Job ID = 8184306 SRX = SRX8047584 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T03:14:42 prefetch.2.10.7: 1) Downloading 'SRR11471309'... 2020-08-10T03:14:42 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T03:17:17 prefetch.2.10.7: HTTPS download succeed 2020-08-10T03:17:17 prefetch.2.10.7: 1) 'SRR11471309' was downloaded successfully Read 58769760 spots for SRR11471309/SRR11471309.sra Written 58769760 spots for SRR11471309/SRR11471309.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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:28:24 58769760 reads; of these: 58769760 (100.00%) were unpaired; of these: 1987626 (3.38%) aligned 0 times 49393047 (84.05%) aligned exactly 1 time 7389087 (12.57%) aligned >1 times 96.62% overall alignment rate Time searching: 00:28:27 Overall time: 00:28:27 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] 19669273 / 56782134 = 0.3464 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 13:00:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.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 13:00:55: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:00:55: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:01:01: 1000000 INFO @ Mon, 10 Aug 2020 13:01:07: 2000000 INFO @ Mon, 10 Aug 2020 13:01:13: 3000000 INFO @ Mon, 10 Aug 2020 13:01:18: 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 13:01:24: 5000000 INFO @ Mon, 10 Aug 2020 13:01:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.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 13:01:25: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:01:25: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:01:30: 6000000 INFO @ Mon, 10 Aug 2020 13:01:31: 1000000 INFO @ Mon, 10 Aug 2020 13:01:36: 7000000 INFO @ Mon, 10 Aug 2020 13:01:38: 2000000 INFO @ Mon, 10 Aug 2020 13:01:43: 8000000 INFO @ Mon, 10 Aug 2020 13:01:44: 3000000 INFO @ Mon, 10 Aug 2020 13:01:49: 9000000 INFO @ Mon, 10 Aug 2020 13:01:50: 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 13:01:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.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 13:01:55: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:01:55: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:01:55: 10000000 INFO @ Mon, 10 Aug 2020 13:01:56: 5000000 INFO @ Mon, 10 Aug 2020 13:02:02: 1000000 INFO @ Mon, 10 Aug 2020 13:02:02: 11000000 INFO @ Mon, 10 Aug 2020 13:02:03: 6000000 INFO @ Mon, 10 Aug 2020 13:02:08: 2000000 INFO @ Mon, 10 Aug 2020 13:02:08: 12000000 INFO @ Mon, 10 Aug 2020 13:02:09: 7000000 INFO @ Mon, 10 Aug 2020 13:02:14: 3000000 INFO @ Mon, 10 Aug 2020 13:02:15: 13000000 INFO @ Mon, 10 Aug 2020 13:02:15: 8000000 INFO @ Mon, 10 Aug 2020 13:02:21: 4000000 INFO @ Mon, 10 Aug 2020 13:02:21: 14000000 INFO @ Mon, 10 Aug 2020 13:02:22: 9000000 INFO @ Mon, 10 Aug 2020 13:02:27: 5000000 INFO @ Mon, 10 Aug 2020 13:02:27: 15000000 INFO @ Mon, 10 Aug 2020 13:02:28: 10000000 INFO @ Mon, 10 Aug 2020 13:02:34: 6000000 INFO @ Mon, 10 Aug 2020 13:02:34: 16000000 INFO @ Mon, 10 Aug 2020 13:02:34: 11000000 INFO @ Mon, 10 Aug 2020 13:02:40: 7000000 INFO @ Mon, 10 Aug 2020 13:02:40: 12000000 INFO @ Mon, 10 Aug 2020 13:02:41: 17000000 INFO @ Mon, 10 Aug 2020 13:02:47: 8000000 INFO @ Mon, 10 Aug 2020 13:02:47: 13000000 INFO @ Mon, 10 Aug 2020 13:02:47: 18000000 INFO @ Mon, 10 Aug 2020 13:02:53: 9000000 INFO @ Mon, 10 Aug 2020 13:02:53: 14000000 INFO @ Mon, 10 Aug 2020 13:02:54: 19000000 INFO @ Mon, 10 Aug 2020 13:03:00: 10000000 INFO @ Mon, 10 Aug 2020 13:03:00: 15000000 INFO @ Mon, 10 Aug 2020 13:03:00: 20000000 INFO @ Mon, 10 Aug 2020 13:03:06: 11000000 INFO @ Mon, 10 Aug 2020 13:03:06: 16000000 INFO @ Mon, 10 Aug 2020 13:03:07: 21000000 INFO @ Mon, 10 Aug 2020 13:03:12: 12000000 INFO @ Mon, 10 Aug 2020 13:03:12: 17000000 INFO @ Mon, 10 Aug 2020 13:03:13: 22000000 INFO @ Mon, 10 Aug 2020 13:03:19: 13000000 INFO @ Mon, 