Job ID = 5721051 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 9,192,252 reads read : 18,384,504 reads written : 18,384,504 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:24:36 9192252 reads; of these: 9192252 (100.00%) were paired; of these: 6906815 (75.14%) aligned concordantly 0 times 731579 (7.96%) aligned concordantly exactly 1 time 1553858 (16.90%) aligned concordantly >1 times ---- 6906815 pairs aligned concordantly 0 times; of these: 72966 (1.06%) aligned discordantly 1 time ---- 6833849 pairs aligned 0 times concordantly or discordantly; of these: 13667698 mates make up the pairs; of these: 12546609 (91.80%) aligned 0 times 214031 (1.57%) aligned exactly 1 time 907058 (6.64%) aligned >1 times 31.75% overall alignment rate Time searching: 00:24:36 Overall time: 00:24:36 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1549331 / 2324562 = 0.6665 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 04:36:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 16 Apr 2020 04:36:03: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:36:03: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:36:11: 1000000 INFO @ Thu, 16 Apr 2020 04:36:20: 2000000 INFO @ Thu, 16 Apr 2020 04:36:26: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 04:36:26: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 04:36:26: #1 total tags in treatment: 773558 INFO @ Thu, 16 Apr 2020 04:36:26: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:36:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 04:36:26: #1 tags after filtering in treatment: 522488 INFO @ Thu, 16 Apr 2020 04:36:26: #1 Redundant rate of treatment: 0.32 INFO @ Thu, 16 Apr 2020 04:36:26: #1 finished! INFO @ Thu, 16 Apr 2020 04:36:26: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:36:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:36:26: #2 number of paired peaks: 3713 INFO @ Thu, 16 Apr 2020 04:36:26: start model_add_line... INFO @ Thu, 16 Apr 2020 04:36:26: start X-correlation... INFO @ Thu, 16 Apr 2020 04:36:26: end of X-cor INFO @ Thu, 16 Apr 2020 04:36:26: #2 finished! INFO @ Thu, 16 Apr 2020 04:36:26: #2 predicted fragment length is 182 bps INFO @ Thu, 16 Apr 2020 04:36:26: #2 alternative fragment length(s) may be 182 bps INFO @ Thu, 16 Apr 2020 04:36:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.05_model.r WARNING @ Thu, 16 Apr 2020 04:36:26: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:36:26: #2 You may need to consider one of the other alternative d(s): 182 WARNING @ Thu, 16 Apr 2020 04:36:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 04:36:26: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:36:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:36:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:36:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.05_peaks.xls INFO @ Thu, 16 Apr 2020 04:36:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:36:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.05_summits.bed INFO @ Thu, 16 Apr 2020 04:36:29: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1925 records, 4 fields): 3 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 04:36:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 16 Apr 2020 04:36:32: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:36:32: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:36:41: 1000000 INFO @ Thu, 16 Apr 2020 04:36:49: 2000000 INFO @ Thu, 16 Apr 2020 04:36:56: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 04:36:56: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 04:36:56: #1 total tags in treatment: 773558 INFO @ Thu, 16 Apr 2020 04:36:56: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:36:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 04:36:56: #1 tags after filtering in treatment: 522488 INFO @ Thu, 16 Apr 2020 04:36:56: #1 Redundant rate of treatment: 0.32 INFO @ Thu, 16 Apr 2020 04:36:56: #1 finished! INFO @ Thu, 16 Apr 2020 04:36:56: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:36:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:36:56: #2 number of paired peaks: 3713 INFO @ Thu, 16 Apr 2020 04:36:56: start model_add_line... INFO @ Thu, 16 Apr 2020 04:36:56: start X-correlation... INFO @ Thu, 16 Apr 2020 04:36:56: end of X-cor INFO @ Thu, 16 Apr 2020 04:36:56: #2 finished! INFO @ Thu, 16 Apr 2020 04:36:56: #2 predicted fragment length is 182 bps INFO @ Thu, 16 Apr 2020 04:36:56: #2 alternative fragment length(s) may be 182 bps INFO @ Thu, 16 Apr 2020 04:36:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.10_model.r WARNING @ Thu, 16 Apr 2020 04:36:56: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:36:56: #2 You may need to consider one of the other alternative d(s): 182 WARNING @ Thu, 16 Apr 2020 04:36:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 04:36:56: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:36:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:36:57: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:36:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.10_peaks.xls INFO @ Thu, 16 Apr 2020 04:36:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:36:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.10_summits.bed INFO @ Thu, 16 Apr 2020 04:36:58: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (946 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 04:37:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 16 Apr 2020 04:37:03: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:37:03: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:37:11: 1000000 INFO @ Thu, 16 Apr 2020 04:37:19: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 04:37:25: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 04:37:25: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 04:37:25: #1 total tags in treatment: 773558 INFO @ Thu, 16 Apr 2020 04:37:25: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:37:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 04:37:25: #1 tags after filtering in treatment: 522488 INFO @ Thu, 16 Apr 2020 04:37:25: #1 Redundant rate of treatment: 0.32 INFO @ Thu, 16 Apr 2020 04:37:25: #1 finished! INFO @ Thu, 16 Apr 2020 04:37:25: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:37:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:37:25: #2 number of paired peaks: 3713 INFO @ Thu, 16 Apr 2020 04:37:25: start model_add_line... INFO @ Thu, 16 Apr 2020 04:37:25: start X-correlation... INFO @ Thu, 16 Apr 2020 04:37:25: end of X-cor INFO @ Thu, 16 Apr 2020 04:37:25: #2 finished! INFO @ Thu, 16 Apr 2020 04:37:25: #2 predicted fragment length is 182 bps INFO @ Thu, 16 Apr 2020 04:37:25: #2 alternative fragment length(s) may be 182 bps INFO @ Thu, 16 Apr 2020 04:37:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.20_model.r WARNING @ Thu, 16 Apr 2020 04:37:25: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:37:25: #2 You may need to consider one of the other alternative d(s): 182 WARNING @ Thu, 16 Apr 2020 04:37:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 04:37:25: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:37:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:37:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:37:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.20_peaks.xls INFO @ Thu, 16 Apr 2020 04:37:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:37:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386784/SRX6386784.20_summits.bed INFO @ Thu, 16 Apr 2020 04:37:27: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (488 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。