Job ID = 8184559 SRX = SRX8047611 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T04:32:00 prefetch.2.10.7: 1) Downloading 'SRR11471335'... 2020-08-10T04:32:00 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:34:57 prefetch.2.10.7: HTTPS download succeed 2020-08-10T04:34:57 prefetch.2.10.7: 1) 'SRR11471335' was downloaded successfully Read 56681502 spots for SRR11471335/SRR11471335.sra Written 56681502 spots for SRR11471335/SRR11471335.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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:24:42 56681502 reads; of these: 56681502 (100.00%) were unpaired; of these: 2001445 (3.53%) aligned 0 times 48532290 (85.62%) aligned exactly 1 time 6147767 (10.85%) aligned >1 times 96.47% overall alignment rate Time searching: 00:24:45 Overall time: 00:24:45 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] 25900080 / 54680057 = 0.4737 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 14:13:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.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 14:13:31: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:13:31: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:13:38: 1000000 INFO @ Mon, 10 Aug 2020 14:13:44: 2000000 INFO @ Mon, 10 Aug 2020 14:13:50: 3000000 INFO @ Mon, 10 Aug 2020 14:13:57: 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 14:14:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.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 14:14:01: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:14:01: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:14:03: 5000000 INFO @ Mon, 10 Aug 2020 14:14:08: 1000000 INFO @ Mon, 10 Aug 2020 14:14:10: 6000000 INFO @ Mon, 10 Aug 2020 14:14:14: 2000000 INFO @ Mon, 10 Aug 2020 14:14:17: 7000000 INFO @ Mon, 10 Aug 2020 14:14:21: 3000000 INFO @ Mon, 10 Aug 2020 14:14:24: 8000000 INFO @ Mon, 10 Aug 2020 14:14:27: 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 14:14:31: 9000000 INFO @ Mon, 10 Aug 2020 14:14:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.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 14:14:31: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:14:31: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:14:33: 5000000 INFO @ Mon, 10 Aug 2020 14:14:38: 10000000 INFO @ Mon, 10 Aug 2020 14:14:38: 1000000 INFO @ Mon, 10 Aug 2020 14:14:40: 6000000 INFO @ Mon, 10 Aug 2020 14:14:45: 11000000 INFO @ Mon, 10 Aug 2020 14:14:45: 2000000 INFO @ Mon, 10 Aug 2020 14:14:46: 7000000 INFO @ Mon, 10 Aug 2020 14:14:52: 12000000 INFO @ Mon, 10 Aug 2020 14:14:52: 3000000 INFO @ Mon, 10 Aug 2020 14:14:53: 8000000 INFO @ Mon, 10 Aug 2020 14:14:59: 13000000 INFO @ Mon, 10 Aug 2020 14:14:59: 4000000 INFO @ Mon, 10 Aug 2020 14:14:59: 9000000 INFO @ Mon, 10 Aug 2020 14:15:06: 10000000 INFO @ Mon, 10 Aug 2020 14:15:06: 14000000 INFO @ Mon, 10 Aug 2020 14:15:06: 5000000 INFO @ Mon, 10 Aug 2020 14:15:12: 11000000 INFO @ Mon, 10 Aug 2020 14:15:13: 15000000 INFO @ Mon, 10 Aug 2020 14:15:14: 6000000 INFO @ Mon, 10 Aug 2020 14:15:19: 12000000 INFO @ Mon, 10 Aug 2020 14:15:21: 16000000 INFO @ Mon, 10 Aug 2020 14:15:21: 7000000 INFO @ Mon, 10 Aug 2020 14:15:25: 13000000 INFO @ Mon, 10 Aug 2020 14:15:28: 17000000 INFO @ Mon, 10 Aug 2020 14:15:29: 8000000 INFO @ Mon, 10 Aug 2020 14:15:31: 14000000 INFO @ Mon, 10 Aug 2020 14:15:36: 18000000 INFO @ Mon, 10 Aug 2020 14:15:36: 9000000 INFO @ Mon, 10 Aug 2020 14:15:38: 15000000 INFO @ Mon, 10 Aug 2020 14:15:43: 19000000 INFO @ Mon, 10 Aug 2020 14:15:44: 10000000 INFO @ Mon, 10 Aug 2020 14:15:44: 16000000 INFO @ Mon, 10 Aug 2020 14:15:51: 20000000 INFO @ Mon, 10 Aug 2020 14:15:51: 17000000 INFO @ Mon, 10 Aug 2020 14:15:51: 11000000 INFO @ Mon, 10 Aug 2020 14:15:57: 18000000 INFO @ Mon, 10 Aug 2020 14:15:58: 21000000 INFO @ Mon, 10 Aug 2020 14:15:59: 12000000 INFO @ Mon, 10 Aug 2020 14:16:04: 19000000 INFO @ Mon, 10 Aug 2020 14:16:06: 22000000 INFO @ Mon, 10 Aug 2020 14:16:06: 13000000 INFO @ Mon, 10 Aug 2020 14:16:10: 20000000 INFO @ Mon, 10 Aug 2020 14:16:14: 23000000 INFO @ Mon, 10 Aug 2020 14:16:14: 14000000 INFO @ Mon, 10 Aug 2020 14:16:17: 21000000 INFO @ Mon, 10 Aug 2020 14:16:21: 24000000 INFO @ Mon, 10 Aug 2020 14:16:21: 15000000 INFO @ Mon, 10 Aug 2020 14:16:23: 22000000 INFO @ Mon, 10 Aug 2020 14:16:28: 25000000 INFO @ Mon, 10 Aug 2020 14:16:29: 16000000 INFO @ Mon, 10 Aug 2020 14:16:30: 23000000 INFO @ Mon, 10 Aug 2020 14:16:36: 26000000 INFO @ Mon, 10 Aug 2020 14:16:36: 24000000 INFO @ Mon, 10 Aug 2020 14:16:36: 17000000 INFO @ Mon, 10 Aug 2020 14:16:43: 25000000 INFO @ Mon, 10 Aug 2020 14:16:43: 27000000 INFO @ Mon, 10 Aug 2020 14:16:44: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 14:16:49: 26000000 INFO @ Mon, 10 Aug 2020 14:16:51: 28000000 INFO @ Mon, 10 Aug 2020 14:16:51: 19000000 INFO @ Mon, 10 Aug 2020 14:16:56: 27000000 INFO @ Mon, 10 Aug 2020 14:16:57: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:16:57: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:16:57: #1 total tags in treatment: 28779977 INFO @ Mon, 10 Aug 2020 14:16:57: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:16:57: #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 14:16:58: #1 tags after filtering in treatment: 28779786 INFO @ Mon, 10 Aug 2020 