Job ID = 8184563 SRX = SRX8047612 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T04:36:46 prefetch.2.10.7: 1) Downloading 'SRR11471336'... 2020-08-10T04:36:46 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:39:19 prefetch.2.10.7: HTTPS download succeed 2020-08-10T04:39:19 prefetch.2.10.7: 1) 'SRR11471336' was downloaded successfully Read 57445702 spots for SRR11471336/SRR11471336.sra Written 57445702 spots for SRR11471336/SRR11471336.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:27:03 57445702 reads; of these: 57445702 (100.00%) were unpaired; of these: 1699907 (2.96%) aligned 0 times 48488764 (84.41%) aligned exactly 1 time 7257031 (12.63%) aligned >1 times 97.04% overall alignment rate Time searching: 00:27:07 Overall time: 00:27:07 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] 20286207 / 55745795 = 0.3639 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 @ Mon, 10 Aug 2020 14:21:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.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 @ Mon, 10 Aug 2020 14:21:02: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:21:02: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:21:08: 1000000 INFO @ Mon, 10 Aug 2020 14:21:14: 2000000 INFO @ Mon, 10 Aug 2020 14:21:19: 3000000 INFO @ Mon, 10 Aug 2020 14:21:25: 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 @ Mon, 10 Aug 2020 14:21:31: 5000000 INFO @ Mon, 10 Aug 2020 14:21:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.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 @ Mon, 10 Aug 2020 14:21:32: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:21:32: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:21:37: 6000000 INFO @ Mon, 10 Aug 2020 14:21:39: 1000000 INFO @ Mon, 10 Aug 2020 14:21:43: 7000000 INFO @ Mon, 10 Aug 2020 14:21:45: 2000000 INFO @ Mon, 10 Aug 2020 14:21:49: 8000000 INFO @ Mon, 10 Aug 2020 14:21:51: 3000000 INFO @ Mon, 10 Aug 2020 14:21:55: 9000000 INFO @ Mon, 10 Aug 2020 14:21:57: 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 @ Mon, 10 Aug 2020 14:22:00: 10000000 INFO @ Mon, 10 Aug 2020 14:22:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.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 @ Mon, 10 Aug 2020 14:22:02: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:22:02: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:22:03: 5000000 INFO @ Mon, 10 Aug 2020 14:22:07: 11000000 INFO @ Mon, 10 Aug 2020 14:22:09: 6000000 INFO @ Mon, 10 Aug 2020 14:22:10: 1000000 INFO @ Mon, 10 Aug 2020 14:22:13: 12000000 INFO @ Mon, 10 Aug 2020 14:22:15: 7000000 INFO @ Mon, 10 Aug 2020 14:22:17: 2000000 INFO @ Mon, 10 Aug 2020 14:22:19: 13000000 INFO @ Mon, 10 Aug 2020 14:22:22: 8000000 INFO @ Mon, 10 Aug 2020 14:22:25: 3000000 INFO @ Mon, 10 Aug 2020 14:22:25: 14000000 INFO @ Mon, 10 Aug 2020 14:22:28: 9000000 INFO @ Mon, 10 Aug 2020 14:22:31: 15000000 INFO @ Mon, 10 Aug 2020 14:22:32: 4000000 INFO @ Mon, 10 Aug 2020 14:22:34: 10000000 INFO @ Mon, 10 Aug 2020 14:22:37: 16000000 INFO @ Mon, 10 Aug 2020 14:22:39: 5000000 INFO @ Mon, 10 Aug 2020 14:22:40: 11000000 INFO @ Mon, 10 Aug 2020 14:22:43: 17000000 INFO @ Mon, 10 Aug 2020 14:22:46: 6000000 INFO @ Mon, 10 Aug 2020 14:22:47: 12000000 INFO @ Mon, 10 Aug 2020 14:22:49: 18000000 INFO @ Mon, 10 Aug 2020 14:22:53: 7000000 INFO @ Mon, 10 Aug 2020 14:22:53: 13000000 INFO @ Mon, 10 Aug 2020 14:22:55: 19000000 INFO @ Mon, 10 Aug 2020 14:22:59: 8000000 INFO @ Mon, 10 Aug 2020 14:22:59: 14000000 INFO @ Mon, 10 Aug 2020 14:23:01: 20000000 INFO @ Mon, 10 Aug 2020 14:23:05: 9000000 INFO @ Mon, 10 Aug 2020 14:23:06: 15000000 INFO @ Mon, 10 Aug 2020 14:23:07: 21000000 INFO @ Mon, 10 Aug 2020 14:23:12: 10000000 INFO @ Mon, 10 Aug 2020 14:23:12: 16000000 INFO @ Mon, 10 Aug 2020 14:23:13: 22000000 INFO @ Mon, 10 Aug 2020 14:23:18: 11000000 INFO @ Mon, 10 