Job ID = 8184558 SRX = SRX8047610 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T04:32:04 prefetch.2.10.7: 1) Downloading 'SRR11471334'... 2020-08-10T04:32:04 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:34:44 prefetch.2.10.7: HTTPS download succeed 2020-08-10T04:34:44 prefetch.2.10.7: 1) 'SRR11471334' was downloaded successfully Read 53858516 spots for SRR11471334/SRR11471334.sra Written 53858516 spots for SRR11471334/SRR11471334.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: 00:00:02 Multiseed full-index search: 00:24:44 53858516 reads; of these: 53858516 (100.00%) were unpaired; of these: 9397536 (17.45%) aligned 0 times 37455420 (69.54%) aligned exactly 1 time 7005560 (13.01%) aligned >1 times 82.55% overall alignment rate Time searching: 00:24:49 Overall time: 00:24:49 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 20 files... [bam_rmdupse_core] 12501679 / 44460980 = 0.2812 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 14:12:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.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 14:12:31: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:12:31: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:12:38: 1000000 INFO @ Mon, 10 Aug 2020 14:12:46: 2000000 INFO @ Mon, 10 Aug 2020 14:12:53: 3000000 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 14:13:00: 4000000 INFO @ Mon, 10 Aug 2020 14:13:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.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 14:13:01: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:13:01: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:13:09: 5000000 INFO @ Mon, 10 Aug 2020 14:13:09: 1000000 INFO @ Mon, 10 Aug 2020 14:13:17: 6000000 INFO @ Mon, 10 Aug 2020 14:13:17: 2000000 INFO @ Mon, 10 Aug 2020 14:13:25: 3000000 INFO @ Mon, 10 Aug 2020 14:13:25: 7000000 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 14:13:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.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 14:13:31: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:13:31: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:13:33: 4000000 INFO @ Mon, 10 Aug 2020 14:13:34: 8000000 INFO @ Mon, 10 Aug 2020 14:13:40: 1000000 INFO @ Mon, 10 Aug 2020 14:13:40: 5000000 INFO @ Mon, 10 Aug 2020 14:13:43: 9000000 INFO @ Mon, 10 Aug 2020 14:13:48: 2000000 INFO @ Mon, 10 Aug 2020 14:13:49: 6000000 INFO @ Mon, 10 Aug 2020 14:13:51: 10000000 INFO @ Mon, 10 Aug 2020 14:13:57: 7000000 INFO @ Mon, 10 Aug 2020 14:13:57: 3000000 INFO @ Mon, 10 Aug 2020 14:14:00: 11000000 INFO @ Mon, 10 Aug 2020 14:14:05: 8000000 INFO @ Mon, 10 Aug 2020 14:14:06: 4000000 INFO @ Mon, 10 Aug 2020 14:14:08: 12000000 INFO @ Mon, 10 Aug 2020 14:14:13: 9000000 INFO @ Mon, 10 Aug 2020 14:14:14: 5000000 INFO @ Mon, 10 Aug 2020 14:14:17: 13000000 INFO @ Mon, 10 Aug 2020 14:14:21: 10000000 INFO @ Mon, 10 Aug 2020 14:14:23: 6000000 INFO @ Mon, 10 Aug 2020 14:14:26: 14000000 INFO @ Mon, 10 Aug 2020 14:14:29: 11000000 INFO @ Mon, 10 Aug 2020 14:14:31: 7000000 INFO @ Mon, 10 Aug 2020 14:14:35: 15000000 INFO @ Mon, 10 Aug 2020 14:14:37: 12000000 INFO @ Mon, 10 Aug 2020 14:14:39: 8000000 INFO @ Mon, 10 Aug 2020 14:14:43: 16000000 INFO @ Mon, 10 Aug 2020 14:14:46: 13000000 INFO @ Mon, 10 Aug 2020 14:14:48: 9000000 INFO @ Mon, 10 Aug 2020 14:14:52: 17000000 INFO @ Mon, 10 Aug 2020 14:14:54: 14000000 INFO @ Mon, 10 Aug 2020 14:14:56: 10000000 INFO @ Mon, 10 Aug 2020 14:15:01: 18000000 INFO @ Mon, 10 Aug 2020 14:15:02: 15000000 INFO @ Mon, 10 Aug 2020 14:15:05: 11000000 INFO @ Mon, 10 Aug 2020 14:15:10: 19000000 INFO @ Mon, 10 Aug 2020 14:15:11: 16000000 