Job ID = 8184179 SRX = SRX8047571 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T02:45:33 prefetch.2.10.7: 1) Downloading 'SRR11471296'... 2020-08-10T02:45:33 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T02:49:03 prefetch.2.10.7: HTTPS download succeed 2020-08-10T02:49:03 prefetch.2.10.7: 1) 'SRR11471296' was downloaded successfully Read 56223227 spots for SRR11471296/SRR11471296.sra Written 56223227 spots for SRR11471296/SRR11471296.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: 00:39:05 56223227 reads; of these: 56223227 (100.00%) were unpaired; of these: 1559183 (2.77%) aligned 0 times 43168707 (76.78%) aligned exactly 1 time 11495337 (20.45%) aligned >1 times 97.23% overall alignment rate Time searching: 00:39:10 Overall time: 00:39:11 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] 11592823 / 54664044 = 0.2121 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 12:44:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.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 12:44:07: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:44:07: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:44:13: 1000000 INFO @ Mon, 10 Aug 2020 12:44:19: 2000000 INFO @ Mon, 10 Aug 2020 12:44:25: 3000000 INFO @ Mon, 10 Aug 2020 12:44:31: 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 12:44:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.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 12:44:37: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:44:37: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:44:37: 5000000 INFO @ Mon, 10 Aug 2020 12:44:43: 1000000 INFO @ Mon, 10 Aug 2020 12:44:45: 6000000 INFO @ Mon, 10 Aug 2020 12:44:50: 2000000 INFO @ Mon, 10 Aug 2020 12:44:53: 7000000 INFO @ Mon, 10 Aug 2020 12:44:57: 3000000 INFO @ Mon, 10 Aug 2020 12:45:01: 8000000 INFO @ Mon, 10 Aug 2020 12:45:04: 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 12:45:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.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 12:45:07: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:45:07: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:45:08: 9000000 INFO @ Mon, 10 Aug 2020 12:45:11: 5000000 INFO @ Mon, 10 Aug 2020 12:45:13: 1000000 INFO @ Mon, 10 Aug 2020 12:45:16: 10000000 INFO @ Mon, 10 Aug 2020 12:45:18: 6000000 INFO @ Mon, 10 Aug 2020 12:45:20: 2000000 INFO @ Mon, 10 Aug 2020 12:45:24: 11000000 INFO @ Mon, 10 Aug 2020 12:45:25: 7000000 INFO @ Mon, 10 Aug 2020 12:45:27: 3000000 INFO @ Mon, 10 Aug 2020 12:45:31: 12000000 INFO @ Mon, 10 Aug 2020 12:45:32: 8000000 INFO @ Mon, 10 Aug 2020 12:45:34: 4000000 INFO @ Mon, 10 Aug 2020 12:45:38: 9000000 INFO @ Mon, 10 Aug 2020 12:45:39: 13000000 INFO @ Mon, 10 Aug 2020 12:45:41: 5000000 INFO @ Mon, 10 Aug 2020 12:45:45: 10000000 INFO @ Mon, 10 Aug 2020 12:45:46: 14000000 INFO @ Mon, 10 Aug 2020 12:45:48: 6000000 INFO @ Mon, 10 Aug 2020 12:45:52: 11000000 INFO @ Mon, 10 Aug 2020 12:45:53: 15000000 INFO @ Mon, 10 Aug 2020 12:45:55: 7000000 INFO @ Mon, 10 Aug 2020 12:45:58: 12000000 INFO @ Mon, 10 Aug 2020 12:46:00: 16000000 INFO @ Mon, 10 Aug 2020 12:46:01: 8000000 INFO @ Mon, 10 Aug 2020 12:46:05: 13000000 INFO @ Mon, 10 Aug 2020 12:46:07: 17000000 INFO @ Mon, 10 Aug 2020 12:46:08: 9000000 INFO @ Mon, 10 Aug 2020 12:46:12: 14000000 INFO @ Mon, 10 Aug 2020 12:46:14: 18000000 INFO @ Mon, 10 Aug 2020 12:46:15: 10000000 INFO @ Mon, 10 Aug 2020 12:46:20: 15000000 INFO @ Mon, 10 Aug 2020 12:46:21: 19000000 INFO @ Mon, 10 Aug 2020 12:46:22: 11000000 INFO @ Mon, 10 Aug 2020 12:46:28: 16000000 INFO @ Mon, 10 Aug 2020 12:46:28: 12000000 INFO @ Mon, 10 Aug 2020 12:46:28: 20000000 INFO @ Mon, 10 Aug 2020 12:46:35: 13000000 INFO @ Mon, 10 Aug 2020 12:46:35: 17000000 INFO @ Mon, 10 Aug 2020 12:46:35: 21000000 INFO @ Mon, 10 Aug 2020 12:46:42: 14000000 INFO @ Mon, 10 Aug 2020 12:46:42: 22000000 INFO @ Mon, 10 Aug 2020 12:46:43: 18000000 INFO @ Mon, 10 Aug 2020 12:46:49: 23000000 INFO @ Mon, 10 Aug 2020 12:46:49: 15000000 INFO @ Mon, 10 Aug 2020 12:46:50: 19000000 INFO @ Mon, 10 Aug 2020 12:46:56: 24000000 INFO @ Mon, 10 Aug 2020 12:46:57: 16000000 INFO @ Mon, 10 Aug 