[2017-09-13 01:24:33,042] multiqc                                            [DEBUG  ]  No MultiQC config found: /share/apps/python3/lib/python3.5/site-packages/multiqc_config.yaml
[2017-09-13 01:24:33,042] multiqc                                            [DEBUG  ]  No MultiQC config found: /home/gencore/.multiqc_config.yaml
[2017-09-13 01:24:33,043] multiqc                                            [DEBUG  ]  No MultiQC config found: multiqc_config.yaml
[2017-09-13 01:24:33,059] multiqc                                            [DEBUG  ]  Loading config settings from: /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml
[2017-09-13 01:24:33,059] multiqc                                            [DEBUG  ]  New config 'custom_content': {'order': ['run_stats', 'demux_report', 'demux_report-1', 'demux_report-2', 'demux_report-3', 'demux_report-4', 'demux_report-5', 'demux_report-6', 'demux_report-7', 'demux_report-8']}
[2017-09-13 01:24:33,059] multiqc                                            [DEBUG  ]  Command used: /share/apps/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/HKWY5BGX3/merged
[2017-09-13 01:24:33,588] multiqc                                            [WARNING]  MultiQC Version v1.2 now available!
[2017-09-13 01:24:33,588] multiqc                                            [INFO   ]  This is MultiQC v1.0.dev0
[2017-09-13 01:24:33,589] multiqc                                            [DEBUG  ]  Command     : /share/apps/python3/bin/multiqc -c /home/mk5636/SCRIPTS/Scanner/mqc_config.yaml /home/mk5636/fastqc-delivery/HKWY5BGX3/merged
[2017-09-13 01:24:33,589] multiqc                                            [DEBUG  ]  Working dir : /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HKWY5BGX3/merged
[2017-09-13 01:24:33,589] multiqc                                            [INFO   ]  Template    : default
[2017-09-13 01:24:33,590] multiqc                                            [INFO   ]  Searching '/home/mk5636/fastqc-delivery/HKWY5BGX3/merged'
[2017-09-13 01:24:33,591] multiqc                                            [DEBUG  ]  Analysing modules: custom_content, peddy, methylQA, qualimap, preseq, quast, rna_seqc, rseqc, busco, goleft_indexcov, snpeff, gatk, htseq, bcftools, featureCounts, picard, prokka, samblaster, samtools, bamtools, bismark, hicup, salmon, kallisto, slamdunk, star, tophat, bowtie2, bowtie1, adapterRemoval, cutadapt, trimmomatic, skewer, sortmerna, fastq_screen, fastqc, clusterflow
[2017-09-13 01:24:33,591] multiqc                                            [DEBUG  ]  Using temporary directory for creating report: /tmp/tmp4dud_sh7
[2017-09-13 01:24:36,381] multiqc.modules.custom_content.custom_content      [INFO   ]  demux_report: Found 24 samples (table)
[2017-09-13 01:24:36,383] multiqc.modules.custom_content.custom_content      [INFO   ]  run_stats: Found 1 samples (table)
[2017-09-13 01:24:36,389] multiqc.modules.peddy.peddy                        [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,394] multiqc.modules.methylQA.methylQA                  [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,399] multiqc.modules.qualimap.QM_BamQC                  [DEBUG  ]  Using default Qualimap thresholds: 1, 5, 10, 30, 50
[2017-09-13 01:24:36,399] multiqc.modules.qualimap.qualimap                  [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,404] multiqc.modules.preseq.preseq                      [DEBUG  ]  Could not find any preseq data in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,408] multiqc.modules.quast.quast                        [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,420] multiqc.modules.rna_seqc.rna_seqc                  [DEBUG  ]  Could not find any RNA-SeQC data in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,436] multiqc.modules.rseqc.rseqc                        [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,454] multiqc.modules.busco.busco                        [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,459] multiqc.modules.goleft_indexcov.goleft_indexcov    [DEBUG  ]  Did not find goleft indexcov outputs in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,463] multiqc.modules.snpeff.snpeff                      [DEBUG  ]  Could not find any data in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,468] multiqc.modules.gatk.gatk                          [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,479] multiqc.modules.htseq.htseq                        [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,484] multiqc.modules.bcftools.bcftools                  [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,488] multiqc.modules.featureCounts.feature_counts       [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,509] multiqc.modules.picard.picard                      [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,514] multiqc.modules.prokka.prokka                      [DEBUG  ]  Could not find any Prokka data in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,518] multiqc.modules.samblaster.samblaster              [DEBUG  ]  Could not find any data in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,525] multiqc.modules.samtools.samtools                  [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,530] multiqc.modules.bamtools.bamtools                  [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,534] multiqc.modules.bismark.bismark                    [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,539] multiqc.modules.hicup.hicup                        [DEBUG  ]  Could not find any HiCUP data in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,544] multiqc.modules.salmon.salmon                      [DEBUG  ]  Could not find any Salmon data in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,548] multiqc.modules.kallisto.kallisto                  [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,553] multiqc.modules.slamdunk.slamdunk                  [DEBUG  ]  No slamdunk reports found.
[2017-09-13 01:24:36,564] multiqc.modules.star.star                          [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,568] multiqc.modules.tophat.tophat                      [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,573] multiqc.modules.bowtie2.bowtie2                    [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,577] multiqc.modules.bowtie1.bowtie1                    [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,582] multiqc.modules.adapterRemoval.adapterRemoval      [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,586] multiqc.modules.cutadapt.cutadapt                  [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,591] multiqc.modules.trimmomatic.trimmomatic            [DEBUG  ]  Could not find any Trimmomatic data in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,595] multiqc.modules.skewer.skewer                      [DEBUG  ]  Could not find any data in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,600] multiqc.modules.sortmerna.sortmerna                [DEBUG  ]  Could not find any SortMeRNA data in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:36,604] multiqc.modules.fastq_screen.fastq_screen          [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:39,916] multiqc.modules.fastqc.fastqc                      [INFO   ]  Found 24 reports
[2017-09-13 01:24:40,271] multiqc.modules.clusterflow.clusterflow            [DEBUG  ]  Could not find any reports in ('/home/mk5636/fastqc-delivery/HKWY5BGX3/merged',)
[2017-09-13 01:24:40,305] multiqc                                            [INFO   ]  Compressing plot data
[2017-09-13 01:24:40,685] multiqc                                            [INFO   ]  Report      : multiqc_report.html
[2017-09-13 01:24:40,702] multiqc                                            [INFO   ]  Data        : multiqc_data
[2017-09-13 01:24:40,702] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmp4dud_sh7/multiqc_data/multiqc_general_stats.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HKWY5BGX3/merged/multiqc_data'
[2017-09-13 01:24:40,706] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmp4dud_sh7/multiqc_data/multiqc_sources.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HKWY5BGX3/merged/multiqc_data'
[2017-09-13 01:24:40,709] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmp4dud_sh7/multiqc_data/multiqc_fastqc.txt' to '/mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HKWY5BGX3/merged/multiqc_data'
[2017-09-13 01:24:40,962] multiqc                                            [INFO   ]  MultiQC complete