Job ID = 8184601 SRX = SRX8047617 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T04:50:49 prefetch.2.10.7: 1) Downloading 'SRR11471341'... 2020-08-10T04:50:49 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:53:04 prefetch.2.10.7: HTTPS download succeed 2020-08-10T04:53:04 prefetch.2.10.7: 1) 'SRR11471341' was downloaded successfully Read 41160009 spots for SRR11471341/SRR11471341.sra Written 41160009 spots for SRR11471341/SRR11471341.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:33:57 41160009 reads; of these: 41160009 (100.00%) were unpaired; of these: 1102390 (2.68%) aligned 0 times 28620938 (69.54%) aligned exactly 1 time 11436681 (27.79%) aligned >1 times 97.32% overall alignment rate Time searching: 00:34:00 Overall time: 00:34:00 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] 3632711 / 40057619 = 0.0907 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 14:39:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.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 14:39:40: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:39:40: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:39:47: 1000000 INFO @ Mon, 10 Aug 2020 14:39:53: 2000000 INFO @ Mon, 10 Aug 2020 14:39:59: 3000000 INFO @ Mon, 10 Aug 2020 14:40:06: 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 14:40:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.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 14:40:10: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:40:10: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:40:12: 5000000 INFO @ Mon, 10 Aug 2020 14:40:18: 1000000 INFO @ Mon, 10 Aug 2020 14:40:20: 6000000 INFO @ Mon, 10 Aug 2020 14:40:26: 2000000 INFO @ Mon, 10 Aug 2020 14:40:28: 7000000 INFO @ Mon, 10 Aug 2020 14:40:35: 3000000 INFO @ Mon, 10 Aug 2020 14:40:36: 8000000 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 14:40:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.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 14:40:40: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:40:40: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:40:43: 4000000 INFO @ Mon, 10 Aug 2020 14:40:44: 9000000 INFO @ Mon, 10 Aug 2020 14:40:48: 1000000 INFO @ Mon, 10 Aug 2020 14:40:52: 10000000 INFO @ Mon, 10 Aug 2020 14:40:52: 5000000 INFO @ Mon, 10 Aug 2020 14:40:57: 2000000 INFO @ Mon, 10 Aug 2020 14:41:00: 11000000 INFO @ Mon, 10 Aug 2020 14:41:00: 6000000 INFO @ Mon, 10 Aug 2020 14:41:05: 3000000 INFO @ Mon, 10 Aug 2020 14:41:08: 12000000 INFO @ Mon, 10 Aug 2020 14:41:09: 7000000 INFO @ Mon, 10 Aug 2020 14:41:14: 4000000 INFO @ Mon, 10 Aug 2020 14:41:16: 13000000 INFO @ Mon, 10 Aug 2020 14:41:17: 8000000 INFO @ Mon, 10 Aug 2020 14:41:23: 5000000 INFO @ Mon, 10 Aug 2020 14:41:24: 14000000 INFO @ Mon, 10 Aug 2020 14:41:26: 9000000 INFO @ Mon, 10 Aug 2020 14:41:32: 15000000 INFO @ Mon, 10 Aug 2020 14:41:32: 6000000 INFO @ Mon, 10 Aug 2020 14:41:34: 10000000 INFO @ Mon, 10 Aug 2020 14:41:40: 16000000 INFO @ Mon, 10 Aug 2020 14:41:41: 7000000 INFO @ Mon, 10 Aug 2020 14:41:43: 11000000 INFO @ Mon, 10 Aug 2020 14:41:48: 17000000 INFO @ Mon, 10 Aug 2020 14:41:49: 8000000 INFO @ Mon, 10 Aug 2020 14:41:51: 12000000 INFO @ Mon, 10 Aug 2020 14:41:56: 18000000 INFO @ Mon, 10 Aug 2020 14:41:58: 9000000 INFO @ Mon, 10 Aug 2020 14:42:00: 13000000 INFO @ Mon, 10 Aug 2020 14:42:04: 19000000 INFO @ Mon, 10 Aug 2020 14:42:06: 10000000 INFO @ Mon, 10 Aug 2020 14:42:08: 14000000 INFO @ Mon, 10 Aug 2020 14:42:12: 20000000 INFO @ Mon, 10 Aug 2020 14:42:15: 11000000 INFO @ Mon, 10 Aug 2020 14:42:17: 15000000 INFO @ Mon, 10 Aug 2020 14:42:20: 21000000 INFO @ Mon, 10 Aug 2020 14:42:23: 12000000 INFO @ Mon, 10 Aug 2020 14:42:26: 16000000 INFO @ Mon, 10 Aug 2020 14:42:28: 22000000 INFO @ Mon, 10 Aug 2020 14:42:32: 13000000 INFO @ Mon, 10 Aug 2020 14:42:34: 17000000 INFO @ Mon, 10 Aug 2020 14:42:36: 23000000 INFO @ Mon, 10 Aug 2020 14:42:40: 14000000 INFO @ Mon, 10 Aug 2020 14:42:43: 18000000 INFO @ Mon, 10 Aug 