Job ID = 8184549 SRX = SRX8047607 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T04:27:23 prefetch.2.10.7: 1) Downloading 'SRR11471331'... 2020-08-10T04:27:23 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:30:37 prefetch.2.10.7: HTTPS download succeed 2020-08-10T04:30:37 prefetch.2.10.7: 1) 'SRR11471331' was downloaded successfully Read 52244352 spots for SRR11471331/SRR11471331.sra Written 52244352 spots for SRR11471331/SRR11471331.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: 00:00:01 Multiseed full-index search: 00:35:45 52244352 reads; of these: 52244352 (100.00%) were unpaired; of these: 8928010 (17.09%) aligned 0 times 32459155 (62.13%) aligned exactly 1 time 10857187 (20.78%) aligned >1 times 82.91% overall alignment rate Time searching: 00:35:50 Overall time: 00:35:50 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] 4446316 / 43316342 = 0.1026 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 14:20:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.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 14:20:20: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:20:20: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:20:26: 1000000 INFO @ Mon, 10 Aug 2020 14:20:31: 2000000 INFO @ Mon, 10 Aug 2020 14:20:36: 3000000 INFO @ Mon, 10 Aug 2020 14:20:41: 4000000 INFO @ Mon, 10 Aug 2020 14:20:47: 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 14:20:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.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 14:20:50: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:20:50: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:20:52: 6000000 INFO @ Mon, 10 Aug 2020 14:20:56: 1000000 INFO @ Mon, 10 Aug 2020 14:20:58: 7000000 INFO @ Mon, 10 Aug 2020 14:21:02: 2000000 INFO @ Mon, 10 Aug 2020 14:21:04: 8000000 INFO @ Mon, 10 Aug 2020 14:21:07: 3000000 INFO @ Mon, 10 Aug 2020 14:21:09: 9000000 INFO @ Mon, 10 Aug 2020 14:21:13: 4000000 INFO @ Mon, 10 Aug 2020 14:21:15: 10000000 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 14:21:19: 5000000 INFO @ Mon, 10 Aug 2020 14:21:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.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 14:21:20: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:21:20: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:21:21: 11000000 INFO @ Mon, 10 Aug 2020 14:21:25: 6000000 INFO @ Mon, 10 Aug 2020 14:21:26: 1000000 INFO @ Mon, 10 Aug 2020 14:21:27: 12000000 INFO @ Mon, 10 Aug 2020 14:21:30: 7000000 INFO @ Mon, 10 Aug 2020 14:21:32: 2000000 INFO @ Mon, 10 Aug 2020 14:21:32: 13000000 INFO @ Mon, 10 Aug 2020 14:21:36: 8000000 INFO @ Mon, 10 Aug 2020 14:21:38: 3000000 INFO @ Mon, 10 Aug 2020 14:21:38: 14000000 INFO @ Mon, 10 Aug 2020 14:21:42: 9000000 INFO @ Mon, 10 Aug 2020 14:21:43: 4000000 INFO @ Mon, 10 Aug 2020 14:21:44: 15000000 INFO @ Mon, 10 Aug 2020 14:21:48: 10000000 INFO @ Mon, 10 Aug 2020 14:21:49: 5000000 INFO @ Mon, 10 Aug 2020 14:21:50: 16000000 INFO @ Mon, 10 Aug 2020 14:21:54: 11000000 INFO @ Mon, 10 Aug 2020 14:21:55: 6000000 INFO @ Mon, 10 Aug 2020 14:21:56: 17000000 INFO @ Mon, 10 Aug 2020 14:22:00: 12000000 INFO @ Mon, 10 Aug 2020 14:22:01: 7000000 INFO @ Mon, 10 Aug 2020 14:22:02: 18000000 INFO @ Mon, 10 Aug 2020 14:22:05: 13000000 INFO @ Mon, 10 Aug 2020 14:22:07: 8000000 INFO @ Mon, 10 Aug 2020 14:22:07: 19000000 INFO @ Mon, 10 Aug 2020 14:22:11: 14000000 INFO @ Mon, 10 Aug 2020 14:22:13: 9000000 INFO @ Mon, 10 Aug 2020 14:22:13: 20000000 INFO @ Mon, 10 Aug 2020 14:22:17: 15000000 INFO @ Mon, 10 Aug 2020 14:22:18: 10000000 INFO @ Mon, 10 Aug 2020 14:22:19: 21000000 INFO @ Mon, 10 Aug 2020 14:22:23: 16000000 INFO @ Mon, 10 Aug 2020 14:22:24: 11000000 INFO @ Mon, 10 Aug 2020 14:22:25: 22000000 INFO @ Mon, 10 Aug 2020 14:22:29: 17000000 INFO @ Mon, 10 Aug 2020 14:22:30: 12000000 INFO @ Mon, 10 Aug 2020 14:22:31: 23000000 INFO @ Mon, 10 Aug 2020 14:22:35: 18000000 INFO @ Mon, 10 Aug 2020 14:22:36: 13000000 INFO @ Mon, 10 Aug 2020 14:22:37: 24000000 INFO @ Mon, 10 Aug 2020 14:22:41: 19000000 INFO @ Mon, 10 Aug 2020 14:22:42: 14000000 INFO @ Mon, 10 Aug 2020 14:22:43: 