Job ID = 5721048 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 35,660,694 reads read : 71,321,388 reads written : 71,321,388 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: 01:27:15 35660694 reads; of these: 35660694 (100.00%) were paired; of these: 14056746 (39.42%) aligned concordantly 0 times 15807178 (44.33%) aligned concordantly exactly 1 time 5796770 (16.26%) aligned concordantly >1 times ---- 14056746 pairs aligned concordantly 0 times; of these: 1176528 (8.37%) aligned discordantly 1 time ---- 12880218 pairs aligned 0 times concordantly or discordantly; of these: 25760436 mates make up the pairs; of these: 23874470 (92.68%) aligned 0 times 791769 (3.07%) aligned exactly 1 time 1094197 (4.25%) aligned >1 times 66.53% overall alignment rate Time searching: 01:27:15 Overall time: 01:27:15 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 36 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] 17437075 / 22727619 = 0.7672 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 06:38:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.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 06:38:38: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:38:38: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:38:45: 1000000 INFO @ Thu, 16 Apr 2020 06:38:51: 2000000 INFO @ Thu, 16 Apr 2020 06:38:58: 3000000 INFO @ Thu, 16 Apr 2020 06:39:04: 4000000 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 06:39:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.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 06:39:08: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:39:08: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:39:11: 5000000 INFO @ Thu, 16 Apr 2020 06:39:14: 1000000 INFO @ Thu, 16 Apr 2020 06:39:18: 6000000 INFO @ Thu, 16 Apr 2020 06:39:21: 2000000 INFO @ Thu, 16 Apr 2020 06:39:25: 7000000 INFO @ Thu, 16 Apr 2020 06:39:28: 3000000 INFO @ Thu, 16 Apr 2020 06:39:32: 8000000 INFO @ Thu, 16 Apr 2020 06:39:34: 4000000 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 06:39:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.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 06:39:38: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:39:38: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:39:38: 9000000 INFO @ Thu, 16 Apr 2020 06:39:41: 5000000 INFO @ Thu, 16 Apr 2020 06:39:44: 1000000 INFO @ Thu, 16 Apr 2020 06:39:45: 10000000 INFO @ Thu, 16 Apr 2020 06:39:48: 6000000 INFO @ Thu, 16 Apr 2020 06:39:51: 2000000 INFO @ Thu, 16 Apr 2020 06:39:51: 11000000 INFO @ Thu, 16 Apr 2020 06:39:54: 7000000 INFO @ Thu, 16 Apr 2020 06:39:58: 3000000 INFO @ Thu, 16 Apr 2020 06:39:58: 12000000 INFO @ Thu, 16 Apr 2020 06:40:01: 8000000 INFO @ Thu, 16 Apr 2020 06:40:02: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 06:40:02: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 06:40:02: #1 total tags in treatment: 4821350 INFO @ Thu, 16 Apr 2020 06:40:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:40:02: #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 06:40:02: #1 tags after filtering in treatment: 4460297 INFO @ Thu, 16 Apr 2020 06:40:02: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 16 Apr 2020 06:40:02: #1 finished! INFO @ Thu, 16 Apr 2020 06:40:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:40:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:40:03: #2 number of paired peaks: 2959 INFO @ Thu, 16 Apr 2020 06:40:03: start model_add_line... INFO @ Thu, 16 Apr 2020 06:40:03: start X-correlation... INFO @ Thu, 16 Apr 2020 06:40:03: end of X-cor INFO @ Thu, 16 Apr 2020 06:40:03: #2 finished! INFO @ Thu, 16 Apr 2020 06:40:03: #2 predicted fragment length is 268 bps INFO @ Thu, 16 Apr 2020 06:40:03: #2 alternative fragment length(s) may be 268 bps INFO @ Thu, 16 Apr 2020 06:40:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.05_model.r WARNING @ Thu, 16 Apr 2020 06:40:03: #2 Since the d (268) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:40:03: #2 You may need to consider one of the other alternative d(s): 268 WARNING @ Thu, 16 Apr 2020 06:40:03: #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 06:40:03: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:40:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:40:05: 4000000 INFO @ Thu, 16 Apr 2020 06:40:07: 9000000 INFO @ Thu, 16 Apr 2020 06:40:11: 5000000 INFO @ Thu, 16 Apr 2020 06:40:14: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:40:14: 10000000 INFO @ Thu, 16 Apr 2020 06:40:18: 6000000 INFO @ Thu, 16 Apr 