Job ID = 5721219 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 22,134,598 reads read : 44,269,196 reads written : 44,269,196 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: 01:56:47 22134598 reads; of these: 22134598 (100.00%) were paired; of these: 6239956 (28.19%) aligned concordantly 0 times 11750387 (53.09%) aligned concordantly exactly 1 time 4144255 (18.72%) aligned concordantly >1 times ---- 6239956 pairs aligned concordantly 0 times; of these: 1767880 (28.33%) aligned discordantly 1 time ---- 4472076 pairs aligned 0 times concordantly or discordantly; of these: 8944152 mates make up the pairs; of these: 5921597 (66.21%) aligned 0 times 395991 (4.43%) aligned exactly 1 time 2626564 (29.37%) aligned >1 times 86.62% overall alignment rate Time searching: 01:56:47 Overall time: 01:56:47 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 16 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] 2986135 / 17478673 = 0.1708 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 08:21:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.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 08:21:33: #1 read tag files... INFO @ Thu, 16 Apr 2020 08:21:33: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 08:21:39: 1000000 INFO @ Thu, 16 Apr 2020 08:21:44: 2000000 INFO @ Thu, 16 Apr 2020 08:21:49: 3000000 INFO @ Thu, 16 Apr 2020 08:21:54: 4000000 INFO @ Thu, 16 Apr 2020 08:22:00: 5000000 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 08:22:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.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 08:22:03: #1 read tag files... INFO @ Thu, 16 Apr 2020 08:22:03: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 08:22:05: 6000000 INFO @ Thu, 16 Apr 2020 08:22:09: 1000000 INFO @ Thu, 16 Apr 2020 08:22:10: 7000000 INFO @ Thu, 16 Apr 2020 08:22:14: 2000000 INFO @ Thu, 16 Apr 2020 08:22:16: 8000000 INFO @ Thu, 16 Apr 2020 08:22:20: 3000000 INFO @ Thu, 16 Apr 2020 08:22:21: 9000000 INFO @ Thu, 16 Apr 2020 08:22:25: 4000000 INFO @ Thu, 16 Apr 2020 08:22:27: 10000000 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 08:22:31: 5000000 INFO @ Thu, 16 Apr 2020 08:22:32: 11000000 INFO @ Thu, 16 Apr 2020 08:22:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.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 08:22:33: #1 read tag files... INFO @ Thu, 16 Apr 2020 08:22:33: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 08:22:36: 6000000 INFO @ Thu, 16 Apr 2020 08:22:38: 12000000 INFO @ Thu, 16 Apr 2020 08:22:39: 1000000 INFO @ Thu, 16 Apr 2020 08:22:42: 7000000 INFO @ Thu, 16 Apr 2020 08:22:44: 13000000 INFO @ Thu, 16 Apr 2020 08:22:45: 2000000 INFO @ Thu, 16 Apr 2020 08:22:48: 8000000 INFO @ Thu, 16 Apr 2020 08:22:49: 14000000 INFO @ Thu, 16 Apr 2020 08:22:50: 3000000 INFO @ Thu, 16 Apr 2020 08:22:53: 9000000 INFO @ Thu, 16 Apr 2020 08:22:55: 15000000 INFO @ Thu, 16 Apr 2020 08:22:56: 4000000 INFO @ Thu, 16 Apr 2020 08:22:59: 10000000 INFO @ Thu, 16 Apr 2020 08:23:00: 16000000 INFO @ Thu, 16 Apr 2020 08:23:02: 5000000 INFO @ Thu, 16 Apr 2020 08:23:05: 11000000 INFO @ Thu, 16 Apr 2020 08:23:06: 17000000 INFO @ Thu, 16 Apr 2020 08:23:07: 6000000 INFO @ Thu, 16 Apr 2020 08:23:11: 12000000 INFO @ Thu, 16 Apr 2020 08:23:12: 18000000 INFO @ Thu, 16 Apr 2020 08:23:13: 7000000 INFO @ Thu, 16 Apr 2020 08:23:16: 13000000 INFO @ Thu, 16 Apr 2020 08:23:17: 19000000 INFO @ Thu, 16 Apr 2020 08:23:19: 8000000 INFO @ Thu, 16 Apr 2020 08:23:22: 14000000 INFO @ Thu, 16 Apr 2020 08:23:23: 20000000 INFO @ Thu, 16 Apr 2020 08:23:25: 9000000 INFO @ Thu, 16 Apr 2020 08:23:28: 15000000 INFO @ Thu, 16 Apr 2020 08:23:28: 21000000 INFO @ Thu, 16 Apr 2020 08:23:30: 10000000 INFO @ Thu, 16 Apr 2020 08:23:34: 16000000 INFO @ Thu, 16 Apr 2020 08:23:34: 22000000 INFO @ Thu, 16 Apr 2020 08:23:36: 11000000 INFO @ Thu, 16 Apr 2020 08:23:39: 17000000 INFO @ Thu, 16 Apr 2020 08:23:39: 