Job ID = 5790657 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 54,156,347 reads read : 108,312,694 reads written : 54,156,347 reads 0-length : 54,156,347 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:29:24 54156347 reads; of these: 54156347 (100.00%) were unpaired; of these: 7409099 (13.68%) aligned 0 times 37496591 (69.24%) aligned exactly 1 time 9250657 (17.08%) aligned >1 times 86.32% overall alignment rate Time searching: 00:29:25 Overall time: 00:29:25 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] 7759930 / 46747248 = 0.1660 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 @ Wed, 22 Apr 2020 05:59:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.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 @ Wed, 22 Apr 2020 05:59:45: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:59:45: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:59:51: 1000000 INFO @ Wed, 22 Apr 2020 05:59:57: 2000000 INFO @ Wed, 22 Apr 2020 06:00:02: 3000000 INFO @ Wed, 22 Apr 2020 06:00:08: 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 @ Wed, 22 Apr 2020 06:00:13: 5000000 INFO @ Wed, 22 Apr 2020 06:00:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.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 @ Wed, 22 Apr 2020 06:00:15: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:00:15: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:00:19: 6000000 INFO @ Wed, 22 Apr 2020 06:00:20: 1000000 INFO @ Wed, 22 Apr 2020 06:00:24: 7000000 INFO @ Wed, 22 Apr 2020 06:00:25: 2000000 INFO @ Wed, 22 Apr 2020 06:00:30: 3000000 INFO @ Wed, 22 Apr 2020 06:00:30: 8000000 INFO @ Wed, 22 Apr 2020 06:00:35: 4000000 INFO @ Wed, 22 Apr 2020 06:00:36: 9000000 INFO @ Wed, 22 Apr 2020 06:00:40: 5000000 BedGraph に変換中... INFO @ Wed, 22 Apr 2020 06:00:42: 10000000 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 @ Wed, 22 Apr 2020 06:00:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.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 @ Wed, 22 Apr 2020 06:00:44: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:00:44: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:00:46: 6000000 INFO @ Wed, 22 Apr 2020 06:00:48: 11000000 INFO @ Wed, 22 Apr 2020 06:00:50: 1000000 INFO @ Wed, 22 Apr 2020 06:00:51: 7000000 INFO @ Wed, 22 Apr 2020 06:00:53: 12000000 INFO @ Wed, 22 Apr 2020 06:00:55: 2000000 INFO @ Wed, 22 Apr 2020 06:00:56: 8000000 INFO @ Wed, 22 Apr 2020 06:00:59: 13000000 INFO @ Wed, 22 Apr 2020 06:01:00: 3000000 INFO @ Wed, 22 Apr 2020 06:01:01: 9000000 INFO @ Wed, 22 Apr 2020 06:01:05: 14000000 INFO @ Wed, 22 Apr 2020 06:01:05: 4000000 INFO @ Wed, 22 Apr 2020 06:01:06: 10000000 INFO @ Wed, 22 Apr 2020 06:01:10: 5000000 INFO @ Wed, 22 Apr 2020 06:01:11: 15000000 INFO @ Wed, 22 Apr 2020 06:01:11: 11000000 INFO @ Wed, 22 Apr 2020 06:01:15: 6000000 INFO @ Wed, 22 Apr 2020 06:01:16: 16000000 INFO @ Wed, 22 Apr 2020 06:01:17: 12000000 INFO @ Wed, 22 Apr 2020 06:01:21: 7000000 INFO @ Wed, 22 Apr 2020 06:01:22: 13000000 INFO @ Wed, 22 Apr 2020 06:01:22: 17000000 INFO @ Wed, 22 Apr 2020 06:01:26: 8000000 INFO @ Wed, 22 Apr 2020 06:01:27: 14000000 INFO @ Wed, 22 Apr 2020 06:01:28: 18000000 INFO @ Wed, 22 Apr 2020 06:01:31: 9000000 INFO @ Wed, 22 Apr 2020 06:01:32: 15000000 INFO @ Wed, 22 Apr 2020 06:01:34: 19000000 INFO @ Wed, 22 Apr 2020 06:01:36: 10000000 INFO @ Wed, 22 Apr 2020 06:01:37: 16000000 INFO @ Wed, 22 Apr 2020 06:01:40: 20000000 INFO @ Wed, 22 Apr 2020 06:01:41: 11000000 INFO @ Wed, 22 Apr 2020 06:01:42: 17000000 INFO @ Wed, 22 Apr 2020 06:01:45: 21000000 INFO @ Wed, 22 Apr 2020 06:01:46: 12000000 INFO @ Wed, 22 Apr 2020 06:01:48: 18000000 INFO @ Wed, 22 Apr 2020 06:01:51: 22000000 INFO @ Wed, 22 Apr 2020 06:01:52: 13000000 INFO @ Wed, 22 Apr 2020 06:01:53: 19000000 INFO @ Wed, 22 Apr 2020 06:01:57: 14000000 INFO @ Wed, 22 Apr 2020 