14:16:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:16:58: #1 finished! INFO @ Mon, 10 Aug 2020 14:16:58: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:16:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:16:58: 20000000 INFO @ Mon, 10 Aug 2020 14:17:02: #2 number of paired peaks: 43789 INFO @ Mon, 10 Aug 2020 14:17:02: start model_add_line... INFO @ Mon, 10 Aug 2020 14:17:02: start X-correlation... INFO @ Mon, 10 Aug 2020 14:17:02: end of X-cor INFO @ Mon, 10 Aug 2020 14:17:02: #2 finished! INFO @ Mon, 10 Aug 2020 14:17:02: #2 predicted fragment length is 118 bps INFO @ Mon, 10 Aug 2020 14:17:02: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 10 Aug 2020 14:17:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.05_model.r INFO @ Mon, 10 Aug 2020 14:17:02: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:17:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:17:02: 28000000 INFO @ Mon, 10 Aug 2020 14:17:06: 21000000 INFO @ Mon, 10 Aug 2020 14:17:08: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:17:08: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:17:08: #1 total tags in treatment: 28779977 INFO @ Mon, 10 Aug 2020 14:17:08: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:17:08: #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 14:17:08: #1 tags after filtering in treatment: 28779786 INFO @ Mon, 10 Aug 2020 14:17:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:17:08: #1 finished! INFO @ Mon, 10 Aug 2020 14:17:08: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:17:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:17:12: #2 number of paired peaks: 43789 INFO @ Mon, 10 Aug 2020 14:17:12: start model_add_line... INFO @ Mon, 10 Aug 2020 14:17:12: 22000000 INFO @ Mon, 10 Aug 2020 14:17:13: start X-correlation... INFO @ Mon, 10 Aug 2020 14:17:13: end of X-cor INFO @ Mon, 10 Aug 2020 14:17:13: #2 finished! INFO @ Mon, 10 Aug 2020 14:17:13: #2 predicted fragment length is 118 bps INFO @ Mon, 10 Aug 2020 14:17:13: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 10 Aug 2020 14:17:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.10_model.r INFO @ Mon, 10 Aug 2020 14:17:13: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:17:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:17:19: 23000000 INFO @ Mon, 10 Aug 2020 14:17:26: 24000000 BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 14:17:32: 25000000 INFO @ Mon, 10 Aug 2020 14:17:39: 26000000 INFO @ Mon, 10 Aug 2020 14:17:45: 27000000 INFO @ Mon, 10 Aug 2020 14:17:52: 28000000 INFO @ Mon, 10 Aug 2020 14:17:58: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:17:58: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:17:58: #1 total tags in treatment: 28779977 INFO @ Mon, 10 Aug 2020 14:17:58: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:17:58: #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 14:17:58: #1 tags after filtering in treatment: 28779786 INFO @ Mon, 10 Aug 2020 14:17:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:17:58: #1 finished! INFO @ Mon, 10 Aug 2020 14:17:58: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:17:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:18:02: #2 number of paired peaks: 43789 INFO @ Mon, 10 Aug 2020 14:18:02: start model_add_line... INFO @ Mon, 10 Aug 2020 14:18:03: start X-correlation... INFO @ Mon, 10 Aug 2020 14:18:03: end of X-cor INFO @ Mon, 10 Aug 2020 14:18:03: #2 finished! INFO @ Mon, 10 Aug 2020 14:18:03: #2 predicted fragment length is 118 bps INFO @ Mon, 10 Aug 2020 14:18:03: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 10 Aug 2020 14:18:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.20_model.r INFO @ Mon, 10 Aug 2020 14:18:03: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:18:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:18:03: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:18:12: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:18:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.05_peaks.xls INFO @ Mon, 10 Aug 2020 14:18:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:18:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.05_summits.bed INFO @ Mon, 10 Aug 2020 14:18:38: Done! pass1 - making usageList (142 chroms): 6 millis pass2 - checking and writing primary data (38455 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:18:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.10_peaks.xls INFO @ Mon, 10 Aug 2020 14:18:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:18:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.10_summits.bed INFO @ Mon, 10 Aug 2020 14:18:46: Done! pass1 - making usageList (125 chroms): 5 millis pass2 - checking and writing primary data (32848 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:19:02: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:19:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.20_peaks.xls INFO @ Mon, 10 Aug 2020 14:19:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:19:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047611/SRX8047611.20_summits.bed INFO @ Mon, 10 Aug 2020 14:19:35: Done! pass1 - making usageList (108 chroms): 4 millis pass2 - checking and writing primary data (27098 records, 4 fields): 29 millis CompletedMACS2peakCalling