Job ID = 8184240 SRX = SRX8047577 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T03:01:19 prefetch.2.10.7: 1) Downloading 'SRR11471302'... 2020-08-10T03:01:19 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T03:06:00 prefetch.2.10.7: HTTPS download succeed 2020-08-10T03:06:00 prefetch.2.10.7: 1) 'SRR11471302' was downloaded successfully Read 56000282 spots for SRR11471302/SRR11471302.sra Written 56000282 spots for SRR11471302/SRR11471302.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: 00:50:24 56000282 reads; of these: 56000282 (100.00%) were unpaired; of these: 10587734 (18.91%) aligned 0 times 33438405 (59.71%) aligned exactly 1 time 11974143 (21.38%) aligned >1 times 81.09% overall alignment rate Time searching: 00:50:29 Overall time: 00:50:29 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] 4799714 / 45412548 = 0.1057 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 13:16:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.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 13:16:26: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:16:26: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:16:32: 1000000 INFO @ Mon, 10 Aug 2020 13:16:37: 2000000 INFO @ Mon, 10 Aug 2020 13:16:42: 3000000 INFO @ Mon, 10 Aug 2020 13:16:48: 4000000 INFO @ Mon, 10 Aug 2020 13:16:53: 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 13:16:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.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 13:16:56: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:16:56: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:16:59: 6000000 INFO @ Mon, 10 Aug 2020 13:17:02: 1000000 INFO @ Mon, 10 Aug 2020 13:17:04: 7000000 INFO @ Mon, 10 Aug 2020 13:17:08: 2000000 INFO @ Mon, 10 Aug 2020 13:17:10: 8000000 INFO @ Mon, 10 Aug 2020 13:17:14: 3000000 INFO @ Mon, 10 Aug 2020 13:17:16: 9000000 INFO @ Mon, 10 Aug 2020 13:17:19: 4000000 INFO @ Mon, 10 Aug 2020 13:17:21: 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 13:17:25: 5000000 INFO @ Mon, 10 Aug 2020 13:17:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.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 13:17:27: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:17:27: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:17:27: 11000000 INFO @ Mon, 10 Aug 2020 13:17:31: 6000000 INFO @ Mon, 10 Aug 2020 13:17:33: 1000000 INFO @ Mon, 10 Aug 2020 13:17:33: 12000000 INFO @ Mon, 10 Aug 2020 13:17:37: 7000000 INFO @ Mon, 10 Aug 2020 13:17:38: 13000000 INFO @ Mon, 10 Aug 2020 13:17:38: 2000000 INFO @ Mon, 10 Aug 2020 13:17:43: 8000000 INFO @ Mon, 10 Aug 2020 13:17:44: 14000000 INFO @ Mon, 10 Aug 2020 13:17:44: 3000000 INFO @ Mon, 10 Aug 2020 13:17:48: 9000000 INFO @ Mon, 10 Aug 2020 13:17:50: 15000000 INFO @ Mon, 10 Aug 2020 13:17:50: 4000000 INFO @ Mon, 10 Aug 2020 13:17:54: 10000000 INFO @ Mon, 10 Aug 2020 13:17:56: 16000000 INFO @ Mon, 10 Aug 2020 13:17:56: 5000000 INFO @ Mon, 10 Aug 2020 13:18:00: 11000000 INFO @ Mon, 10 Aug 2020 13:18:02: 17000000 INFO @ Mon, 10 Aug 2020 13:18:02: 6000000 INFO @ Mon, 10 Aug 2020 13:18:05: 12000000 INFO @ Mon, 10 Aug 2020 13:18:07: 18000000 INFO @ Mon, 10 Aug 2020 13:18:08: 7000000 INFO @ Mon, 10 Aug 2020 13:18:11: 13000000 INFO @ Mon, 10 Aug 2020 13:18:13: 19000000 INFO @ Mon, 10 Aug 2020 13:18:13: 8000000 INFO @ Mon, 10 Aug 2020 13:18:17: 14000000 INFO @ Mon, 10 Aug 2020 13:18:19: 20000000 INFO @ Mon, 10 Aug 2020 13:18:19: 9000000 INFO @ Mon, 10 Aug 2020 13:18:23: 15000000 INFO @ Mon, 10 Aug 2020 13:18:25: 10000000 INFO @ Mon, 10 Aug 2020 13:18:25: 21000000 INFO @ Mon, 10 Aug 2020 13:18:29: 16000000 INFO @ Mon, 10 Aug 2020 13:18:31: 11000000 INFO @ Mon, 10 Aug 2020 13:18:31: 22000000 INFO @ Mon, 10 Aug 2020 13:18:34: 17000000 INFO @ Mon, 10 Aug 2020 13:18:36: 12000000 INFO @ Mon, 10 Aug 2020 13:18:37: 23000000 INFO @ Mon, 10 Aug 2020 13:18:40: 18000000 INFO @ Mon, 10 Aug 2020 13:18:42: 13000000 INFO @ Mon, 10 Aug 2020 13:18:42: 24000000 INFO @ Mon, 10 Aug 2020 13:18:46: 19000000 INFO @ Mon, 10 Aug 2020 13:18:48: 14000000 INFO @ Mon, 10 Aug 2020 13:18:48: 25000000 INFO @ Mon, 10 Aug 2020 13:18:52: 20000000 INFO @ Mon, 10 Aug 2020 13:18:54: 15000000 INFO @ Mon, 10 Aug 2020 13:18:54: 