2020 12:46:58: 20000000 INFO @ Mon, 10 Aug 2020 12:47:03: 25000000 INFO @ Mon, 10 Aug 2020 12:47:04: 17000000 INFO @ Mon, 10 Aug 2020 12:47:05: 21000000 INFO @ Mon, 10 Aug 2020 12:47:10: 26000000 INFO @ Mon, 10 Aug 2020 12:47:12: 18000000 INFO @ Mon, 10 Aug 2020 12:47:13: 22000000 INFO @ Mon, 10 Aug 2020 12:47:17: 27000000 INFO @ Mon, 10 Aug 2020 12:47:19: 19000000 INFO @ Mon, 10 Aug 2020 12:47:21: 23000000 INFO @ Mon, 10 Aug 2020 12:47:24: 28000000 INFO @ Mon, 10 Aug 2020 12:47:27: 20000000 INFO @ Mon, 10 Aug 2020 12:47:28: 24000000 INFO @ Mon, 10 Aug 2020 12:47:30: 29000000 INFO @ Mon, 10 Aug 2020 12:47:34: 21000000 INFO @ Mon, 10 Aug 2020 12:47:36: 25000000 INFO @ Mon, 10 Aug 2020 12:47:37: 30000000 INFO @ Mon, 10 Aug 2020 12:47:42: 22000000 INFO @ Mon, 10 Aug 2020 12:47:44: 26000000 INFO @ Mon, 10 Aug 2020 12:47:44: 31000000 INFO @ Mon, 10 Aug 2020 12:47:50: 23000000 INFO @ Mon, 10 Aug 2020 12:47:51: 32000000 INFO @ Mon, 10 Aug 2020 12:47:51: 27000000 INFO @ Mon, 10 Aug 2020 12:47:58: 24000000 INFO @ Mon, 10 Aug 2020 12:47:58: 33000000 INFO @ Mon, 10 Aug 2020 12:47:59: 28000000 INFO @ Mon, 10 Aug 2020 12:48:05: 34000000 INFO @ Mon, 10 Aug 2020 12:48:05: 25000000 INFO @ Mon, 10 Aug 2020 12:48:06: 29000000 INFO @ Mon, 10 Aug 2020 12:48:12: 35000000 INFO @ Mon, 10 Aug 2020 12:48:13: 26000000 INFO @ Mon, 10 Aug 2020 12:48:14: 30000000 INFO @ Mon, 10 Aug 2020 12:48:19: 36000000 INFO @ Mon, 10 Aug 2020 12:48:21: 27000000 INFO @ Mon, 10 Aug 2020 12:48:22: 31000000 INFO @ Mon, 10 Aug 2020 12:48:26: 37000000 INFO @ Mon, 10 Aug 2020 12:48:28: 28000000 INFO @ Mon, 10 Aug 2020 12:48:30: 32000000 INFO @ Mon, 10 Aug 2020 12:48:33: 38000000 INFO @ Mon, 10 Aug 2020 12:48:36: 29000000 INFO @ Mon, 10 Aug 2020 12:48:38: 33000000 INFO @ Mon, 10 Aug 2020 12:48:40: 39000000 INFO @ Mon, 10 Aug 2020 12:48:44: 30000000 INFO @ Mon, 10 Aug 2020 12:48:46: 34000000 INFO @ Mon, 10 Aug 2020 12:48:47: 40000000 INFO @ Mon, 10 Aug 2020 12:48:52: 31000000 INFO @ Mon, 10 Aug 2020 12:48:53: 35000000 INFO @ Mon, 10 Aug 2020 12:48:54: 41000000 INFO @ Mon, 10 Aug 2020 12:48:59: 32000000 INFO @ Mon, 10 Aug 2020 12:49:01: 42000000 INFO @ Mon, 10 Aug 2020 12:49:01: 36000000 INFO @ Mon, 10 Aug 2020 12:49:07: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 12:49:08: 43000000 INFO @ Mon, 10 Aug 2020 12:49:09: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 12:49:09: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 12:49:09: #1 total tags in treatment: 43071221 INFO @ Mon, 10 Aug 2020 12:49:09: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 12:49:09: #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 12:49:09: 37000000 INFO @ Mon, 10 Aug 2020 12:49:10: #1 tags after filtering in treatment: 43071143 INFO @ Mon, 10 Aug 2020 12:49:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 12:49:10: #1 finished! INFO @ Mon, 10 Aug 2020 12:49:10: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 12:49:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 12:49:14: 34000000 INFO @ Mon, 10 Aug 2020 12:49:14: #2 number of paired peaks: 38246 INFO @ Mon, 10 Aug 2020 12:49:14: start model_add_line... INFO @ Mon, 10 Aug 2020 12:49:15: start X-correlation... INFO @ Mon, 10 Aug 2020 12:49:15: end of X-cor INFO @ Mon, 10 Aug 2020 12:49:15: #2 finished! INFO @ Mon, 10 Aug 2020 12:49:15: #2 predicted fragment length is 132 bps INFO @ Mon, 10 Aug 2020 12:49:15: #2 alternative fragment length(s) may be 132 bps INFO @ Mon, 10 Aug 2020 12:49:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.05_model.r INFO @ Mon, 10 Aug 2020 12:49:15: #3 Call peaks... INFO @ Mon, 10 Aug 2020 12:49:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 12:49:17: 38000000 INFO @ Mon, 10 Aug 2020 12:49:22: 35000000 INFO @ Mon, 10 Aug 2020 12:49:25: 39000000 INFO @ Mon, 10 Aug 2020 12:49:30: 36000000 INFO @ Mon, 10 Aug 2020 12:49:32: 40000000 INFO @ Mon, 10 Aug 2020 12:49:37: 37000000 INFO @ Mon, 10 Aug 2020 12:49:40: 41000000 INFO @ Mon, 10 Aug 2020 12:49:45: 38000000 INFO @ Mon, 10 Aug 2020 12:49:48: 42000000 INFO @ Mon, 10 Aug 2020 12:49:53: 39000000 INFO @ Mon, 10 Aug 2020 12:49:56: 43000000 INFO @ Mon, 10 Aug 2020 