Job ID = 5790658 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 60,195,950 reads read : 120,391,900 reads written : 60,195,950 reads 0-length : 60,195,950 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:35:57 60195950 reads; of these: 60195950 (100.00%) were unpaired; of these: 6549615 (10.88%) aligned 0 times 43596624 (72.42%) aligned exactly 1 time 10049711 (16.69%) aligned >1 times 89.12% overall alignment rate Time searching: 00:35:58 Overall time: 00:35:58 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 24 files... [bam_rmdupse_core] 9827513 / 53646335 = 0.1832 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 @ Wed, 22 Apr 2020 06:11:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 06:11:36: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:11:36: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:11:41: 1000000 INFO @ Wed, 22 Apr 2020 06:11:46: 2000000 INFO @ Wed, 22 Apr 2020 06:11:52: 3000000 INFO @ Wed, 22 Apr 2020 06:11:57: 4000000 INFO @ Wed, 22 Apr 2020 06:12:02: 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 @ Wed, 22 Apr 2020 06:12:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 06:12:06: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:12:06: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:12:07: 6000000 INFO @ Wed, 22 Apr 2020 06:12:11: 1000000 INFO @ Wed, 22 Apr 2020 06:12:12: 7000000 INFO @ Wed, 22 Apr 2020 06:12:16: 2000000 INFO @ Wed, 22 Apr 2020 06:12:17: 8000000 INFO @ Wed, 22 Apr 2020 06:12:22: 3000000 INFO @ Wed, 22 Apr 2020 06:12:22: 9000000 INFO @ Wed, 22 Apr 2020 06:12:27: 4000000 INFO @ Wed, 22 Apr 2020 06:12:27: 10000000 INFO @ Wed, 22 Apr 2020 06:12:32: 5000000 INFO @ Wed, 22 Apr 2020 06:12:32: 11000000 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 @ Wed, 22 Apr 2020 06:12:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 06:12:36: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:12:36: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:12:37: 6000000 INFO @ Wed, 22 Apr 2020 06:12:38: 12000000 INFO @ Wed, 22 Apr 2020 06:12:41: 1000000 INFO @ Wed, 22 Apr 2020 06:12:42: 7000000 INFO @ Wed, 22 Apr 2020 06:12:43: 13000000 INFO @ Wed, 22 Apr 2020 06:12:47: 2000000 INFO @ Wed, 22 Apr 2020 06:12:47: 8000000 INFO @ Wed, 22 Apr 2020 06:12:48: 14000000 INFO @ Wed, 22 Apr 2020 06:12:52: 3000000 INFO @ Wed, 22 Apr 2020 06:12:52: 9000000 INFO @ Wed, 22 Apr 2020 06:12:53: 15000000 INFO @ Wed, 22 Apr 2020 06:12:57: 4000000 INFO @ Wed, 22 Apr 2020 06:12:58: 10000000 INFO @ Wed, 22 Apr 2020 06:12:58: 16000000 INFO @ Wed, 22 Apr 2020 06:13:02: 5000000 INFO @ Wed, 22 Apr 2020 06:13:03: 11000000 INFO @ Wed, 22 Apr 2020 06:13:03: 17000000 INFO @ Wed, 22 Apr 2020 06:13:07: 6000000 INFO @ Wed, 22 Apr 2020 06:13:08: 12000000 INFO @ Wed, 22 Apr 2020 06:13:09: 18000000 INFO @ Wed, 22 Apr 2020 06:13:13: 7000000 INFO @ Wed, 22 Apr 2020 06:13:13: 13000000 INFO @ Wed, 22 Apr 2020 06:13:14: 19000000 INFO @ Wed, 22 Apr 2020 06:13:18: 8000000 INFO @ Wed, 22 Apr 2020 06:13:18: 14000000 INFO @ Wed, 22 Apr 2020 06:13:19: 20000000 INFO @ Wed, 22 Apr 2020 06:13:23: 9000000 INFO @ Wed, 22 Apr 2020 06:13:23: 15000000 INFO @ Wed, 22 Apr 2020 06:13:24: 21000000 INFO @ Wed, 22 Apr 2020 06:13:28: 10000000 INFO @ Wed, 22 Apr 2020 06:13:29: 16000000 INFO @ Wed, 22 Apr 2020 06:13:29: 22000000 INFO @ Wed, 22 Apr 2020 06:13:33: 11000000 INFO @ Wed, 22 Apr 2020 06:13:34: 17000000 INFO @ Wed, 22 Apr 2020 06:13:34: 23000000 INFO @ Wed, 22 Apr 2020 06:13:39: 12000000 INFO @ Wed, 22 Apr 2020 06:13:39: 18000000 INFO @ Wed, 22 Apr 2020 06:13:40: 24000000 INFO @ Wed, 22 Apr 2020 06:13:44: 13000000 INFO @ Wed, 22 Apr 2020 06:13:44: 19000000 INFO @ Wed, 22 Apr 2020 06:13:45: 25000000 INFO @ Wed, 22 Apr 2020 06:13:49: 14000000 INFO @ Wed, 22 Apr 2020 06:13:49: 20000000 INFO @ Wed, 22 Apr 2020 06:13:50: 26000000 INFO @ Wed, 22 Apr 2020 06:13:54: 21000000 INFO @ Wed, 22 Apr 2020 06:13:54: 15000000 INFO @ Wed, 22 Apr 2020 06:13:55: 27000000 INFO @ Wed, 22 Apr 2020 