INFO @ Mon, 10 Aug 2020 14:15:14: 12000000 INFO @ Mon, 10 Aug 2020 14:15:19: 17000000 INFO @ Mon, 10 Aug 2020 14:15:19: 20000000 INFO @ Mon, 10 Aug 2020 14:15:22: 13000000 INFO @ Mon, 10 Aug 2020 14:15:27: 18000000 INFO @ Mon, 10 Aug 2020 14:15:28: 21000000 INFO @ Mon, 10 Aug 2020 14:15:31: 14000000 INFO @ Mon, 10 Aug 2020 14:15:35: 19000000 INFO @ Mon, 10 Aug 2020 14:15:37: 22000000 INFO @ Mon, 10 Aug 2020 14:15:40: 15000000 INFO @ Mon, 10 Aug 2020 14:15:44: 20000000 INFO @ Mon, 10 Aug 2020 14:15:46: 23000000 INFO @ Mon, 10 Aug 2020 14:15:49: 16000000 INFO @ Mon, 10 Aug 2020 14:15:52: 21000000 INFO @ Mon, 10 Aug 2020 14:15:55: 24000000 INFO @ Mon, 10 Aug 2020 14:15:57: 17000000 INFO @ Mon, 10 Aug 2020 14:16:00: 22000000 INFO @ Mon, 10 Aug 2020 14:16:04: 25000000 INFO @ Mon, 10 Aug 2020 14:16:06: 18000000 INFO @ Mon, 10 Aug 2020 14:16:09: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 14:16:12: 26000000 INFO @ Mon, 10 Aug 2020 14:16:15: 19000000 INFO @ Mon, 10 Aug 2020 14:16:17: 24000000 INFO @ Mon, 10 Aug 2020 14:16:21: 27000000 INFO @ Mon, 10 Aug 2020 14:16:24: 20000000 INFO @ Mon, 10 Aug 2020 14:16:25: 25000000 INFO @ Mon, 10 Aug 2020 14:16:30: 28000000 INFO @ Mon, 10 Aug 2020 14:16:33: 21000000 INFO @ Mon, 10 Aug 2020 14:16:34: 26000000 INFO @ Mon, 10 Aug 2020 14:16:39: 29000000 INFO @ Mon, 10 Aug 2020 14:16:42: 22000000 INFO @ Mon, 10 Aug 2020 14:16:42: 27000000 INFO @ Mon, 10 Aug 2020 14:16:48: 30000000 INFO @ Mon, 10 Aug 2020 14:16:50: 28000000 INFO @ Mon, 10 Aug 2020 14:16:51: 23000000 INFO @ Mon, 10 Aug 2020 14:16:57: 31000000 INFO @ Mon, 10 Aug 2020 14:16:59: 29000000 INFO @ Mon, 10 Aug 2020 14:16:59: 24000000 BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 14:17:06: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:17:06: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:17:06: #1 total tags in treatment: 31959301 INFO @ Mon, 10 Aug 2020 14:17:06: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:17:06: #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 14:17:07: 30000000 INFO @ Mon, 10 Aug 2020 14:17:07: #1 tags after filtering in treatment: 31959153 INFO @ Mon, 10 Aug 2020 14:17:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:17:07: #1 finished! INFO @ Mon, 10 Aug 2020 14:17:07: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:17:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:17:08: 25000000 INFO @ Mon, 10 Aug 2020 14:17:11: #2 number of paired peaks: 39716 INFO @ Mon, 10 Aug 2020 14:17:11: start model_add_line... INFO @ Mon, 10 Aug 2020 14:17:12: start X-correlation... INFO @ Mon, 10 Aug 2020 14:17:12: end of X-cor INFO @ Mon, 10 Aug 2020 14:17:12: #2 finished! INFO @ Mon, 10 Aug 2020 14:17:12: #2 predicted fragment length is 110 bps INFO @ Mon, 10 Aug 2020 14:17:12: #2 alternative fragment length(s) may be 110 bps INFO @ Mon, 10 Aug 2020 14:17:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.05_model.r INFO @ Mon, 10 Aug 2020 14:17:12: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:17:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:17:15: 31000000 INFO @ Mon, 10 Aug 2020 14:17:17: 26000000 INFO @ Mon, 10 Aug 2020 14:17:23: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:17:23: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:17:23: #1 total tags in treatment: 31959301 INFO @ Mon, 10 Aug 2020 14:17:23: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:17:23: #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 14:17:24: #1 tags after filtering in treatment: 31959153 INFO @ Mon, 10 Aug 2020 14:17:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:17:24: #1 finished! INFO @ Mon, 10 Aug 2020 