12:49:57: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 12:49:57: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 12:49:57: #1 total tags in treatment: 43071221 INFO @ Mon, 10 Aug 2020 12:49:57: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 12:49:57: #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 12:49:58: #1 tags after filtering in treatment: 43071143 INFO @ Mon, 10 Aug 2020 12:49:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 12:49:58: #1 finished! INFO @ Mon, 10 Aug 2020 12:49:58: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 12:49:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 12:50:00: 40000000 INFO @ Mon, 10 Aug 2020 12:50:02: #2 number of paired peaks: 38246 INFO @ Mon, 10 Aug 2020 12:50:02: start model_add_line... INFO @ Mon, 10 Aug 2020 12:50:03: start X-correlation... INFO @ Mon, 10 Aug 2020 12:50:03: end of X-cor INFO @ Mon, 10 Aug 2020 12:50:03: #2 finished! INFO @ Mon, 10 Aug 2020 12:50:03: #2 predicted fragment length is 132 bps INFO @ Mon, 10 Aug 2020 12:50:03: #2 alternative fragment length(s) may be 132 bps INFO @ Mon, 10 Aug 2020 12:50:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.10_model.r INFO @ Mon, 10 Aug 2020 12:50:03: #3 Call peaks... INFO @ Mon, 10 Aug 2020 12:50:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 12:50:07: 41000000 INFO @ Mon, 10 Aug 2020 12:50:14: 42000000 INFO @ Mon, 10 Aug 2020 12:50:21: 43000000 INFO @ Mon, 10 Aug 2020 12:50:22: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 12:50:22: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 12:50:22: #1 total tags in treatment: 43071221 INFO @ Mon, 10 Aug 2020 12:50:22: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 12:50:22: #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 12:50:22: #1 tags after filtering in treatment: 43071143 INFO @ Mon, 10 Aug 2020 12:50:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 12:50:22: #1 finished! INFO @ Mon, 10 Aug 2020 12:50:22: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 12:50:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 12:50:27: #2 number of paired peaks: 38246 INFO @ Mon, 10 Aug 2020 12:50:27: start model_add_line... INFO @ Mon, 10 Aug 2020 12:50:27: start X-correlation... INFO @ Mon, 10 Aug 2020 12:50:28: end of X-cor INFO @ Mon, 10 Aug 2020 12:50:28: #2 finished! INFO @ Mon, 10 Aug 2020 12:50:28: #2 predicted fragment length is 132 bps INFO @ Mon, 10 Aug 2020 12:50:28: #2 alternative fragment length(s) may be 132 bps INFO @ Mon, 10 Aug 2020 12:50:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.20_model.r INFO @ Mon, 10 Aug 2020 12:50:28: #3 Call peaks... INFO @ Mon, 10 Aug 2020 12:50:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 12:50:53: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 12:51:43: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 12:51:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.05_peaks.xls INFO @ Mon, 10 Aug 2020 12:51:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 12:51:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.05_summits.bed INFO @ Mon, 10 Aug 2020 12:51:45: Done! pass1 - making usageList (115 chroms): 4 millis pass2 - checking and writing primary data (25549 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 12:52:07: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 12:52:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.10_peaks.xls INFO @ Mon, 10 Aug 2020 12:52:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 12:52:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.10_summits.bed INFO @ Mon, 10 Aug 2020 12:52:35: Done! pass1 - making usageList (92 chroms): 2 millis pass2 - checking and writing primary data (15746 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 12:52:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.20_peaks.xls INFO @ Mon, 10 Aug 2020 12:52:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 12:52:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047571/SRX8047571.20_summits.bed INFO @ Mon, 10 Aug 2020 12:52:58: Done! pass1 - making usageList (60 chroms): 2 millis pass2 - checking and writing primary data (8078 records, 4 fields): 12 millis CompletedMACS2peakCalling