25000000 INFO @ Mon, 10 Aug 2020 14:22:47: 20000000 INFO @ Mon, 10 Aug 2020 14:22:48: 15000000 INFO @ Mon, 10 Aug 2020 14:22:49: 26000000 INFO @ Mon, 10 Aug 2020 14:22:52: 21000000 INFO @ Mon, 10 Aug 2020 14:22:53: 16000000 INFO @ Mon, 10 Aug 2020 14:22:55: 27000000 INFO @ Mon, 10 Aug 2020 14:22:58: 22000000 INFO @ Mon, 10 Aug 2020 14:22:59: 17000000 INFO @ Mon, 10 Aug 2020 14:23:01: 28000000 INFO @ Mon, 10 Aug 2020 14:23:04: 23000000 INFO @ Mon, 10 Aug 2020 14:23:05: 18000000 INFO @ Mon, 10 Aug 2020 14:23:07: 29000000 INFO @ Mon, 10 Aug 2020 14:23:10: 24000000 INFO @ Mon, 10 Aug 2020 14:23:11: 19000000 INFO @ Mon, 10 Aug 2020 14:23:13: 30000000 INFO @ Mon, 10 Aug 2020 14:23:16: 25000000 INFO @ Mon, 10 Aug 2020 14:23:17: 20000000 INFO @ Mon, 10 Aug 2020 14:23:19: 31000000 INFO @ Mon, 10 Aug 2020 14:23:22: 26000000 INFO @ Mon, 10 Aug 2020 14:23:23: 21000000 INFO @ Mon, 10 Aug 2020 14:23:25: 32000000 INFO @ Mon, 10 Aug 2020 14:23:27: 27000000 INFO @ Mon, 10 Aug 2020 14:23:28: 22000000 INFO @ Mon, 10 Aug 2020 14:23:31: 33000000 INFO @ Mon, 10 Aug 2020 14:23:33: 28000000 INFO @ Mon, 10 Aug 2020 14:23:34: 23000000 INFO @ Mon, 10 Aug 2020 14:23:36: 34000000 INFO @ Mon, 10 Aug 2020 14:23:39: 29000000 INFO @ Mon, 10 Aug 2020 14:23:40: 24000000 INFO @ Mon, 10 Aug 2020 14:23:42: 35000000 INFO @ Mon, 10 Aug 2020 14:23:45: 30000000 INFO @ Mon, 10 Aug 2020 14:23:46: 25000000 INFO @ Mon, 10 Aug 2020 14:23:48: 36000000 INFO @ Mon, 10 Aug 2020 14:23:51: 31000000 INFO @ Mon, 10 Aug 2020 14:23:52: 26000000 INFO @ Mon, 10 Aug 2020 14:23:54: 37000000 INFO @ Mon, 10 Aug 2020 14:23:57: 32000000 INFO @ Mon, 10 Aug 2020 14:23:57: 27000000 INFO @ Mon, 10 Aug 2020 14:24:00: 38000000 INFO @ Mon, 10 Aug 2020 14:24:02: 33000000 INFO @ Mon, 10 Aug 2020 14:24:03: 28000000 INFO @ Mon, 10 Aug 2020 14:24:05: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:24:05: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:24:05: #1 total tags in treatment: 38870026 INFO @ Mon, 10 Aug 2020 14:24:05: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:24:05: #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 14:24:06: #1 tags after filtering in treatment: 38869933 INFO @ Mon, 10 Aug 2020 14:24:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:24:06: #1 finished! INFO @ Mon, 10 Aug 2020 14:24:06: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:24:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:24:08: 34000000 INFO @ Mon, 10 Aug 2020 14:24:09: 29000000 INFO @ Mon, 10 Aug 2020 14:24:09: #2 number of paired peaks: 17785 INFO @ Mon, 10 Aug 2020 14:24:09: start model_add_line... INFO @ Mon, 10 Aug 2020 14:24:10: start X-correlation... INFO @ Mon, 10 Aug 2020 14:24:10: end of X-cor INFO @ Mon, 10 Aug 2020 14:24:10: #2 finished! INFO @ Mon, 10 Aug 2020 14:24:10: #2 predicted fragment length is 91 bps INFO @ Mon, 10 Aug 2020 14:24:10: #2 alternative fragment length(s) may be 91 bps INFO @ Mon, 10 Aug 2020 14:24:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.05_model.r WARNING @ Mon, 10 Aug 2020 14:24:10: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:24:10: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Mon, 10 Aug 2020 14:24:10: #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 14:24:10: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:24:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:24:14: 35000000 INFO @ Mon, 10 Aug 2020 14:24:15: 30000000 INFO @ Mon, 10 Aug 2020 14:24:20: 36000000 INFO @ Mon, 10 Aug 2020 14:24:20: 31000000 INFO @ Mon, 10 Aug 2020 14:24:25: 37000000 INFO @ Mon, 10 Aug 2020 14:24:26: 32000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 14:24:31: 38000000 INFO @ Mon, 10 Aug 2020 14:24:32: 33000000 INFO @ Mon, 10 Aug 2020 14:24:36: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:24:36: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:24:36: #1 total tags in treatment: 38870026 INFO @ Mon, 10 Aug 2020 14:24:36: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:24:36: #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 14:24:37: #1 tags after filtering in treatment: 38869933 INFO @ Mon, 10 Aug 2020 