14:17:24: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:17:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:17:25: 27000000 INFO @ Mon, 10 Aug 2020 14:17:28: #2 number of paired peaks: 39716 INFO @ Mon, 10 Aug 2020 14:17:28: start model_add_line... INFO @ Mon, 10 Aug 2020 14:17:28: start X-correlation... INFO @ Mon, 10 Aug 2020 14:17:28: end of X-cor INFO @ Mon, 10 Aug 2020 14:17:28: #2 finished! INFO @ Mon, 10 Aug 2020 14:17:28: #2 predicted fragment length is 110 bps INFO @ Mon, 10 Aug 2020 14:17:28: #2 alternative fragment length(s) may be 110 bps INFO @ Mon, 10 Aug 2020 14:17:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.10_model.r INFO @ Mon, 10 Aug 2020 14:17:28: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:17:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:17:33: 28000000 INFO @ Mon, 10 Aug 2020 14:17:40: 29000000 INFO @ Mon, 10 Aug 2020 14:17:48: 30000000 INFO @ Mon, 10 Aug 2020 14:17:56: 31000000 INFO @ Mon, 10 Aug 2020 14:18:03: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:18:03: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:18:03: #1 total tags in treatment: 31959301 INFO @ Mon, 10 Aug 2020 14:18:03: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:18:03: #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 14:18:04: #1 tags after filtering in treatment: 31959153 INFO @ Mon, 10 Aug 2020 14:18:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:18:04: #1 finished! INFO @ Mon, 10 Aug 2020 14:18:04: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:18:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:18:08: #2 number of paired peaks: 39716 INFO @ Mon, 10 Aug 2020 14:18:08: start model_add_line... INFO @ Mon, 10 Aug 2020 14:18:08: start X-correlation... INFO @ Mon, 10 Aug 2020 14:18:08: end of X-cor INFO @ Mon, 10 Aug 2020 14:18:08: #2 finished! INFO @ Mon, 10 Aug 2020 14:18:08: #2 predicted fragment length is 110 bps INFO @ Mon, 10 Aug 2020 14:18:08: #2 alternative fragment length(s) may be 110 bps INFO @ Mon, 10 Aug 2020 14:18:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.20_model.r INFO @ Mon, 10 Aug 2020 14:18:08: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:18:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:18:20: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:18:35: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:18:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.05_peaks.xls INFO @ Mon, 10 Aug 2020 14:18:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:18:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.05_summits.bed INFO @ Mon, 10 Aug 2020 14:18:57: Done! pass1 - making usageList (142 chroms): 5 millis pass2 - checking and writing primary data (35368 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:19:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.10_peaks.xls INFO @ Mon, 10 Aug 2020 14:19:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:19:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.10_summits.bed INFO @ Mon, 10 Aug 2020 14:19:14: Done! pass1 - making usageList (126 chroms): 5 millis pass2 - checking and writing primary data (30113 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:19:15: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:19:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.20_peaks.xls INFO @ Mon, 10 Aug 2020 14:19:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:19:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047610/SRX8047610.20_summits.bed INFO @ Mon, 10 Aug 2020 14:19:51: Done! pass1 - making usageList (111 chroms): 4 millis pass2 - checking and writing primary data (24787 records, 4 fields): 26 millis CompletedMACS2peakCalling