Job ID = 8184178 SRX = SRX8047570 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T02:45:15 prefetch.2.10.7: 1) Downloading 'SRR11471295'... 2020-08-10T02:45:15 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T02:48:56 prefetch.2.10.7: HTTPS download succeed 2020-08-10T02:48:56 prefetch.2.10.7: 1) 'SRR11471295' was downloaded successfully Read 67257698 spots for SRR11471295/SRR11471295.sra Written 67257698 spots for SRR11471295/SRR11471295.sra 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: 00:00:01 Multiseed full-index search: 00:48:26 67257698 reads; of these: 67257698 (100.00%) were unpaired; of these: 1815121 (2.70%) aligned 0 times 51905643 (77.17%) aligned exactly 1 time 13536934 (20.13%) aligned >1 times 97.30% overall alignment rate Time searching: 00:48:30 Overall time: 00:48:30 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 28 files... [bam_rmdupse_core] 23524807 / 65442577 = 0.3595 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 12:55:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.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 12:55:11: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:55:11: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:55:16: 1000000 INFO @ Mon, 10 Aug 2020 12:55:22: 2000000 INFO @ Mon, 10 Aug 2020 12:55:27: 3000000 INFO @ Mon, 10 Aug 2020 12:55:33: 4000000 INFO @ Mon, 10 Aug 2020 12:55:39: 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 @ Mon, 10 Aug 2020 12:55:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.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 12:55:41: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:55:41: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:55:45: 6000000 INFO @ Mon, 10 Aug 2020 12:55:47: 1000000 INFO @ Mon, 10 Aug 2020 12:55:51: 7000000 INFO @ Mon, 10 Aug 2020 12:55:53: 2000000 INFO @ Mon, 10 Aug 2020 12:55:57: 8000000 INFO @ Mon, 10 Aug 2020 12:55:59: 3000000 INFO @ Mon, 10 Aug 2020 12:56:03: 9000000 INFO @ Mon, 10 Aug 2020 12:56:05: 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 12:56:10: 10000000 INFO @ Mon, 10 Aug 2020 12:56:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.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 12:56:11: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:56:11: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:56:12: 5000000 INFO @ Mon, 10 Aug 2020 12:56:16: 11000000 INFO @ Mon, 10 Aug 2020 12:56:17: 1000000 INFO @ Mon, 10 Aug 2020 12:56:18: 6000000 INFO @ Mon, 10 Aug 2020 12:56:22: 12000000 INFO @ Mon, 10 Aug 2020 12:56:24: 2000000 INFO @ Mon, 10 Aug 2020 12:56:24: 7000000 INFO @ Mon, 10 Aug 2020 12:56:29: 13000000 INFO @ Mon, 10 Aug 2020 12:56:30: 3000000 INFO @ Mon, 10 Aug 2020 12:56:31: 8000000 INFO @ Mon, 10 Aug 2020 12:56:35: 14000000 INFO @ Mon, 10 Aug 2020 12:56:37: 4000000 INFO @ Mon, 10 Aug 2020 12:56:37: 9000000 INFO @ Mon, 10 Aug 2020 12:56:42: 15000000 INFO @ Mon, 10 Aug 2020 12:56:43: 5000000 INFO @ Mon, 10 Aug 2020 12:56:44: 10000000 INFO @ Mon, 10 Aug 2020 12:56:48: 16000000 INFO @ Mon, 10 Aug 2020 12:56:50: 6000000 INFO @ Mon, 10 Aug 2020 12:56:50: 11000000 INFO @ Mon, 10 Aug 2020 12:56:54: 17000000 INFO @ Mon, 10 Aug 2020 12:56:56: 7000000 INFO @ Mon, 10 Aug 2020 12:56:57: 12000000 INFO @ Mon, 10 Aug 2020 12:57:01: 18000000 INFO @ Mon, 10 Aug 2020 12:57:03: 8000000 INFO @ Mon, 10 Aug 2020 12:57:03: 13000000 INFO @ Mon, 10 Aug 2020 12:57:07: 19000000 INFO @ Mon, 10 Aug 2020 12:57:09: 9000000 INFO @ Mon, 10 Aug 2020 12:57:09: 14000000 INFO @ Mon, 10 Aug 2020 12:57:13: 20000000 INFO @ Mon, 10 Aug 2020 12:57:15: 10000000 INFO @ Mon, 10 Aug 2020 12:57:16: 15000000 INFO @ Mon, 10 Aug 2020 12:57:20: 21000000 INFO @ Mon, 10 Aug 2020 12:57:22: 11000000 INFO @ Mon, 10 Aug 2020 12:57:22: 16000000 INFO @ Mon, 10 Aug 2020 12:57:26: 22000000 INFO @ Mon, 10 Aug 2020 12:57:28: 12000000 INFO @ Mon, 10 Aug 2020 12:57:28: 17000000 INFO @ Mon, 10 Aug 2020 12:57:32: 23000000 INFO @ Mon, 10 Aug 2020 12:57:34: 13000000 INFO @ Mon, 10 Aug 2020 12:57:35: 18000000 INFO @ Mon, 10 Aug 2020 12:57:39: 24000000 INFO @ Mon, 10 Aug 2020 12:57:41: 