2020 06:40:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:40:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:40:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.05_summits.bed INFO @ Thu, 16 Apr 2020 06:40:19: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5956 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:40:21: 11000000 INFO @ Thu, 16 Apr 2020 06:40:25: 7000000 INFO @ Thu, 16 Apr 2020 06:40:27: 12000000 INFO @ Thu, 16 Apr 2020 06:40:31: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 06:40:31: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 06:40:31: #1 total tags in treatment: 4821350 INFO @ Thu, 16 Apr 2020 06:40:31: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:40:31: #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 06:40:31: #1 tags after filtering in treatment: 4460297 INFO @ Thu, 16 Apr 2020 06:40:31: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 16 Apr 2020 06:40:31: #1 finished! INFO @ Thu, 16 Apr 2020 06:40:31: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:40:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:40:31: 8000000 INFO @ Thu, 16 Apr 2020 06:40:32: #2 number of paired peaks: 2959 INFO @ Thu, 16 Apr 2020 06:40:32: start model_add_line... INFO @ Thu, 16 Apr 2020 06:40:32: start X-correlation... INFO @ Thu, 16 Apr 2020 06:40:32: end of X-cor INFO @ Thu, 16 Apr 2020 06:40:32: #2 finished! INFO @ Thu, 16 Apr 2020 06:40:32: #2 predicted fragment length is 268 bps INFO @ Thu, 16 Apr 2020 06:40:32: #2 alternative fragment length(s) may be 268 bps INFO @ Thu, 16 Apr 2020 06:40:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.10_model.r WARNING @ Thu, 16 Apr 2020 06:40:32: #2 Since the d (268) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:40:32: #2 You may need to consider one of the other alternative d(s): 268 WARNING @ Thu, 16 Apr 2020 06:40:32: #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 06:40:32: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:40:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:40:38: 9000000 INFO @ Thu, 16 Apr 2020 06:40:43: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:40:44: 10000000 INFO @ Thu, 16 Apr 2020 06:40:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:40:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:40:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.10_summits.bed INFO @ Thu, 16 Apr 2020 06:40:48: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3828 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:40:51: 11000000 INFO @ Thu, 16 Apr 2020 06:40:58: 12000000 INFO @ Thu, 16 Apr 2020 06:41:02: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 06:41:02: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 06:41:02: #1 total tags in treatment: 4821350 INFO @ Thu, 16 Apr 2020 06:41:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:41:02: #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 06:41:02: #1 tags after filtering in treatment: 4460297 INFO @ Thu, 16 Apr 2020 06:41:02: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 16 Apr 2020 06:41:02: #1 finished! INFO @ Thu, 16 Apr 2020 06:41:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:41:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:41:02: #2 number of paired peaks: 2959 INFO @ Thu, 16 Apr 2020 06:41:02: start model_add_line... INFO @ Thu, 16 Apr 2020 06:41:02: start X-correlation... INFO @ Thu, 16 Apr 2020 06:41:02: end of X-cor INFO @ Thu, 16 Apr 2020 06:41:02: #2 finished! INFO @ Thu, 16 Apr 2020 06:41:02: #2 predicted fragment length is 268 bps INFO @ Thu, 16 Apr 2020 06:41:02: #2 alternative fragment length(s) may be 268 bps INFO @ Thu, 16 Apr 2020 06:41:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.20_model.r WARNING @ Thu, 16 Apr 2020 06:41:02: #2 Since the d (268) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:41:02: #2 You may need to consider one of the other alternative d(s): 268 WARNING @ Thu, 16 Apr 2020 06:41:02: #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 06:41:02: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:41:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:41:13: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:41:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:41:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:41:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386781/SRX6386781.20_summits.bed INFO @ Thu, 16 Apr 2020 06:41:18: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2241 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。