26000000 INFO @ Mon, 10 Aug 2020 13:18:58: 21000000 INFO @ Mon, 10 Aug 2020 13:18:59: 16000000 INFO @ Mon, 10 Aug 2020 13:19:00: 27000000 INFO @ Mon, 10 Aug 2020 13:19:04: 22000000 INFO @ Mon, 10 Aug 2020 13:19:05: 28000000 INFO @ Mon, 10 Aug 2020 13:19:05: 17000000 INFO @ Mon, 10 Aug 2020 13:19:10: 23000000 INFO @ Mon, 10 Aug 2020 13:19:11: 29000000 INFO @ Mon, 10 Aug 2020 13:19:11: 18000000 INFO @ Mon, 10 Aug 2020 13:19:15: 24000000 INFO @ Mon, 10 Aug 2020 13:19:17: 30000000 INFO @ Mon, 10 Aug 2020 13:19:17: 19000000 INFO @ Mon, 10 Aug 2020 13:19:21: 25000000 INFO @ Mon, 10 Aug 2020 13:19:22: 31000000 INFO @ Mon, 10 Aug 2020 13:19:23: 20000000 INFO @ Mon, 10 Aug 2020 13:19:27: 26000000 INFO @ Mon, 10 Aug 2020 13:19:28: 32000000 INFO @ Mon, 10 Aug 2020 13:19:29: 21000000 INFO @ Mon, 10 Aug 2020 13:19:32: 27000000 INFO @ Mon, 10 Aug 2020 13:19:34: 33000000 INFO @ Mon, 10 Aug 2020 13:19:35: 22000000 INFO @ Mon, 10 Aug 2020 13:19:38: 28000000 INFO @ Mon, 10 Aug 2020 13:19:40: 34000000 INFO @ Mon, 10 Aug 2020 13:19:40: 23000000 INFO @ Mon, 10 Aug 2020 13:19:44: 29000000 INFO @ Mon, 10 Aug 2020 13:19:45: 35000000 INFO @ Mon, 10 Aug 2020 13:19:46: 24000000 INFO @ Mon, 10 Aug 2020 13:19:50: 30000000 INFO @ Mon, 10 Aug 2020 13:19:51: 36000000 INFO @ Mon, 10 Aug 2020 13:19:52: 25000000 INFO @ Mon, 10 Aug 2020 13:19:55: 31000000 INFO @ Mon, 10 Aug 2020 13:19:57: 37000000 INFO @ Mon, 10 Aug 2020 13:19:58: 26000000 INFO @ Mon, 10 Aug 2020 13:20:01: 32000000 INFO @ Mon, 10 Aug 2020 13:20:03: 38000000 INFO @ Mon, 10 Aug 2020 13:20:03: 27000000 INFO @ Mon, 10 Aug 2020 13:20:07: 33000000 INFO @ Mon, 10 Aug 2020 13:20:09: 39000000 INFO @ Mon, 10 Aug 2020 13:20:09: 28000000 INFO @ Mon, 10 Aug 2020 13:20:12: 34000000 INFO @ Mon, 10 Aug 2020 13:20:14: 40000000 INFO @ Mon, 10 Aug 2020 13:20:15: 29000000 INFO @ Mon, 10 Aug 2020 13:20:18: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:20:18: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:20:18: #1 total tags in treatment: 40612834 INFO @ Mon, 10 Aug 2020 13:20:18: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:20:18: #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 13:20:18: 35000000 INFO @ Mon, 10 Aug 2020 13:20:19: #1 tags after filtering in treatment: 40612749 INFO @ Mon, 10 Aug 2020 13:20:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:20:19: #1 finished! INFO @ Mon, 10 Aug 2020 13:20:19: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:20:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:20:20: 30000000 INFO @ Mon, 10 Aug 2020 13:20:23: #2 number of paired peaks: 17241 INFO @ Mon, 10 Aug 2020 13:20:23: start model_add_line... INFO @ Mon, 10 Aug 2020 13:20:23: start X-correlation... INFO @ Mon, 10 Aug 2020 13:20:23: end of X-cor INFO @ Mon, 10 Aug 2020 13:20:23: #2 finished! INFO @ Mon, 10 Aug 2020 13:20:23: #2 predicted fragment length is 92 bps INFO @ Mon, 10 Aug 2020 13:20:23: #2 alternative fragment length(s) may be 92 bps INFO @ Mon, 10 Aug 2020 13:20:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.05_model.r WARNING @ Mon, 10 Aug 2020 13:20:23: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:20:23: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Mon, 10 Aug 2020 13:20:23: #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 13:20:23: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:20:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:20:24: 36000000 INFO @ Mon, 10 Aug 2020 13:20:26: 31000000 INFO @ Mon, 10 Aug 2020 13:20:30: 37000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 13:20:32: 32000000 INFO @ Mon, 10 Aug 2020 13:20:35: 38000000 INFO @ Mon, 10 Aug 2020 13:20:38: 33000000 INFO @ Mon, 10 Aug 2020 13:20:41: 39000000 INFO @ Mon, 10 Aug 2020 13:20:43: 34000000 INFO @ Mon, 10 Aug 2020 13:20:47: 40000000 INFO @ Mon, 10 Aug 2020 13:20:49: 35000000 INFO @ Mon, 10 Aug 2020 13:20:51: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:20:51: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:20:51: #1 total tags in treatment: 40612834 INFO @ Mon, 10 Aug 2020 13:20:51: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:20:51: #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 13:20:51: #1 tags after filtering in treatment: 40612749 