2014-08-13

Mapping Pipeline Error:

INFO: 2014/08/13 07:54:17 Mapping.pm (3112): Report location: /Bioinformatics/NGS_analyses/automated/RNA-Seq/Mapping/000854_JrWen_BC13_Details_TEST_WU/report.html
INFO: 2014/08/13 07:54:17 Mapping.pm (3137): Searching /Bioinformatics/NGS_analyses/automated/RNA-Seq/Mapping/000854_JrWen_BC13_Details_TEST_WU/JrWen_RNAseq_BC_13 for .bw files
INFO: 2014/08/13 07:54:17 Mapping.pm (3158): Folder: /Bioinformatics/NGS_analyses/automated/RNA-Seq/Mapping/000854_JrWen_BC13_Details_TEST_WU/JrWen_RNAseq_BC_13/005_bigwig/accepted_hits_filtered_dust_4.bam / Bigwig file:/Bioinformatics/NGS_analyses/automated/RNA-Seq/Mapping/000854_JrWen_BC13_Details_TEST_WU/JrWen_RNAseq_BC_13/005_bigwig/accepted_hits_filtered_dust_4.bam/accepted_hits.sorted.bw
INFO: 2014/08/13 07:54:17 Mapping.pm (3171): Folder: /Bioinformatics/NGS_analyses/automated/RNA-Seq/Mapping/000854_JrWen_BC13_Details_TEST_WU/JrWen_RNAseq_BC_13/005_bigwig/accepted_hits_filtered_dust_4_unique.bam / Bigwig file:/Bioinformatics/NGS_analyses/automated/RNA-Seq/Mapping/000854_JrWen_BC13_Details_TEST_WU/JrWen_RNAseq_BC_13/005_bigwig/accepted_hits_filtered_dust_4_unique.bam/accepted_hits.sorted.bw
WARN: 2014/08/13 07:54:17 Pipeline.pm (1017): Creating new parameter 'ALL_TRACKS_URL' and setting its value to 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr19&hgt.customText=https://informaticsdata.liai.org/NGS_analyses/automated/RNA-Seq/Mapping/000854_JrWen_BC13_Details_TEST_WU/allTracks.txt'
WARN: 2014/08/13 07:54:17 Pipeline.pm (1017): Creating new parameter 'ALL_TRACKS_UNIQUE_URL' and setting its value to 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr19&hgt.customText=https://informaticsdata.liai.org/NGS_analyses/automated/RNA-Seq/Mapping/000854_JrWen_BC13_Details_TEST_WU/allTracksUnique.txt'
Use of uninitialized value $bowtie_dir in concatenation (.) or string at /Bioinformatics/apps/NGS_pipeline_dev/src/NGSPipeline/Pipeline/Mapping.pm line 3323.
INFO: 2014/08/13 07:54:17 Mapping.pm (3323): premapping_dir:001_premapping_filter tophat:002_tophat bowtie:  low_complexity:003_low_complexity_filter bigwig:005_bigwig bamMetrics:004_bam_metrics HTSeq:006_HTSeq calc_rpkm:007_calc_rpkm
Use of uninitialized value $bowtie_dir in concatenation (.) or string at /Bioinformatics/apps/NGS_pipeline_dev/src/NGSPipeline/Pipeline/Mapping.pm line 3328.
INFO: 2014/08/13 07:54:17 Mapping.pm (3360): Error log was found /Bioinformatics/NGS_analyses/automated/RNA-Seq/Mapping/000854_JrWen_BC13_Details_TEST_WU/JrWen_RNAseq_BC_13/mapHiSeq2500Reads.err
INFO: 2014/08/13 07:54:18 Mapping.pm (3373): Dust Filtered Reads: 582601
readline() on closed filehandle $INF at /Bioinformatics/apps/NGS_pipeline_dev/src/NGSPipeline/Utils.pm line 36.
Use of uninitialized value $value in scalar chomp at /Bioinformatics/apps/NGS_pipeline_dev/src/NGSPipeline/Utils.pm line 39.
Use of uninitialized value in addition (+) at /Bioinformatics/apps/NGS_pipeline_dev/src/NGSPipeline/Pipeline/Mapping.pm line 3402.
INFO: 2014/08/13 07:54:18 Mapping.pm (3413): Adaptor Reads: 0
INFO: 2014/08/13 07:54:18 Mapping.pm (3416): Good Illumina Reads: 49979864
INFO: 2014/08/13 07:54:18 Mapping.pm (3424): 00002_13: JrWen_RNAseq_BC_13
INFO: 2014/08/13 07:54:18 Mapping.pm (3425): Mapped reads: 33334388
INFO: 2014/08/13 07:54:18 Mapping.pm (3426): Uniquely Mapped reads: 30441021
INFO: 2014/08/13 07:54:18 Mapping.pm (3477): Expected 51330230 Total Reads the sum of the parts is 51330230
INFO: 2014/08/13 07:54:18 Mapping.pm (3478): Expected 100% the sum of the percentages is 100.000
Can't locate object method "get_param" via package "https://informaticsdata.liai.org/NGS_analyses/automated/RNA-Seq/Mapping/000854_JrWen_BC13_Details_TEST_WU/JrWen_RNAseq_BC_13/005_bigwig/accepted_hits_filtered_dust_4.bam/accepted_hits.sorted.bw" (perhaps you forgot to load "https://informaticsdata.liai.org/NGS_analyses/automated/RNA-Seq/Mapping/000854_JrWen_BC13_Details_TEST_WU/JrWen_RNAseq_BC_13/005_bigwig/accepted_hits_filtered_dust_4.bam/accepted_hits.sorted.bw"?) at /Bioinformatics/apps/NGS_pipeline_dev/src/NGSPipeline/Pipeline/Mapping.pm line 4034.