Job ID = 5720776 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 23,472,422 reads read : 46,944,844 reads written : 46,944,844 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: 02:09:31 23472422 reads; of these: 23472422 (100.00%) were paired; of these: 5558777 (23.68%) aligned concordantly 0 times 6737342 (28.70%) aligned concordantly exactly 1 time 11176303 (47.61%) aligned concordantly >1 times ---- 5558777 pairs aligned concordantly 0 times; of these: 806624 (14.51%) aligned discordantly 1 time ---- 4752153 pairs aligned 0 times concordantly or discordantly; of these: 9504306 mates make up the pairs; of these: 3436914 (36.16%) aligned 0 times 1034113 (10.88%) aligned exactly 1 time 5033279 (52.96%) aligned >1 times 92.68% overall alignment rate Time searching: 02:09:31 Overall time: 02:09:31 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 20 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] 2404885 / 18571380 = 0.1295 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 04:12:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.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 04:12:03: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:12:03: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:12:08: 1000000 INFO @ Thu, 16 Apr 2020 04:12:14: 2000000 INFO @ Thu, 16 Apr 2020 04:12:20: 3000000 INFO @ Thu, 16 Apr 2020 04:12:26: 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 04:12:32: 5000000 INFO @ Thu, 16 Apr 2020 04:12:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.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 04:12:33: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:12:33: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:12:39: 6000000 INFO @ Thu, 16 Apr 2020 04:12:40: 1000000 INFO @ Thu, 16 Apr 2020 04:12:46: 7000000 INFO @ Thu, 16 Apr 2020 04:12:47: 2000000 INFO @ Thu, 16 Apr 2020 04:12:53: 8000000 INFO @ Thu, 16 Apr 2020 04:12:53: 3000000 INFO @ Thu, 16 Apr 2020 04:12:59: 9000000 INFO @ Thu, 16 Apr 2020 04:13:00: 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 04:13:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.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 04:13:03: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:13:03: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:13:07: 10000000 INFO @ Thu, 16 Apr 2020 04:13:07: 5000000 INFO @ Thu, 16 Apr 2020 04:13:10: 1000000 INFO @ Thu, 16 Apr 2020 04:13:14: 11000000 INFO @ Thu, 16 Apr 2020 04:13:14: 6000000 INFO @ Thu, 16 Apr 2020 04:13:18: 2000000 INFO @ Thu, 16 Apr 2020 04:13:21: 12000000 INFO @ Thu, 16 Apr 2020 04:13:22: 7000000 INFO @ Thu, 16 Apr 2020 04:13:26: 3000000 INFO @ Thu, 16 Apr 2020 04:13:28: 13000000 INFO @ Thu, 16 Apr 2020 04:13:29: 8000000 INFO @ Thu, 16 Apr 2020 04:13:34: 4000000 INFO @ Thu, 16 Apr 2020 04:13:35: 14000000 INFO @ Thu, 16 Apr 2020 04:13:36: 9000000 INFO @ Thu, 16 Apr 2020 04:13:42: 5000000 INFO @ Thu, 16 Apr 2020 04:13:42: 15000000 INFO @ Thu, 16 Apr 2020 04:13:44: 10000000 INFO @ Thu, 16 Apr 2020 04:13:49: 16000000 INFO @ Thu, 16 Apr 2020 04:13:50: 6000000 INFO @ Thu, 16 Apr 2020 04:13:51: 11000000 INFO @ Thu, 16 Apr 2020 04:13:57: 17000000 INFO @ Thu, 16 Apr 2020 04:13:57: 7000000 INFO @ Thu, 16 Apr 2020 04:13:58: 12000000 INFO @ Thu, 16 Apr 2020 04:14:04: 18000000 INFO @ Thu, 16 Apr 2020 04:14:05: 8000000 INFO @ Thu, 16 Apr 2020 04:14:05: 13000000 INFO @ Thu, 16 Apr 2020 04:14:11: 19000000 INFO @ Thu, 16 Apr 2020 04:14:12: 14000000 INFO @ Thu, 16 Apr 2020 04:14:13: 9000000 INFO @ Thu, 16 Apr 2020 04:14:18: 20000000 INFO @ Thu, 16 Apr 2020 04:14:20: 15000000 INFO @ Thu, 16 Apr 2020 04:14:21: 10000000 INFO @ Thu, 16 Apr 2020 04:14:26: 21000000 INFO @ Thu, 16 Apr 2020 04:14:27: 16000000 INFO @ Thu, 16 Apr 2020 04:14:29: 11000000 INFO @ Thu, 16 Apr 2020 04:14:33: 22000000 INFO @ Thu, 16 Apr 2020 04:14:34: 17000000 INFO @ Thu, 16 Apr 2020 04:14:36: 12000000 INFO @ Thu, 16 