14000000 INFO @ Mon, 10 Aug 2020 12:57:41: 19000000 INFO @ Mon, 10 Aug 2020 12:57:45: 25000000 INFO @ Mon, 10 Aug 2020 12:57:47: 15000000 INFO @ Mon, 10 Aug 2020 12:57:48: 20000000 INFO @ Mon, 10 Aug 2020 12:57:51: 26000000 INFO @ Mon, 10 Aug 2020 12:57:53: 16000000 INFO @ Mon, 10 Aug 2020 12:57:54: 21000000 INFO @ Mon, 10 Aug 2020 12:57:58: 27000000 INFO @ Mon, 10 Aug 2020 12:58:00: 17000000 INFO @ Mon, 10 Aug 2020 12:58:01: 22000000 INFO @ Mon, 10 Aug 2020 12:58:04: 28000000 INFO @ Mon, 10 Aug 2020 12:58:06: 18000000 INFO @ Mon, 10 Aug 2020 12:58:07: 23000000 INFO @ Mon, 10 Aug 2020 12:58:11: 29000000 INFO @ Mon, 10 Aug 2020 12:58:12: 19000000 INFO @ Mon, 10 Aug 2020 12:58:13: 24000000 INFO @ Mon, 10 Aug 2020 12:58:17: 30000000 INFO @ Mon, 10 Aug 2020 12:58:18: 20000000 INFO @ Mon, 10 Aug 2020 12:58:20: 25000000 INFO @ Mon, 10 Aug 2020 12:58:23: 31000000 INFO @ Mon, 10 Aug 2020 12:58:25: 21000000 INFO @ Mon, 10 Aug 2020 12:58:26: 26000000 INFO @ Mon, 10 Aug 2020 12:58:30: 32000000 INFO @ Mon, 10 Aug 2020 12:58:31: 22000000 INFO @ Mon, 10 Aug 2020 12:58:32: 27000000 INFO @ Mon, 10 Aug 2020 12:58:36: 33000000 INFO @ Mon, 10 Aug 2020 12:58:37: 23000000 INFO @ Mon, 10 Aug 2020 12:58:39: 28000000 INFO @ Mon, 10 Aug 2020 12:58:42: 34000000 INFO @ Mon, 10 Aug 2020 12:58:43: 24000000 INFO @ Mon, 10 Aug 2020 12:58:45: 29000000 INFO @ Mon, 10 Aug 2020 12:58:48: 35000000 INFO @ Mon, 10 Aug 2020 12:58:49: 25000000 INFO @ Mon, 10 Aug 2020 12:58:51: 30000000 INFO @ Mon, 10 Aug 2020 12:58:55: 36000000 INFO @ Mon, 10 Aug 2020 12:58:55: 26000000 INFO @ Mon, 10 Aug 2020 12:58:57: 31000000 INFO @ Mon, 10 Aug 2020 12:59:01: 37000000 INFO @ Mon, 10 Aug 2020 12:59:02: 27000000 INFO @ Mon, 10 Aug 2020 12:59:04: 32000000 INFO @ Mon, 10 Aug 2020 12:59:07: 38000000 INFO @ Mon, 10 Aug 2020 12:59:08: 28000000 INFO @ Mon, 10 Aug 2020 12:59:10: 33000000 INFO @ Mon, 10 Aug 2020 12:59:14: 39000000 INFO @ Mon, 10 Aug 2020 12:59:14: 29000000 INFO @ Mon, 10 Aug 2020 12:59:16: 34000000 INFO @ Mon, 10 Aug 2020 12:59:20: 30000000 INFO @ Mon, 10 Aug 2020 12:59:20: 40000000 INFO @ Mon, 10 Aug 2020 12:59:23: 35000000 INFO @ Mon, 10 Aug 2020 12:59:27: 31000000 INFO @ Mon, 10 Aug 2020 12:59:27: 41000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 12:59:29: 36000000 INFO @ Mon, 10 Aug 2020 12:59:33: 32000000 INFO @ Mon, 10 Aug 2020 12:59:34: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 12:59:34: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 12:59:34: #1 total tags in treatment: 41917770 INFO @ Mon, 10 Aug 2020 12:59:34: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 12:59:34: #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 12:59:34: #1 tags after filtering in treatment: 41917685 INFO @ Mon, 10 Aug 2020 12:59:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 12:59:34: #1 finished! INFO @ Mon, 10 Aug 2020 12:59:34: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 12:59:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 12:59:36: 37000000 INFO @ Mon, 10 Aug 2020 12:59:39: #2 number of paired peaks: 40065 INFO @ Mon, 10 Aug 2020 12:59:39: start model_add_line... INFO @ Mon, 10 Aug 2020 12:59:39: 33000000 INFO @ Mon, 10 Aug 2020 12:59:40: start X-correlation... INFO @ Mon, 10 Aug 2020 12:59:40: end of X-cor INFO @ Mon, 10 Aug 2020 12:59:40: #2 finished! INFO @ Mon, 10 Aug 2020 12:59:40: #2 predicted fragment length is 126 bps INFO @ Mon, 10 Aug 2020 12:59:40: #2 alternative fragment length(s) may be 126 bps INFO @ Mon, 10 Aug 2020 12:59:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.05_model.r INFO @ Mon, 10 Aug 2020 12:59:40: #3 Call peaks... INFO @ Mon, 10 Aug 2020 12:59:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 12:59:42: 38000000 INFO @ Mon, 10 Aug 2020 12:59:45: 34000000 INFO @ Mon, 10 Aug 2020 12:59:48: 39000000 INFO @ Mon, 10 Aug 2020 12:59:52: 35000000 INFO @ Mon, 10 Aug 2020 12:59:54: 40000000 INFO @ Mon, 10 Aug 2020 12:59:58: 36000000 INFO @ Mon, 10 Aug 2020 13:00:01: 41000000 INFO @ Mon, 10 Aug 2020 13:00:04: 37000000 INFO @ Mon, 10 Aug 2020 