Aug 2020 14:23:18: 17000000 INFO @ Mon, 10 Aug 2020 14:23:19: 23000000 INFO @ Mon, 10 Aug 2020 14:23:24: 12000000 INFO @ Mon, 10 Aug 2020 14:23:24: 18000000 INFO @ Mon, 10 Aug 2020 14:23:25: 24000000 INFO @ Mon, 10 Aug 2020 14:23:31: 13000000 INFO @ Mon, 10 Aug 2020 14:23:31: 19000000 INFO @ Mon, 10 Aug 2020 14:23:31: 25000000 INFO @ Mon, 10 Aug 2020 14:23:37: 14000000 INFO @ Mon, 10 Aug 2020 14:23:37: 20000000 INFO @ Mon, 10 Aug 2020 14:23:37: 26000000 INFO @ Mon, 10 Aug 2020 14:23:43: 15000000 INFO @ Mon, 10 Aug 2020 14:23:43: 21000000 INFO @ Mon, 10 Aug 2020 14:23:43: 27000000 INFO @ Mon, 10 Aug 2020 14:23:49: 16000000 INFO @ Mon, 10 Aug 2020 14:23:49: 22000000 INFO @ Mon, 10 Aug 2020 14:23:49: 28000000 INFO @ Mon, 10 Aug 2020 14:23:54: 29000000 INFO @ Mon, 10 Aug 2020 14:23:54: 17000000 INFO @ Mon, 10 Aug 2020 14:23:55: 23000000 INFO @ Mon, 10 Aug 2020 14:24:00: 30000000 INFO @ Mon, 10 Aug 2020 14:24:00: 18000000 INFO @ Mon, 10 Aug 2020 14:24:00: 24000000 INFO @ Mon, 10 Aug 2020 14:24:06: 31000000 INFO @ Mon, 10 Aug 2020 14:24:06: 19000000 INFO @ Mon, 10 Aug 2020 14:24:06: 25000000 INFO @ Mon, 10 Aug 2020 14:24:12: 32000000 INFO @ Mon, 10 Aug 2020 14:24:12: 20000000 INFO @ Mon, 10 Aug 2020 14:24:12: 26000000 INFO @ Mon, 10 Aug 2020 14:24:18: 33000000 INFO @ Mon, 10 Aug 2020 14:24:18: 21000000 INFO @ Mon, 10 Aug 2020 14:24:18: 27000000 INFO @ Mon, 10 Aug 2020 14:24:24: 34000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 14:24:24: 22000000 INFO @ Mon, 10 Aug 2020 14:24:24: 28000000 INFO @ Mon, 10 Aug 2020 14:24:30: 35000000 INFO @ Mon, 10 Aug 2020 14:24:30: 23000000 INFO @ Mon, 10 Aug 2020 14:24:30: 29000000 INFO @ Mon, 10 Aug 2020 14:24:33: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:24:33: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:24:33: #1 total tags in treatment: 35459588 INFO @ Mon, 10 Aug 2020 14:24:33: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:24:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 14:24:33: #1 tags after filtering in treatment: 35459419 INFO @ Mon, 10 Aug 2020 14:24:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:24:33: #1 finished! INFO @ Mon, 10 Aug 2020 14:24:33: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:24:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:24:36: 24000000 INFO @ Mon, 10 Aug 2020 14:24:36: 30000000 INFO @ Mon, 10 Aug 2020 14:24:38: #2 number of paired peaks: 45243 INFO @ Mon, 10 Aug 2020 14:24:38: start model_add_line... INFO @ Mon, 10 Aug 2020 14:24:38: start X-correlation... INFO @ Mon, 10 Aug 2020 14:24:38: end of X-cor INFO @ Mon, 10 Aug 2020 14:24:38: #2 finished! INFO @ Mon, 10 Aug 2020 14:24:38: #2 predicted fragment length is 117 bps INFO @ Mon, 10 Aug 2020 14:24:38: #2 alternative fragment length(s) may be 117 bps INFO @ Mon, 10 Aug 2020 14:24:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.05_model.r INFO @ Mon, 10 Aug 2020 14:24:38: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:24:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:24:41: 25000000 INFO @ Mon, 10 Aug 2020 14:24:41: 31000000 INFO @ Mon, 10 Aug 2020 14:24:47: 26000000 INFO @ Mon, 10 Aug 2020 14:24:47: 32000000 INFO @ Mon, 10 Aug 2020 14:24:53: 27000000 INFO @ Mon, 10 Aug 2020 14:24:53: 33000000 INFO @ Mon, 10 Aug 2020 14:24:58: 28000000 INFO @ Mon, 10 Aug 2020 14:24:58: 34000000 INFO @ Mon, 10 Aug 2020 14:25:04: 29000000 INFO @ Mon, 10 Aug 2020 14:25:04: 35000000 INFO @ Mon, 10 Aug 2020 14:25:07: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:25:07: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:25:07: #1 total tags in treatment: 35459588 INFO @ Mon, 10 Aug 2020 14:25:07: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:25:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 14:25:07: #1 tags after filtering in treatment: 35459419 INFO @ Mon, 10 Aug 2020 