06:13:59: 22000000 INFO @ Wed, 22 Apr 2020 06:14:00: 16000000 INFO @ Wed, 22 Apr 2020 06:14:00: 28000000 INFO @ Wed, 22 Apr 2020 06:14:04: 23000000 INFO @ Wed, 22 Apr 2020 06:14:05: 17000000 INFO @ Wed, 22 Apr 2020 06:14:06: 29000000 INFO @ Wed, 22 Apr 2020 06:14:10: 24000000 INFO @ Wed, 22 Apr 2020 06:14:10: 18000000 INFO @ Wed, 22 Apr 2020 06:14:11: 30000000 INFO @ Wed, 22 Apr 2020 06:14:15: 25000000 INFO @ Wed, 22 Apr 2020 06:14:15: 19000000 INFO @ Wed, 22 Apr 2020 06:14:16: 31000000 INFO @ Wed, 22 Apr 2020 06:14:20: 26000000 INFO @ Wed, 22 Apr 2020 06:14:20: 20000000 INFO @ Wed, 22 Apr 2020 06:14:22: 32000000 INFO @ Wed, 22 Apr 2020 06:14:25: 27000000 INFO @ Wed, 22 Apr 2020 06:14:25: 21000000 INFO @ Wed, 22 Apr 2020 06:14:27: 33000000 INFO @ Wed, 22 Apr 2020 06:14:30: 28000000 INFO @ Wed, 22 Apr 2020 06:14:31: 22000000 INFO @ Wed, 22 Apr 2020 06:14:32: 34000000 INFO @ Wed, 22 Apr 2020 06:14:35: 29000000 INFO @ Wed, 22 Apr 2020 06:14:36: 23000000 INFO @ Wed, 22 Apr 2020 06:14:38: 35000000 INFO @ Wed, 22 Apr 2020 06:14:40: 30000000 INFO @ Wed, 22 Apr 2020 06:14:41: 24000000 INFO @ Wed, 22 Apr 2020 06:14:43: 36000000 INFO @ Wed, 22 Apr 2020 06:14:45: 31000000 INFO @ Wed, 22 Apr 2020 06:14:46: 25000000 INFO @ Wed, 22 Apr 2020 06:14:48: 37000000 INFO @ Wed, 22 Apr 2020 06:14:51: 32000000 INFO @ Wed, 22 Apr 2020 06:14:51: 26000000 INFO @ Wed, 22 Apr 2020 06:14:54: 38000000 INFO @ Wed, 22 Apr 2020 06:14:56: 33000000 INFO @ Wed, 22 Apr 2020 06:14:57: 27000000 INFO @ Wed, 22 Apr 2020 06:14:59: 39000000 INFO @ Wed, 22 Apr 2020 06:15:01: 34000000 INFO @ Wed, 22 Apr 2020 06:15:02: 28000000 INFO @ Wed, 22 Apr 2020 06:15:04: 40000000 INFO @ Wed, 22 Apr 2020 06:15:06: 35000000 INFO @ Wed, 22 Apr 2020 06:15:07: 29000000 INFO @ Wed, 22 Apr 2020 06:15:10: 41000000 INFO @ Wed, 22 Apr 2020 06:15:11: 36000000 INFO @ Wed, 22 Apr 2020 06:15:12: 30000000 INFO @ Wed, 22 Apr 2020 06:15:15: 42000000 INFO @ Wed, 22 Apr 2020 06:15:17: 37000000 INFO @ Wed, 22 Apr 2020 06:15:17: 31000000 INFO @ Wed, 22 Apr 2020 06:15:20: 43000000 INFO @ Wed, 22 Apr 2020 06:15:22: 38000000 INFO @ Wed, 22 Apr 2020 06:15:22: 32000000 INFO @ Wed, 22 Apr 2020 06:15:25: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 06:15:25: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 06:15:25: #1 total tags in treatment: 43818822 INFO @ Wed, 22 Apr 2020 06:15:25: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:15:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:15:26: #1 tags after filtering in treatment: 43818716 INFO @ Wed, 22 Apr 2020 06:15:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:15:26: #1 finished! INFO @ Wed, 22 Apr 2020 06:15:26: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:15:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:15:27: 39000000 INFO @ Wed, 22 Apr 2020 06:15:28: 33000000 INFO @ Wed, 22 Apr 2020 06:15:32: #2 number of paired peaks: 73990 INFO @ Wed, 22 Apr 2020 06:15:32: start model_add_line... INFO @ Wed, 22 Apr 2020 06:15:32: start X-correlation... INFO @ Wed, 22 Apr 2020 06:15:32: end of X-cor INFO @ Wed, 22 Apr 2020 06:15:32: #2 finished! INFO @ Wed, 22 Apr 2020 06:15:32: #2 predicted fragment length is 173 bps INFO @ Wed, 22 Apr 2020 06:15:32: #2 alternative fragment length(s) may be 173 bps INFO @ Wed, 22 Apr 2020 06:15:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.05_model.r INFO @ Wed, 22 Apr 2020 06:15:32: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:15:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:15:33: 40000000 INFO @ Wed, 22 Apr 2020 06:15:33: 34000000 INFO @ Wed, 22 Apr 2020 06:15:38: 41000000 INFO @ Wed, 22 Apr 2020 06:15:38: 35000000 INFO @ Wed, 22 Apr 2020 06:15:43: 42000000 INFO @ Wed, 22 Apr 2020 06:15:43: 36000000 INFO @ Wed, 22 Apr 2020 06:15:49: 43000000 INFO @ Wed, 22 Apr 2020 06:15:49: 37000000 INFO @ Wed, 22 Apr 2020 06:15:53: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 06:15:53: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 06:15:53: #1 total tags in treatment: 43818822 INFO @ Wed, 22 Apr 2020 06:15:53: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:15:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:15:54: #1 tags after filtering in treatment: 43818716 INFO @ Wed, 22 Apr 2020 06:15:54: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:15:54: #1 finished! INFO @ Wed, 22 Apr 2020 06:15:54: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:15:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:15:54: 38000000 INFO @ Wed, 22 Apr 2020 06:16:00: 39000000 INFO @ Wed, 22 Apr 2020 06:16:00: #2 number of paired peaks: 73990 INFO @ Wed, 22 Apr 2020 06:16:00: start model_add_line... INFO @ Wed, 22 Apr 2020 06:16:01: start X-correlation... INFO @ Wed, 22 Apr 2020 06:16:01: end of X-cor INFO @ Wed, 22 Apr 2020 06:16:01: #2 finished! INFO @ Wed, 22 Apr 2020 06:16:01: #2 predicted fragment length is 173 bps INFO @ Wed, 22 Apr 2020 06:16:01: #2 alternative fragment length(s) may be 173 bps INFO @ Wed, 22 Apr 2020 06:16:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.10_model.r INFO @ Wed, 22 Apr 2020 06:16:01: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:16:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:16:05: 40000000 INFO @ Wed, 22 Apr 2020 06:16:10: 41000000 INFO @ Wed, 22 Apr 2020 06:16:16: 42000000 INFO @ Wed, 22 Apr 2020 06:16:21: 43000000 INFO @ Wed, 22 Apr 2020 06:16:26: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 06:16:26: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 06:16:26: #1 total tags in treatment: 43818822 INFO @ Wed, 22 Apr 2020 06:16:26: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:16:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:16:26: #1 tags after filtering in treatment: 43818716 INFO @ Wed, 22 Apr 2020 06:16:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:16:26: #1 finished! INFO @ Wed, 22 Apr 2020 06:16:26: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:16:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:16:32: #2 number of paired peaks: 73990 INFO @ Wed, 22 Apr 2020 06:16:32: start model_add_line... INFO @ Wed, 22 Apr 2020 06:16:33: start X-correlation... INFO @ Wed, 22 Apr 2020 06:16:33: end of X-cor INFO @ Wed, 22 Apr 2020 06:16:33: #2 finished! INFO @ Wed, 22 Apr 2020 06:16:33: #2 predicted fragment length is 173 bps INFO @ Wed, 22 Apr 2020 06:16:33: #2 alternative fragment length(s) may be 173 bps INFO @ Wed, 22 Apr 2020 06:16:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.20_model.r INFO @ Wed, 22 Apr 2020 06:16:33: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:16:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:17:23: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:17:48: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:18:19: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:18:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:18:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:18:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.05_summits.bed INFO @ Wed, 22 Apr 2020 06:18:23: Done! pass1 - making usageList (123 chroms): 3 millis pass2 - checking and writing primary data (18853 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:18:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:18:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:18:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.10_summits.bed INFO @ Wed, 22 Apr 2020 06:18:45: Done! pass1 - making usageList (107 chroms): 2 millis pass2 - checking and writing primary data (14846 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:19:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:19:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:19:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5433269/SRX5433269.20_summits.bed INFO @ Wed, 22 Apr 2020 06:19:15: Done! pass1 - making usageList (89 chroms): 2 millis pass2 - checking and writing primary data (11221 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。