14:24:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:24:37: #1 finished! INFO @ Mon, 10 Aug 2020 14:24:37: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:24:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:24:38: 34000000 INFO @ Mon, 10 Aug 2020 14:24:41: #2 number of paired peaks: 17785 INFO @ Mon, 10 Aug 2020 14:24:41: start model_add_line... INFO @ Mon, 10 Aug 2020 14:24:41: start X-correlation... INFO @ Mon, 10 Aug 2020 14:24:41: end of X-cor INFO @ Mon, 10 Aug 2020 14:24:41: #2 finished! INFO @ Mon, 10 Aug 2020 14:24:41: #2 predicted fragment length is 91 bps INFO @ Mon, 10 Aug 2020 14:24:41: #2 alternative fragment length(s) may be 91 bps INFO @ Mon, 10 Aug 2020 14:24:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.10_model.r WARNING @ Mon, 10 Aug 2020 14:24:41: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:24:41: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Mon, 10 Aug 2020 14:24:41: #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 14:24:41: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:24:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:24:43: 35000000 INFO @ Mon, 10 Aug 2020 14:24:49: 36000000 INFO @ Mon, 10 Aug 2020 14:24:54: 37000000 INFO @ Mon, 10 Aug 2020 14:25:00: 38000000 INFO @ Mon, 10 Aug 2020 14:25:04: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:25:04: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:25:04: #1 total tags in treatment: 38870026 INFO @ Mon, 10 Aug 2020 14:25:04: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:25:04: #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 14:25:05: #1 tags after filtering in treatment: 38869933 INFO @ Mon, 10 Aug 2020 14:25:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:25:05: #1 finished! INFO @ Mon, 10 Aug 2020 14:25:05: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:25:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:25:09: #2 number of paired peaks: 17785 INFO @ Mon, 10 Aug 2020 14:25:09: start model_add_line... INFO @ Mon, 10 Aug 2020 14:25:09: start X-correlation... INFO @ Mon, 10 Aug 2020 14:25:09: end of X-cor INFO @ Mon, 10 Aug 2020 14:25:09: #2 finished! INFO @ Mon, 10 Aug 2020 14:25:09: #2 predicted fragment length is 91 bps INFO @ Mon, 10 Aug 2020 14:25:09: #2 alternative fragment length(s) may be 91 bps INFO @ Mon, 10 Aug 2020 14:25:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.20_model.r WARNING @ Mon, 10 Aug 2020 14:25:09: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:25:09: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Mon, 10 Aug 2020 14:25:09: #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 14:25:09: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:25:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:25:37: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 14:26:09: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:26:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.05_peaks.xls INFO @ Mon, 10 Aug 2020 14:26:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:26:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.05_summits.bed INFO @ Mon, 10 Aug 2020 14:26:21: Done! pass1 - making usageList (96 chroms): 1 millis pass2 - checking and writing primary data (3852 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:26:37: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:26:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.10_peaks.xls INFO @ Mon, 10 Aug 2020 14:26:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:26:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.10_summits.bed INFO @ Mon, 10 Aug 2020 14:26:54: Done! pass1 - making usageList (63 chroms): 1 millis pass2 - checking and writing primary data (1464 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:27:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.20_peaks.xls INFO @ Mon, 10 Aug 2020 14:27:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:27:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047607/SRX8047607.20_summits.bed INFO @ Mon, 10 Aug 2020 14:27:22: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (535 records, 4 fields): 3 millis CompletedMACS2peakCalling