2020 14:42:44: 24000000 INFO @ Mon, 10 Aug 2020 14:42:49: 15000000 INFO @ Mon, 10 Aug 2020 14:42:51: 19000000 INFO @ Mon, 10 Aug 2020 14:42:52: 25000000 INFO @ Mon, 10 Aug 2020 14:42:58: 16000000 INFO @ Mon, 10 Aug 2020 14:43:00: 20000000 INFO @ Mon, 10 Aug 2020 14:43:00: 26000000 INFO @ Mon, 10 Aug 2020 14:43:06: 17000000 INFO @ Mon, 10 Aug 2020 14:43:08: 27000000 INFO @ Mon, 10 Aug 2020 14:43:08: 21000000 INFO @ Mon, 10 Aug 2020 14:43:15: 18000000 INFO @ Mon, 10 Aug 2020 14:43:16: 28000000 INFO @ Mon, 10 Aug 2020 14:43:17: 22000000 INFO @ Mon, 10 Aug 2020 14:43:23: 19000000 INFO @ Mon, 10 Aug 2020 14:43:24: 29000000 INFO @ Mon, 10 Aug 2020 14:43:25: 23000000 INFO @ Mon, 10 Aug 2020 14:43:31: 20000000 INFO @ Mon, 10 Aug 2020 14:43:32: 30000000 INFO @ Mon, 10 Aug 2020 14:43:34: 24000000 INFO @ Mon, 10 Aug 2020 14:43:40: 31000000 INFO @ Mon, 10 Aug 2020 14:43:40: 21000000 INFO @ Mon, 10 Aug 2020 14:43:42: 25000000 INFO @ Mon, 10 Aug 2020 14:43:48: 32000000 INFO @ Mon, 10 Aug 2020 14:43:49: 22000000 INFO @ Mon, 10 Aug 2020 14:43:51: 26000000 INFO @ Mon, 10 Aug 2020 14:43:56: 33000000 INFO @ Mon, 10 Aug 2020 14:43:57: 23000000 INFO @ Mon, 10 Aug 2020 14:43:59: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 14:44:04: 34000000 INFO @ Mon, 10 Aug 2020 14:44:05: 24000000 INFO @ Mon, 10 Aug 2020 14:44:08: 28000000 INFO @ Mon, 10 Aug 2020 14:44:12: 35000000 INFO @ Mon, 10 Aug 2020 14:44:14: 25000000 INFO @ Mon, 10 Aug 2020 14:44:16: 29000000 INFO @ Mon, 10 Aug 2020 14:44:20: 36000000 INFO @ Mon, 10 Aug 2020 14:44:22: 26000000 INFO @ Mon, 10 Aug 2020 14:44:24: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:44:24: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:44:24: #1 total tags in treatment: 36424908 INFO @ Mon, 10 Aug 2020 14:44:24: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:44:24: #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 14:44:24: #1 tags after filtering in treatment: 36424828 INFO @ Mon, 10 Aug 2020 14:44:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:44:24: #1 finished! INFO @ Mon, 10 Aug 2020 14:44:24: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:44:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:44:25: 30000000 INFO @ Mon, 10 Aug 2020 14:44:27: #2 number of paired peaks: 6053 INFO @ Mon, 10 Aug 2020 14:44:27: start model_add_line... INFO @ Mon, 10 Aug 2020 14:44:28: start X-correlation... INFO @ Mon, 10 Aug 2020 14:44:28: end of X-cor INFO @ Mon, 10 Aug 2020 14:44:28: #2 finished! INFO @ Mon, 10 Aug 2020 14:44:28: #2 predicted fragment length is 52 bps INFO @ Mon, 10 Aug 2020 14:44:28: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 10 Aug 2020 14:44:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.05_model.r WARNING @ Mon, 10 Aug 2020 14:44:28: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:44:28: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 10 Aug 2020 14:44:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 14:44:28: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:44:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:44:31: 27000000 INFO @ Mon, 10 Aug 2020 14:44:33: 31000000 INFO @ Mon, 10 Aug 2020 14:44:39: 28000000 INFO @ Mon, 10 Aug 2020 14:44:41: 32000000 INFO @ Mon, 10 Aug 2020 14:44:48: 29000000 INFO @ Mon, 10 Aug 2020 14:44:50: 33000000 INFO @ Mon, 10 Aug 2020 14:44:56: 30000000 INFO @ Mon, 10 Aug 2020 14:44:58: 34000000 INFO @ Mon, 10 Aug 2020 14:45:04: 31000000 INFO @ Mon, 10 Aug 2020 14:45:07: 35000000 INFO @ Mon, 10 Aug 2020 14:45:13: 32000000 INFO @ Mon, 10 Aug 2020 14:45:15: 36000000 INFO @ Mon, 10 Aug 2020 14:45:19: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:45:19: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:45:19: #1 total tags in treatment: 36424908 INFO @ Mon, 10 Aug 2020 14:45:19: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:45:19: #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 14:45:19: #1 tags after filtering in treatment: 36424828 INFO @ Mon, 10 Aug 2020 