06:01:57: 23000000 INFO @ Wed, 22 Apr 2020 06:01:58: 20000000 INFO @ Wed, 22 Apr 2020 06:02:02: 15000000 INFO @ Wed, 22 Apr 2020 06:02:03: 24000000 INFO @ Wed, 22 Apr 2020 06:02:03: 21000000 INFO @ Wed, 22 Apr 2020 06:02:07: 16000000 INFO @ Wed, 22 Apr 2020 06:02:08: 22000000 INFO @ Wed, 22 Apr 2020 06:02:08: 25000000 INFO @ Wed, 22 Apr 2020 06:02:12: 17000000 INFO @ Wed, 22 Apr 2020 06:02:14: 23000000 INFO @ Wed, 22 Apr 2020 06:02:14: 26000000 INFO @ Wed, 22 Apr 2020 06:02:18: 18000000 INFO @ Wed, 22 Apr 2020 06:02:19: 24000000 INFO @ Wed, 22 Apr 2020 06:02:20: 27000000 INFO @ Wed, 22 Apr 2020 06:02:23: 19000000 INFO @ Wed, 22 Apr 2020 06:02:24: 25000000 INFO @ Wed, 22 Apr 2020 06:02:26: 28000000 INFO @ Wed, 22 Apr 2020 06:02:28: 20000000 INFO @ Wed, 22 Apr 2020 06:02:29: 26000000 INFO @ Wed, 22 Apr 2020 06:02:32: 29000000 INFO @ Wed, 22 Apr 2020 06:02:33: 21000000 INFO @ Wed, 22 Apr 2020 06:02:34: 27000000 INFO @ Wed, 22 Apr 2020 06:02:37: 30000000 INFO @ Wed, 22 Apr 2020 06:02:38: 22000000 INFO @ Wed, 22 Apr 2020 06:02:39: 28000000 INFO @ Wed, 22 Apr 2020 06:02:43: 31000000 INFO @ Wed, 22 Apr 2020 06:02:44: 23000000 INFO @ Wed, 22 Apr 2020 06:02:45: 29000000 INFO @ Wed, 22 Apr 2020 06:02:49: 24000000 INFO @ Wed, 22 Apr 2020 06:02:49: 32000000 INFO @ Wed, 22 Apr 2020 06:02:50: 30000000 INFO @ Wed, 22 Apr 2020 06:02:54: 25000000 INFO @ Wed, 22 Apr 2020 06:02:55: 33000000 INFO @ Wed, 22 Apr 2020 06:02:55: 31000000 INFO @ Wed, 22 Apr 2020 06:02:59: 26000000 INFO @ Wed, 22 Apr 2020 06:03:00: 32000000 INFO @ Wed, 22 Apr 2020 06:03:00: 34000000 INFO @ Wed, 22 Apr 2020 06:03:04: 27000000 INFO @ Wed, 22 Apr 2020 06:03:05: 33000000 INFO @ Wed, 22 Apr 2020 06:03:06: 35000000 INFO @ Wed, 22 Apr 2020 06:03:09: 28000000 INFO @ Wed, 22 Apr 2020 06:03:10: 34000000 INFO @ Wed, 22 Apr 2020 06:03:12: 36000000 INFO @ Wed, 22 Apr 2020 06:03:15: 29000000 INFO @ Wed, 22 Apr 2020 06:03:15: 35000000 INFO @ Wed, 22 Apr 2020 06:03:17: 37000000 INFO @ Wed, 22 Apr 2020 06:03:20: 30000000 INFO @ Wed, 22 Apr 2020 06:03:20: 36000000 INFO @ Wed, 22 Apr 2020 06:03:23: 38000000 INFO @ Wed, 22 Apr 2020 06:03:25: 31000000 INFO @ Wed, 22 Apr 2020 06:03:26: 37000000 INFO @ Wed, 22 Apr 2020 06:03:29: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 06:03:29: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 06:03:29: #1 total tags in treatment: 38987318 INFO @ Wed, 22 Apr 2020 06:03:29: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:03:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:03:30: #1 tags after filtering in treatment: 38987210 INFO @ Wed, 22 Apr 2020 06:03:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:03:30: #1 finished! INFO @ Wed, 22 Apr 2020 06:03:30: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:03:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:03:30: 32000000 INFO @ Wed, 22 Apr 2020 06:03:31: 38000000 INFO @ Wed, 22 Apr 2020 06:03:35: #2 number of paired peaks: 70335 INFO @ Wed, 22 Apr 2020 06:03:35: start model_add_line... INFO @ Wed, 22 Apr 2020 06:03:35: 33000000 INFO @ Wed, 22 Apr 2020 06:03:36: start X-correlation... INFO @ Wed, 22 Apr 2020 06:03:36: end of X-cor INFO @ Wed, 22 Apr 2020 06:03:36: #2 finished! INFO @ Wed, 22 Apr 2020 06:03:36: #2 predicted fragment length is 165 bps INFO @ Wed, 22 Apr 2020 06:03:36: #2 alternative fragment length(s) may be 165 bps INFO @ Wed, 22 Apr 2020 06:03:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.05_model.r INFO @ Wed, 22 Apr 2020 06:03:36: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:03:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:03:36: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 06:03:36: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 06:03:36: #1 total tags in treatment: 38987318 INFO @ Wed, 22 Apr 2020 06:03:36: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:03:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:03:37: #1 tags after filtering in treatment: 38987210 INFO @ Wed, 22 Apr 2020 06:03:37: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:03:37: #1 finished! INFO @ Wed, 22 Apr 2020 06:03:37: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:03:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:03:40: 34000000 INFO @ Wed, 22 Apr 2020 06:03:42: #2 number of paired peaks: 70335 INFO @ Wed, 22 Apr 2020 06:03:42: start model_add_line... INFO @ Wed, 22 Apr 2020 06:03:42: start X-correlation... INFO @ Wed, 22 Apr 2020 06:03:42: end of X-cor INFO @ Wed, 22 Apr 2020 06:03:43: #2 finished! INFO @ Wed, 22 Apr 2020 06:03:43: #2 predicted fragment length is 165 bps INFO @ Wed, 22 Apr 2020 06:03:43: #2 alternative fragment length(s) may be 165 bps INFO @ Wed, 22 Apr 2020 06:03:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.10_model.r INFO @ Wed, 22 Apr 2020 06:03:43: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:03:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:03:45: 35000000 INFO @ Wed, 22 Apr 2020 06:03:50: 36000000 INFO @ Wed, 22 Apr 2020 06:03:55: 37000000 INFO @ Wed, 22 Apr 2020 06:03:59: 38000000 INFO @ Wed, 22 Apr 2020 06:04:04: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 06:04:04: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 06:04:04: #1 total tags in treatment: 38987318 INFO @ Wed, 22 Apr 2020 06:04:04: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:04:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:04:05: #1 tags after filtering in treatment: 38987210 INFO @ Wed, 22 Apr 2020 06:04:05: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:04:05: #1 finished! INFO @ Wed, 22 Apr 2020 06:04:05: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:04:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:04:10: #2 number of paired peaks: 70335 INFO @ Wed, 22 Apr 2020 06:04:10: start model_add_line... INFO @ Wed, 22 Apr 2020 06:04:11: start X-correlation... INFO @ Wed, 22 Apr 2020 06:04:11: end of X-cor INFO @ Wed, 22 Apr 2020 06:04:11: #2 finished! INFO @ Wed, 22 Apr 2020 06:04:11: #2 predicted fragment length is 165 bps INFO @ Wed, 22 Apr 2020 06:04:11: #2 alternative fragment length(s) may be 165 bps INFO @ Wed, 22 Apr 2020 06:04:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.20_model.r INFO @ Wed, 22 Apr 2020 06:04:11: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:04:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:05:07: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:05:09: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:05:43: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:05:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:05:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:05:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.05_summits.bed INFO @ Wed, 22 Apr 2020 06:05:56: Done! INFO @ Wed, 22 Apr 2020 06:05:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:05:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:05:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.10_summits.bed INFO @ Wed, 22 Apr 2020 06:05:57: Done! pass1 - making usageList (118 chroms): 2 millis pass2 - checking and writing primary data (17595 records, 4 fields): 19 millis CompletedMACS2peakCalling pass1 - making usageList (102 chroms): 3 millis pass2 - checking and writing primary data (13556 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:06:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:06:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:06:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5433268/SRX5433268.20_summits.bed INFO @ Wed, 22 Apr 2020 06:06:33: Done! pass1 - making usageList (83 chroms): 5 millis pass2 - checking and writing primary data (9552 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。