10 Aug 2020 13:03:19: 18000000 INFO @ Mon, 10 Aug 2020 13:03:19: 23000000 INFO @ Mon, 10 Aug 2020 13:03:25: 14000000 INFO @ Mon, 10 Aug 2020 13:03:25: 19000000 INFO @ Mon, 10 Aug 2020 13:03:26: 24000000 INFO @ Mon, 10 Aug 2020 13:03:31: 15000000 INFO @ Mon, 10 Aug 2020 13:03:32: 20000000 INFO @ Mon, 10 Aug 2020 13:03:32: 25000000 INFO @ Mon, 10 Aug 2020 13:03:38: 16000000 INFO @ Mon, 10 Aug 2020 13:03:38: 21000000 INFO @ Mon, 10 Aug 2020 13:03:38: 26000000 INFO @ Mon, 10 Aug 2020 13:03:44: 17000000 INFO @ Mon, 10 Aug 2020 13:03:44: 22000000 INFO @ Mon, 10 Aug 2020 13:03:45: 27000000 INFO @ Mon, 10 Aug 2020 13:03:50: 18000000 INFO @ Mon, 10 Aug 2020 13:03:51: 23000000 INFO @ Mon, 10 Aug 2020 13:03:51: 28000000 INFO @ Mon, 10 Aug 2020 13:03:57: 19000000 INFO @ Mon, 10 Aug 2020 13:03:57: 24000000 INFO @ Mon, 10 Aug 2020 13:03:57: 29000000 INFO @ Mon, 10 Aug 2020 13:04:03: 20000000 INFO @ Mon, 10 Aug 2020 13:04:04: 30000000 INFO @ Mon, 10 Aug 2020 13:04:04: 25000000 INFO @ Mon, 10 Aug 2020 13:04:10: 21000000 INFO @ Mon, 10 Aug 2020 13:04:10: 31000000 INFO @ Mon, 10 Aug 2020 13:04:10: 26000000 INFO @ Mon, 10 Aug 2020 13:04:16: 22000000 INFO @ Mon, 10 Aug 2020 13:04:16: 27000000 INFO @ Mon, 10 Aug 2020 13:04:17: 32000000 INFO @ Mon, 10 Aug 2020 13:04:22: 23000000 INFO @ Mon, 10 Aug 2020 13:04:23: 33000000 INFO @ Mon, 10 Aug 2020 13:04:23: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 13:04:29: 24000000 INFO @ Mon, 10 Aug 2020 13:04:29: 34000000 INFO @ Mon, 10 Aug 2020 13:04:29: 29000000 INFO @ Mon, 10 Aug 2020 13:04:35: 25000000 INFO @ Mon, 10 Aug 2020 13:04:36: 35000000 INFO @ Mon, 10 Aug 2020 13:04:36: 30000000 INFO @ Mon, 10 Aug 2020 13:04:42: 26000000 INFO @ Mon, 10 Aug 2020 13:04:42: 36000000 INFO @ Mon, 10 Aug 2020 13:04:42: 31000000 INFO @ Mon, 10 Aug 2020 13:04:48: 27000000 INFO @ Mon, 10 Aug 2020 13:04:48: 37000000 INFO @ Mon, 10 Aug 2020 13:04:48: 32000000 INFO @ Mon, 10 Aug 2020 13:04:49: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:04:49: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:04:49: #1 total tags in treatment: 37112861 INFO @ Mon, 10 Aug 2020 13:04:49: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:04:49: #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 13:04:50: #1 tags after filtering in treatment: 37112711 INFO @ Mon, 10 Aug 2020 13:04:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:04:50: #1 finished! INFO @ Mon, 10 Aug 2020 13:04:50: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:04:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:04:54: 28000000 INFO @ Mon, 10 Aug 2020 13:04:55: 33000000 INFO @ Mon, 10 Aug 2020 13:04:55: #2 number of paired peaks: 53592 INFO @ Mon, 10 Aug 2020 13:04:55: start model_add_line... INFO @ Mon, 10 Aug 2020 13:04:56: start X-correlation... INFO @ Mon, 10 Aug 2020 13:04:56: end of X-cor INFO @ Mon, 10 Aug 2020 13:04:56: #2 finished! INFO @ Mon, 10 Aug 2020 13:04:56: #2 predicted fragment length is 139 bps INFO @ Mon, 10 Aug 2020 13:04:56: #2 alternative fragment length(s) may be 139 bps INFO @ Mon, 10 Aug 2020 13:04:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.05_model.r INFO @ Mon, 10 Aug 2020 13:04:56: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:04:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:05:01: 29000000 INFO @ Mon, 10 Aug 2020 13:05:01: 34000000 INFO @ Mon, 10 Aug 2020 13:05:07: 30000000 INFO @ Mon, 10 Aug 2020 13:05:08: 35000000 INFO @ Mon, 10 Aug 2020 13:05:13: 31000000 INFO @ Mon, 10 Aug 2020 13:05:14: 36000000 INFO @ Mon, 10 Aug 2020 13:05:20: 32000000 INFO @ Mon, 10 Aug 2020 13:05:21: 37000000 INFO @ Mon, 10 Aug 2020 13:05:21: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:05:21: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:05:21: #1 total tags in treatment: 37112861 INFO @ Mon, 10 Aug 2020 13:05:21: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:05:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 