23000000 INFO @ Thu, 16 Apr 2020 08:23:42: 12000000 INFO @ Thu, 16 Apr 2020 08:23:45: 24000000 INFO @ Thu, 16 Apr 2020 08:23:45: 18000000 INFO @ Thu, 16 Apr 2020 08:23:48: 13000000 INFO @ Thu, 16 Apr 2020 08:23:50: 25000000 INFO @ Thu, 16 Apr 2020 08:23:51: 19000000 INFO @ Thu, 16 Apr 2020 08:23:53: 14000000 INFO @ Thu, 16 Apr 2020 08:23:56: 26000000 INFO @ Thu, 16 Apr 2020 08:23:56: 20000000 INFO @ Thu, 16 Apr 2020 08:23:59: 15000000 INFO @ Thu, 16 Apr 2020 08:24:01: 27000000 INFO @ Thu, 16 Apr 2020 08:24:02: 21000000 INFO @ Thu, 16 Apr 2020 08:24:04: 16000000 INFO @ Thu, 16 Apr 2020 08:24:07: 28000000 INFO @ Thu, 16 Apr 2020 08:24:07: 22000000 INFO @ Thu, 16 Apr 2020 08:24:10: 17000000 INFO @ Thu, 16 Apr 2020 08:24:12: 29000000 INFO @ Thu, 16 Apr 2020 08:24:13: 23000000 INFO @ Thu, 16 Apr 2020 08:24:15: 18000000 INFO @ Thu, 16 Apr 2020 08:24:18: 30000000 INFO @ Thu, 16 Apr 2020 08:24:18: 24000000 INFO @ Thu, 16 Apr 2020 08:24:21: 19000000 INFO @ Thu, 16 Apr 2020 08:24:23: 31000000 INFO @ Thu, 16 Apr 2020 08:24:24: 25000000 INFO @ Thu, 16 Apr 2020 08:24:26: 20000000 INFO @ Thu, 16 Apr 2020 08:24:28: 32000000 INFO @ Thu, 16 Apr 2020 08:24:29: 26000000 INFO @ Thu, 16 Apr 2020 08:24:30: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 08:24:30: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 08:24:30: #1 total tags in treatment: 13158250 INFO @ Thu, 16 Apr 2020 08:24:30: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 08:24:30: #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 08:24:31: #1 tags after filtering in treatment: 11961862 INFO @ Thu, 16 Apr 2020 08:24:31: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 16 Apr 2020 08:24:31: #1 finished! INFO @ Thu, 16 Apr 2020 08:24:31: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 08:24:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 08:24:32: #2 number of paired peaks: 1182 INFO @ Thu, 16 Apr 2020 08:24:32: start model_add_line... INFO @ Thu, 16 Apr 2020 08:24:32: start X-correlation... INFO @ Thu, 16 Apr 2020 08:24:32: end of X-cor INFO @ Thu, 16 Apr 2020 08:24:32: #2 finished! INFO @ Thu, 16 Apr 2020 08:24:32: #2 predicted fragment length is 154 bps INFO @ Thu, 16 Apr 2020 08:24:32: #2 alternative fragment length(s) may be 154 bps INFO @ Thu, 16 Apr 2020 08:24:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.05_model.r WARNING @ Thu, 16 Apr 2020 08:24:32: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 08:24:32: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Thu, 16 Apr 2020 08:24:32: #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 08:24:32: #3 Call peaks... INFO @ Thu, 16 Apr 2020 08:24:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 08:24:32: 21000000 INFO @ Thu, 16 Apr 2020 08:24:34: 27000000 INFO @ Thu, 16 Apr 2020 08:24:37: 22000000 INFO @ Thu, 16 Apr 2020 08:24:40: 28000000 INFO @ Thu, 16 Apr 2020 08:24:43: 23000000 INFO @ Thu, 16 Apr 2020 08:24:45: 29000000 INFO @ Thu, 16 Apr 2020 08:24:48: 24000000 INFO @ Thu, 16 Apr 2020 08:24:51: 30000000 INFO @ Thu, 16 Apr 2020 08:24:55: 25000000 INFO @ Thu, 16 Apr 2020 08:24:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 08:24:59: 31000000 INFO @ Thu, 16 Apr 2020 08:25:03: 26000000 INFO @ Thu, 16 Apr 2020 08:25:07: 32000000 INFO @ Thu, 16 Apr 2020 08:25:10: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 08:25:10: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 08:25:10: #1 total tags in treatment: 13158250 INFO @ Thu, 16 Apr 2020 08:25:10: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 08:25:10: #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 08:25:10: #1 tags after filtering in treatment: 11961862 INFO @ Thu, 16 Apr 2020 08:25:10: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 16 Apr 2020 08:25:10: #1 finished! INFO @ Thu, 16 Apr 2020 08:25:10: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 08:25:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 