13:00:07: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:00:07: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:00:07: #1 total tags in treatment: 41917770 INFO @ Mon, 10 Aug 2020 13:00:07: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:00:07: #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 13:00:08: #1 tags after filtering in treatment: 41917685 INFO @ Mon, 10 Aug 2020 13:00:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:00:08: #1 finished! INFO @ Mon, 10 Aug 2020 13:00:08: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:00:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:00:10: 38000000 INFO @ Mon, 10 Aug 2020 13:00:12: #2 number of paired peaks: 40065 INFO @ Mon, 10 Aug 2020 13:00:12: start model_add_line... INFO @ Mon, 10 Aug 2020 13:00:13: start X-correlation... INFO @ Mon, 10 Aug 2020 13:00:13: end of X-cor INFO @ Mon, 10 Aug 2020 13:00:13: #2 finished! INFO @ Mon, 10 Aug 2020 13:00:13: #2 predicted fragment length is 126 bps INFO @ Mon, 10 Aug 2020 13:00:13: #2 alternative fragment length(s) may be 126 bps INFO @ Mon, 10 Aug 2020 13:00:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.10_model.r INFO @ Mon, 10 Aug 2020 13:00:13: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:00:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:00:16: 39000000 INFO @ Mon, 10 Aug 2020 13:00:22: 40000000 INFO @ Mon, 10 Aug 2020 13:00:27: 41000000 INFO @ Mon, 10 Aug 2020 13:00:33: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:00:33: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:00:33: #1 total tags in treatment: 41917770 INFO @ Mon, 10 Aug 2020 13:00:33: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:00:33: #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 13:00:33: #1 tags after filtering in treatment: 41917685 INFO @ Mon, 10 Aug 2020 13:00:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:00:33: #1 finished! INFO @ Mon, 10 Aug 2020 13:00:33: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:00:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:00:38: #2 number of paired peaks: 40065 INFO @ Mon, 10 Aug 2020 13:00:38: start model_add_line... INFO @ Mon, 10 Aug 2020 13:00:38: start X-correlation... INFO @ Mon, 10 Aug 2020 13:00:38: end of X-cor INFO @ Mon, 10 Aug 2020 13:00:38: #2 finished! INFO @ Mon, 10 Aug 2020 13:00:38: #2 predicted fragment length is 126 bps INFO @ Mon, 10 Aug 2020 13:00:38: #2 alternative fragment length(s) may be 126 bps INFO @ Mon, 10 Aug 2020 13:00:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.20_model.r INFO @ Mon, 10 Aug 2020 13:00:38: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:00:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 13:01:15: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:01:44: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:02:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.05_peaks.xls INFO @ Mon, 10 Aug 2020 13:02:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:02:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.05_summits.bed INFO @ Mon, 10 Aug 2020 13:02:05: Done! pass1 - making usageList (117 chroms): 4 millis pass2 - checking and writing primary data (25685 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:02:14: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:02:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.10_peaks.xls INFO @ Mon, 10 Aug 2020 13:02:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:02:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.10_summits.bed INFO @ Mon, 10 Aug 2020 13:02:35: Done! pass1 - making usageList (91 chroms): 3 millis pass2 - checking and writing primary data (15998 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:03:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.20_peaks.xls INFO @ Mon, 10 Aug 2020 13:03:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:03:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047570/SRX8047570.20_summits.bed INFO @ Mon, 10 Aug 2020 13:03:04: Done! pass1 - making usageList (68 chroms): 1 millis pass2 - checking and writing primary data (8306 records, 4 fields): 11 millis CompletedMACS2peakCalling