Apr 2020 04:14:40: 23000000 INFO @ Thu, 16 Apr 2020 04:14:41: 18000000 INFO @ Thu, 16 Apr 2020 04:14:44: 13000000 INFO @ Thu, 16 Apr 2020 04:14:47: 24000000 INFO @ Thu, 16 Apr 2020 04:14:48: 19000000 INFO @ Thu, 16 Apr 2020 04:14:52: 14000000 INFO @ Thu, 16 Apr 2020 04:14:55: 25000000 INFO @ Thu, 16 Apr 2020 04:14:55: 20000000 INFO @ Thu, 16 Apr 2020 04:15:00: 15000000 INFO @ Thu, 16 Apr 2020 04:15:02: 26000000 INFO @ Thu, 16 Apr 2020 04:15:03: 21000000 INFO @ Thu, 16 Apr 2020 04:15:08: 16000000 INFO @ Thu, 16 Apr 2020 04:15:09: 27000000 INFO @ Thu, 16 Apr 2020 04:15:10: 22000000 INFO @ Thu, 16 Apr 2020 04:15:15: 17000000 INFO @ Thu, 16 Apr 2020 04:15:16: 28000000 INFO @ Thu, 16 Apr 2020 04:15:17: 23000000 INFO @ Thu, 16 Apr 2020 04:15:23: 29000000 INFO @ Thu, 16 Apr 2020 04:15:23: 18000000 INFO @ Thu, 16 Apr 2020 04:15:24: 24000000 INFO @ Thu, 16 Apr 2020 04:15:30: 30000000 INFO @ Thu, 16 Apr 2020 04:15:31: 19000000 INFO @ Thu, 16 Apr 2020 04:15:32: 25000000 INFO @ Thu, 16 Apr 2020 04:15:37: 31000000 INFO @ Thu, 16 Apr 2020 04:15:39: 26000000 INFO @ Thu, 16 Apr 2020 04:15:39: 20000000 INFO @ Thu, 16 Apr 2020 04:15:44: 32000000 INFO @ Thu, 16 Apr 2020 04:15:46: 27000000 INFO @ Thu, 16 Apr 2020 04:15:47: 21000000 INFO @ Thu, 16 Apr 2020 04:15:51: 33000000 INFO @ Thu, 16 Apr 2020 04:15:53: 28000000 INFO @ Thu, 16 Apr 2020 04:15:55: 22000000 INFO @ Thu, 16 Apr 2020 04:15:58: 34000000 INFO @ Thu, 16 Apr 2020 04:16:00: 29000000 INFO @ Thu, 16 Apr 2020 04:16:02: 23000000 INFO @ Thu, 16 Apr 2020 04:16:06: 35000000 INFO @ Thu, 16 Apr 2020 04:16:07: 30000000 INFO @ Thu, 16 Apr 2020 04:16:10: 24000000 INFO @ Thu, 16 Apr 2020 04:16:13: 36000000 INFO @ Thu, 16 Apr 2020 04:16:14: 31000000 INFO @ Thu, 16 Apr 2020 04:16:18: 25000000 INFO @ Thu, 16 Apr 2020 04:16:20: 37000000 INFO @ Thu, 16 Apr 2020 04:16:21: 32000000 INFO @ Thu, 16 Apr 2020 04:16:25: 26000000 INFO @ Thu, 16 Apr 2020 04:16:27: 38000000 INFO @ Thu, 16 Apr 2020 04:16:29: 33000000 INFO @ Thu, 16 Apr 2020 04:16:32: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:16:32: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:16:32: #1 total tags in treatment: 15593228 INFO @ Thu, 16 Apr 2020 04:16:32: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:16:32: #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 04:16:33: #1 tags after filtering in treatment: 13282477 INFO @ Thu, 16 Apr 2020 04:16:33: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 04:16:33: #1 finished! INFO @ Thu, 16 Apr 2020 04:16:33: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:16:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:16:33: 27000000 INFO @ Thu, 16 Apr 2020 04:16:34: #2 number of paired peaks: 2853 INFO @ Thu, 16 Apr 2020 04:16:34: start model_add_line... INFO @ Thu, 16 Apr 2020 04:16:34: start X-correlation... INFO @ Thu, 16 Apr 2020 04:16:34: end of X-cor INFO @ Thu, 16 Apr 2020 04:16:34: #2 finished! INFO @ Thu, 16 Apr 2020 04:16:34: #2 predicted fragment length is 210 bps INFO @ Thu, 16 Apr 2020 04:16:34: #2 alternative fragment length(s) may be 210 bps INFO @ Thu, 16 Apr 2020 04:16:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.05_model.r INFO @ Thu, 16 Apr 2020 04:16:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:16:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:16:36: 34000000 INFO @ Thu, 16 Apr 2020 04:16:41: 28000000 INFO @ Thu, 16 Apr 2020 04:16:43: 35000000 INFO @ Thu, 16 Apr 2020 04:16:48: 29000000 INFO @ Thu, 16 Apr 2020 04:16:50: 36000000 INFO @ Thu, 16 Apr 2020 04:16:56: 30000000 INFO @ Thu, 16 Apr 2020 04:16:57: 37000000 INFO @ Thu, 16 Apr 2020 04:17:03: 31000000 INFO @ Thu, 16 Apr 2020 04:17:04: 38000000 INFO @ Thu, 16 Apr 2020 04:17:06: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:17:09: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:17:09: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:17:09: #1 total tags in treatment: 15593228 INFO @ Thu, 16 Apr 2020 04:17:09: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:17:09: #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 04:17:09: #1 tags after filtering in treatment: 13282477 INFO @ Thu, 16 Apr 2020 04:17:09: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 04:17:09: #1 finished! INFO @ Thu, 16 Apr 2020 04:17:09: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:17:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:17:10: #2 number of paired peaks: 2853 INFO @ Thu, 16 Apr 2020 04:17:10: start model_add_line... INFO @ Thu, 16 Apr 2020 04:17:10: start X-correlation... INFO @ Thu, 16 Apr 2020 04:17:10: end of X-cor INFO @ Thu, 16 Apr 2020 04:17:10: #2 finished! INFO @ Thu, 16 Apr 2020 04:17:10: #2 predicted fragment length is 210 bps INFO @ Thu, 16 Apr 2020 04:17:10: #2 alternative fragment length(s) may be 210 bps INFO @ Thu, 16 Apr 2020 04:17:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.10_model.r INFO @ Thu, 16 Apr 2020 04:17:10: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:17:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:17:11: 32000000 INFO @ Thu, 16 Apr 2020 04:17:18: 33000000 INFO @ Thu, 16 Apr 2020 04:17:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.05_peaks.xls INFO @ Thu, 16 Apr 2020 04:17:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:17:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.05_summits.bed INFO @ Thu, 16 Apr 2020 04:17:23: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (14537 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:17:26: 34000000 INFO @ Thu, 16 Apr 2020 04:17:34: 35000000 INFO @ Thu, 16 Apr 2020 04:17:41: 36000000 INFO @ Thu, 16 Apr 2020 04:17:45: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:17:49: 37000000 INFO @ Thu, 16 Apr 2020 04:17:56: 38000000 INFO @ Thu, 16 Apr 2020 04:18:01: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:18:01: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:18:01: #1 total tags in treatment: 15593228 INFO @ Thu, 16 Apr 2020 04:18:01: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:18:01: #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 04:18:02: #1 tags after filtering in treatment: 13282477 INFO @ Thu, 16 Apr 2020 04:18:02: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 04:18:02: #1 finished! INFO @ Thu, 16 Apr 2020 04:18:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:18:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:18:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.10_peaks.xls INFO @ Thu, 16 Apr 2020 04:18:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:18:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.10_summits.bed INFO @ Thu, 16 Apr 2020 04:18:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (9821 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:18:03: #2 number of paired peaks: 2853 INFO @ Thu, 16 Apr 2020 04:18:03: start model_add_line... INFO @ Thu, 16 Apr 2020 04:18:03: start X-correlation... INFO @ Thu, 16 Apr 2020 04:18:03: end of X-cor INFO @ Thu, 16 Apr 2020 04:18:03: #2 finished! INFO @ Thu, 16 Apr 2020 04:18:03: #2 predicted fragment length is 210 bps INFO @ Thu, 16 Apr 2020 04:18:03: #2 alternative fragment length(s) may be 210 bps INFO @ Thu, 16 Apr 2020 04:18:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.20_model.r INFO @ Thu, 16 Apr 2020 04:18:03: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:18:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:18:37: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 04:18:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.20_peaks.xls INFO @ Thu, 16 Apr 2020 04:18:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:18:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246869/SRX5246869.20_summits.bed INFO @ Thu, 16 Apr 2020 04:18:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5474 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。