14:45:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:45:19: #1 finished! INFO @ Mon, 10 Aug 2020 14:45:19: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:45:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:45:21: 33000000 INFO @ Mon, 10 Aug 2020 14:45:22: #2 number of paired peaks: 6053 INFO @ Mon, 10 Aug 2020 14:45:22: start model_add_line... INFO @ Mon, 10 Aug 2020 14:45:23: start X-correlation... INFO @ Mon, 10 Aug 2020 14:45:23: end of X-cor INFO @ Mon, 10 Aug 2020 14:45:23: #2 finished! INFO @ Mon, 10 Aug 2020 14:45:23: #2 predicted fragment length is 52 bps INFO @ Mon, 10 Aug 2020 14:45:23: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 10 Aug 2020 14:45:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.10_model.r WARNING @ Mon, 10 Aug 2020 14:45:23: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:45:23: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 10 Aug 2020 14:45:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 14:45:23: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:45:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 14:45:28: 34000000 INFO @ Mon, 10 Aug 2020 14:45:36: 35000000 INFO @ Mon, 10 Aug 2020 14:45:43: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:45:44: 36000000 INFO @ Mon, 10 Aug 2020 14:45:47: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:45:47: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:45:47: #1 total tags in treatment: 36424908 INFO @ Mon, 10 Aug 2020 14:45:47: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:45:47: #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 14:45:48: #1 tags after filtering in treatment: 36424828 INFO @ Mon, 10 Aug 2020 14:45:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:45:48: #1 finished! INFO @ Mon, 10 Aug 2020 14:45:48: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:45:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:45:51: #2 number of paired peaks: 6053 INFO @ Mon, 10 Aug 2020 14:45:51: start model_add_line... INFO @ Mon, 10 Aug 2020 14:45:51: start X-correlation... INFO @ Mon, 10 Aug 2020 14:45:51: end of X-cor INFO @ Mon, 10 Aug 2020 14:45:51: #2 finished! INFO @ Mon, 10 Aug 2020 14:45:51: #2 predicted fragment length is 52 bps INFO @ Mon, 10 Aug 2020 14:45:51: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 10 Aug 2020 14:45:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.20_model.r WARNING @ Mon, 10 Aug 2020 14:45:51: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:45:51: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 10 Aug 2020 14:45:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 14:45:51: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:45:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:46:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.05_peaks.xls INFO @ Mon, 10 Aug 2020 14:46:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:46:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.05_summits.bed INFO @ Mon, 10 Aug 2020 14:46:23: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (3188 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:46:38: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:47:07: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:47:17: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.10_peaks.xls INFO @ Mon, 10 Aug 2020 14:47:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:47:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.10_summits.bed INFO @ Mon, 10 Aug 2020 14:47:17: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (1521 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:47:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.20_peaks.xls INFO @ Mon, 10 Aug 2020 14:47:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:47:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047617/SRX8047617.20_summits.bed INFO @ Mon, 10 Aug 2020 14:47:46: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (669 records, 4 fields): 3 millis CompletedMACS2peakCalling