13:05:22: #1 tags after filtering in treatment: 37112711 INFO @ Mon, 10 Aug 2020 13:05:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:05:22: #1 finished! INFO @ Mon, 10 Aug 2020 13:05:22: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:05:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:05:26: 33000000 INFO @ Mon, 10 Aug 2020 13:05:27: #2 number of paired peaks: 53592 INFO @ Mon, 10 Aug 2020 13:05:27: start model_add_line... INFO @ Mon, 10 Aug 2020 13:05:28: start X-correlation... INFO @ Mon, 10 Aug 2020 13:05:28: end of X-cor INFO @ Mon, 10 Aug 2020 13:05:28: #2 finished! INFO @ Mon, 10 Aug 2020 13:05:28: #2 predicted fragment length is 139 bps INFO @ Mon, 10 Aug 2020 13:05:28: #2 alternative fragment length(s) may be 139 bps INFO @ Mon, 10 Aug 2020 13:05:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.10_model.r INFO @ Mon, 10 Aug 2020 13:05:28: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:05:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:05:32: 34000000 INFO @ Mon, 10 Aug 2020 13:05:38: 35000000 INFO @ Mon, 10 Aug 2020 13:05:44: 36000000 INFO @ Mon, 10 Aug 2020 13:05:49: 37000000 INFO @ Mon, 10 Aug 2020 13:05:50: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:05:50: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:05:50: #1 total tags in treatment: 37112861 INFO @ Mon, 10 Aug 2020 13:05:50: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:05:50: #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 13:05:51: #1 tags after filtering in treatment: 37112711 INFO @ Mon, 10 Aug 2020 13:05:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:05:51: #1 finished! INFO @ Mon, 10 Aug 2020 13:05:51: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:05:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:05:56: #2 number of paired peaks: 53592 INFO @ Mon, 10 Aug 2020 13:05:56: start model_add_line... INFO @ Mon, 10 Aug 2020 13:05:56: start X-correlation... INFO @ Mon, 10 Aug 2020 13:05:57: end of X-cor INFO @ Mon, 10 Aug 2020 13:05:57: #2 finished! INFO @ Mon, 10 Aug 2020 13:05:57: #2 predicted fragment length is 139 bps INFO @ Mon, 10 Aug 2020 13:05:57: #2 alternative fragment length(s) may be 139 bps INFO @ Mon, 10 Aug 2020 13:05:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.20_model.r INFO @ Mon, 10 Aug 2020 13:05:57: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:05:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:06:18: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:06:48: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:07:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.05_peaks.xls INFO @ Mon, 10 Aug 2020 13:07:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:07:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.05_summits.bed INFO @ Mon, 10 Aug 2020 13:07:01: Done! pass1 - making usageList (152 chroms): 7 millis pass2 - checking and writing primary data (40605 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:07:20: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:07:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.10_peaks.xls INFO @ Mon, 10 Aug 2020 13:07:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:07:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.10_summits.bed INFO @ Mon, 10 Aug 2020 13:07:31: Done! pass1 - making usageList (133 chroms): 5 millis pass2 - checking and writing primary data (33551 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:08:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.20_peaks.xls INFO @ Mon, 10 Aug 2020 13:08:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:08:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047584/SRX8047584.20_summits.bed INFO @ Mon, 10 Aug 2020 13:08:06: Done! pass1 - making usageList (116 chroms): 4 millis pass2 - checking and writing primary data (27677 records, 4 fields): 30 millis CompletedMACS2peakCalling