14:25:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:25:07: #1 finished! INFO @ Mon, 10 Aug 2020 14:25:07: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:25:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:25:09: 30000000 INFO @ Mon, 10 Aug 2020 14:25:12: #2 number of paired peaks: 45243 INFO @ Mon, 10 Aug 2020 14:25:12: start model_add_line... INFO @ Mon, 10 Aug 2020 14:25:13: start X-correlation... INFO @ Mon, 10 Aug 2020 14:25:13: end of X-cor INFO @ Mon, 10 Aug 2020 14:25:13: #2 finished! INFO @ Mon, 10 Aug 2020 14:25:13: #2 predicted fragment length is 117 bps INFO @ Mon, 10 Aug 2020 14:25:13: #2 alternative fragment length(s) may be 117 bps INFO @ Mon, 10 Aug 2020 14:25:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.10_model.r INFO @ Mon, 10 Aug 2020 14:25:13: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:25:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 14:25:14: 31000000 INFO @ Mon, 10 Aug 2020 14:25:20: 32000000 INFO @ Mon, 10 Aug 2020 14:25:25: 33000000 INFO @ Mon, 10 Aug 2020 14:25:31: 34000000 INFO @ Mon, 10 Aug 2020 14:25:36: 35000000 INFO @ Mon, 10 Aug 2020 14:25:39: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:25:39: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:25:39: #1 total tags in treatment: 35459588 INFO @ Mon, 10 Aug 2020 14:25:39: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:25:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 14:25:39: #1 tags after filtering in treatment: 35459419 INFO @ Mon, 10 Aug 2020 14:25:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:25:39: #1 finished! INFO @ Mon, 10 Aug 2020 14:25:39: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:25:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:25:44: #2 number of paired peaks: 45243 INFO @ Mon, 10 Aug 2020 14:25:44: start model_add_line... INFO @ Mon, 10 Aug 2020 14:25:45: start X-correlation... INFO @ Mon, 10 Aug 2020 14:25:45: end of X-cor INFO @ Mon, 10 Aug 2020 14:25:45: #2 finished! INFO @ Mon, 10 Aug 2020 14:25:45: #2 predicted fragment length is 117 bps INFO @ Mon, 10 Aug 2020 14:25:45: #2 alternative fragment length(s) may be 117 bps INFO @ Mon, 10 Aug 2020 14:25:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.20_model.r INFO @ Mon, 10 Aug 2020 14:25:45: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:25:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:25:51: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:26:27: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:26:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.05_peaks.xls INFO @ Mon, 10 Aug 2020 14:26:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:26:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.05_summits.bed INFO @ Mon, 10 Aug 2020 14:26:31: Done! pass1 - making usageList (149 chroms): 5 millis pass2 - checking and writing primary data (39867 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:27:01: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:27:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.10_peaks.xls INFO @ Mon, 10 Aug 2020 14:27:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:27:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.10_summits.bed INFO @ Mon, 10 Aug 2020 14:27:08: Done! pass1 - making usageList (135 chroms): 5 millis pass2 - checking and writing primary data (33638 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:27:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.20_peaks.xls INFO @ Mon, 10 Aug 2020 14:27:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:27:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047612/SRX8047612.20_summits.bed INFO @ Mon, 10 Aug 2020 14:27:43: Done! pass1 - making usageList (110 chroms): 4 millis pass2 - checking and writing primary data (27391 records, 4 fields): 28 millis CompletedMACS2peakCalling