08:25:11: 27000000 INFO @ Thu, 16 Apr 2020 08:25:11: #2 number of paired peaks: 1182 INFO @ Thu, 16 Apr 2020 08:25:11: start model_add_line... INFO @ Thu, 16 Apr 2020 08:25:11: start X-correlation... INFO @ Thu, 16 Apr 2020 08:25:11: end of X-cor INFO @ Thu, 16 Apr 2020 08:25:11: #2 finished! INFO @ Thu, 16 Apr 2020 08:25:11: #2 predicted fragment length is 154 bps INFO @ Thu, 16 Apr 2020 08:25:11: #2 alternative fragment length(s) may be 154 bps INFO @ Thu, 16 Apr 2020 08:25:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.10_model.r WARNING @ Thu, 16 Apr 2020 08:25:12: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 08:25:12: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Thu, 16 Apr 2020 08:25:12: #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 08:25:12: #3 Call peaks... INFO @ Thu, 16 Apr 2020 08:25:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 08:25:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.05_peaks.xls INFO @ Thu, 16 Apr 2020 08:25:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 08:25:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.05_summits.bed INFO @ Thu, 16 Apr 2020 08:25:13: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3637 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 08:25:19: 28000000 INFO @ Thu, 16 Apr 2020 08:25:29: 29000000 INFO @ Thu, 16 Apr 2020 08:25:37: 30000000 INFO @ Thu, 16 Apr 2020 08:25:43: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 08:25:44: 31000000 INFO @ Thu, 16 Apr 2020 08:25:52: 32000000 INFO @ Thu, 16 Apr 2020 08:25:54: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 08:25:54: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 08:25:54: #1 total tags in treatment: 13158250 INFO @ Thu, 16 Apr 2020 08:25:54: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 08:25:54: #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 08:25:54: #1 tags after filtering in treatment: 11961862 INFO @ Thu, 16 Apr 2020 08:25:54: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 16 Apr 2020 08:25:54: #1 finished! INFO @ Thu, 16 Apr 2020 08:25:54: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 08:25:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 08:25:55: #2 number of paired peaks: 1182 INFO @ Thu, 16 Apr 2020 08:25:55: start model_add_line... INFO @ Thu, 16 Apr 2020 08:25:56: start X-correlation... INFO @ Thu, 16 Apr 2020 08:25:56: end of X-cor INFO @ Thu, 16 Apr 2020 08:25:56: #2 finished! INFO @ Thu, 16 Apr 2020 08:25:56: #2 predicted fragment length is 154 bps INFO @ Thu, 16 Apr 2020 08:25:56: #2 alternative fragment length(s) may be 154 bps INFO @ Thu, 16 Apr 2020 08:25:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.20_model.r WARNING @ Thu, 16 Apr 2020 08:25:56: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 08:25:56: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Thu, 16 Apr 2020 08:25:56: #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 08:25:56: #3 Call peaks... INFO @ Thu, 16 Apr 2020 08:25:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 08:25:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.10_peaks.xls INFO @ Thu, 16 Apr 2020 08:25:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 08:25:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.10_summits.bed INFO @ Thu, 16 Apr 2020 08:25:57: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1798 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 08:26:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 08:26:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.20_peaks.xls INFO @ Thu, 16 Apr 2020 08:26:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 08:26:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6845077/SRX6845077.20_summits.bed INFO @ Thu, 16 Apr 2020 08:26:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (902 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。