INFO @ Mon, 10 Aug 2020 13:20:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:20:51: #1 finished! INFO @ Mon, 10 Aug 2020 13:20:51: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:20:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:20:54: 36000000 INFO @ Mon, 10 Aug 2020 13:20:55: #2 number of paired peaks: 17241 INFO @ Mon, 10 Aug 2020 13:20:55: start model_add_line... INFO @ Mon, 10 Aug 2020 13:20:55: start X-correlation... INFO @ Mon, 10 Aug 2020 13:20:55: end of X-cor INFO @ Mon, 10 Aug 2020 13:20:55: #2 finished! INFO @ Mon, 10 Aug 2020 13:20:55: #2 predicted fragment length is 92 bps INFO @ Mon, 10 Aug 2020 13:20:55: #2 alternative fragment length(s) may be 92 bps INFO @ Mon, 10 Aug 2020 13:20:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.10_model.r WARNING @ Mon, 10 Aug 2020 13:20:55: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:20:55: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Mon, 10 Aug 2020 13:20:55: #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 13:20:55: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:20:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:21:00: 37000000 INFO @ Mon, 10 Aug 2020 13:21:05: 38000000 INFO @ Mon, 10 Aug 2020 13:21:10: 39000000 INFO @ Mon, 10 Aug 2020 13:21:16: 40000000 INFO @ Mon, 10 Aug 2020 13:21:19: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:21:19: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:21:19: #1 total tags in treatment: 40612834 INFO @ Mon, 10 Aug 2020 13:21:19: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:21:19: #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 13:21:20: #1 tags after filtering in treatment: 40612749 INFO @ Mon, 10 Aug 2020 13:21:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:21:20: #1 finished! INFO @ Mon, 10 Aug 2020 13:21:20: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:21:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:21:24: #2 number of paired peaks: 17241 INFO @ Mon, 10 Aug 2020 13:21:24: start model_add_line... INFO @ Mon, 10 Aug 2020 13:21:24: start X-correlation... INFO @ Mon, 10 Aug 2020 13:21:24: end of X-cor INFO @ Mon, 10 Aug 2020 13:21:24: #2 finished! INFO @ Mon, 10 Aug 2020 13:21:24: #2 predicted fragment length is 92 bps INFO @ Mon, 10 Aug 2020 13:21:24: #2 alternative fragment length(s) may be 92 bps INFO @ Mon, 10 Aug 2020 13:21:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.20_model.r WARNING @ Mon, 10 Aug 2020 13:21:24: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:21:24: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Mon, 10 Aug 2020 13:21:24: #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 13:21:24: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:21:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:21:49: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 13:22:20: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:22:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.05_peaks.xls INFO @ Mon, 10 Aug 2020 13:22:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:22:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.05_summits.bed INFO @ Mon, 10 Aug 2020 13:22:36: Done! pass1 - making usageList (88 chroms): 1 millis pass2 - checking and writing primary data (3523 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:22:49: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:23:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.10_peaks.xls INFO @ Mon, 10 Aug 2020 13:23:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:23:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.10_summits.bed INFO @ Mon, 10 Aug 2020 13:23:06: Done! pass1 - making usageList (69 chroms): 1 millis pass2 - checking and writing primary data (1556 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:23:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.20_peaks.xls INFO @ Mon, 10 Aug 2020 13:23:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:23:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047577/SRX8047577.20_summits.bed INFO @ Mon, 10 Aug 2020 13:23:35: Done! pass1 - making usageList (46 chroms): 1 millis pass2 - checking and writing primary data (636 records, 4 fields): 3 millis CompletedMACS2peakCalling