqc, anglerfish, multivcfanalyzer, clusterflow, checkqc, bcl2fastq, bclconvert, interop, ivar, flash, seqyclean, optitype, whatshap, xenome, xengsort [2023-12-14 13:40:43,262] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmplae7l698 [2023-12-14 13:40:43,265] multiqc [INFO ] Search path : data1 [2023-12-14 13:40:43,265] multiqc [INFO ] Search path : data2 [2023-12-14 13:40:43,265] multiqc [INFO ] Search path : data3 | searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 12/12
[2023-12-14 13:40:43,396] multiqc [DEBUG ] Summary of files that were skipped by the search: [skipped_module_specific_max_filesize: 72] // [skipped_no_match: 6] [2023-12-14 13:40:44,060] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.5.3 [2023-12-14 13:40:44,072] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.5.3 [2023-12-14 13:40:44,073] multiqc [DEBUG ] No samples found: custom_content [2023-12-14 13:40:44,095] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2023-12-14 13:40:44,140] multiqc.utils.software_versions [DEBUG ] Reading sof [DEBUG ] Command used: /home/alunos/AMRplusplus/envs/AMR++_env-f6a872478a3709bc95dfc426aba819e3/bin/multiqc -v data1 data2 data3 --interactive -f --cl-config max_table_rows: 3000 [2023-12-14 13:40:43,261] multiqc [DEBUG ] Latest MultiQC version is v1.17 [2023-12-14 13:40:43,262] multiqc [DEBUG ] Working dir : /home/alunos/AMRplusplus/work/ba/e8077a574beebf1ae9ed49c8640509 [2023-12-14 13:40:43,262] multiqc [DEBUG ] Template : default [2023-12-14 13:40:43,262] multiqc [DEBUG ] Running Python 3.9.15 | packaged by conda-forge | (main, Nov 22 2022, 08:45:29) [GCC 10.4.0] [2023-12-14 13:40:43,262] multiqc [INFO ] Report title: AMR++ Bioinformatic pipeline [2023-12-14 13:40:43,262] multiqc [DEBUG ] Analysing modules: custom_content, ccs, ngsderive, purple, conpair, lima, peddy, somalier, methylQA, mosdepth, phantompeakqualtools, qualimap, preseq, hifiasm, quast, qorts, rna_seqc, rockhopper, rsem, rseqc, busco, bustools, goleft_indexcov, gffcompare, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, mirtop, sambamba, gopeaks, homer, hops, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, fgbio, dragen, dragen_fastqc, dedup, pbmarkdup, damageprofiler, mapdamage, biobambam2, jcvi, mtnucratio, picard, vep, bakta, prokka, qc3C, nanostat, samblaster, samtools, sexdeterrmine, seqera_cli, eigenstratdatabasetools, bamtools, jellyfish, vcftools, longranger, stacks, varscan2, snippy, umitools, truvari, bbmap, bismark, biscuit, diamond, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, cellranger, snpsplit, odgi, pangolin, nextclade, freyja, humid, kat, leehom, librarian, adapterRemoval, bbduk, clipandmerge, cutadapt, flexbar, sourmash, kaiju, bracken, kraken, malt, motus, trimmomatic, sickle, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, filtlong, prinseqplusplus, pychopper, porechop, pycoqc, minionqc, anglerfish, multivcfanalyzer, clusterflow, checkqc, bcl2fastq, bclconvert, interop, ivar, flash, seqyclean, optitype, whatshap, xenome, xengsort [2023-12-14 13:40:43,262] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmplae7l698 [2023-12-14 13:40:43,265] multiqc [INFO ] Search path : data1 [2023-12-14 13:40:43,265] multiqc [INFO ] Search path : data2 [2023-12-14 13:40:43,265] multiqc [INFO ] Search path : data3 | searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 12/12
[2023-12-14 13:40:43,396] multiqc [DEBUG ] Summary of files that were skipped by the search: [skipped_module_specific_max_filesize: 72] // [skipped_no_match: 6] [2023-12-14 13:40:44,060] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.5.3 [2023-12-14 13:40:44,072] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.5.3 [2023-12-14 13:40:44,073] multiqc [DEBUG ] No samples found: custom_content [2023-12-14 13:40:44,095] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2023-12-14 13:40:44,140] multiqc.utils.software_versions [DEBUG ] Reading software versions from config.software_versions [2023-12-14 13:40:44,159] multiqc [DEBUG ] Compressing plot data [2023-12-14 13:40:44,311] multiqc [INFO ] Report : AMR-Bioinformatic-pipeline_multiqc_report.html [2023-12-14 13:40:44,312] multiqc [INFO ] Data : AMR-Bioinformatic-pipeline_multiqc_report_data [2023-12-14 13:40:44,312] multiqc

stalbrec commented 11 months ago

I had the same issue. The changes i proposed in #32 fixes this issue for me.

cbryansantos commented 11 months ago

it works but now i have other error

ERROR ~ Error executing process > 'FAST_AMRplusplus:FASTQ_RESISTOME_WF:build_dependencies (null)'

Caused by: Process FAST_AMRplusplus:FASTQ_RESISTOME_WF:build_dependencies (null) terminated with an error exit status (128)

Command executed:

Uncomment these sections once the v2 rarefactionanalyzer and resistomeanalyzer repositories are updated, remove cp lines

git clone https://github.com/cdeanj/rarefactionanalyzer.git

cd rarefactionanalyzer

make

chmod 777 rarefaction

mv rarefaction ../

cd ../

rm -rf rarefactionanalyzer

cp /home/alunos/AMRplusplus/bin/rarefaction .

git clone https://github.com/cdeanj/resistomeanalyzer.git

cd resistomeanalyzer

make

chmod 777 resistome

mv resistome ../

cd ../

rm -rf resistomeanalyzer

cp /home/alunos/AMRplusplus/bin/resistome .

git clone https://github.com/Isabella136/AmrPlusPlus_SNP.git chmod -R 777 AmrPlusPlus_SNP/

Command exit status: 128

Command output: (empty)

Command error: Cloning into 'AmrPlusPlus_SNP'... error: 793 bytes of body are still expected fetch-pack: unexpected disconnect while reading sideband packet fatal: early EOF fatal: fetch-pack: invalid index-pack output

Work dir: /home/alunos/AMRplusplus/work/b9/a68dd31d45ce9690ab07a5355b0c16

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- Check '.nextflow.log' file for details

rbtoscan commented 11 months ago

Interested in the resolution.

EnriqueDoster commented 8 months ago

@cbryansantos, thanks for the report. Looks like the issue was that the latest version of multiqc changed so that the title in the config.yaml was now being used to name the report and output folder. I've updated the command for that module so it should work for you now if you download the latest AMR++ code from github. Not sure how you fixed it on your end, but hopefully we've addressed it now.

The second error seems like there was an issue in the download of the AmrPlusPlus_SNP github repository. Did you happen to run it with SLURM or another scheduling system? I've run into an issue where you need to load a module or otherwise specify a way that your computing node can access the internet. If you're not sure about that, you can download the repository by itself prior to running AMR++.

From the AMR++ repository, you could run this:

git clone https://github.com/Isabella136/AmrPlusPlus_SNP.git

# And move the repository the bin/ directory
mv AmrPlusPlus_SNP/ bin/

Then try running AMR++ again, hopefully that works!