Job ID = 5790674 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 44,977,671 reads read : 44,977,671 reads written : 44,977,671 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR8982411.sra.cache’: 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:27 44977671 reads; of these: 44977671 (100.00%) were unpaired; of these: 6465041 (14.37%) aligned 0 times 29488679 (65.56%) aligned exactly 1 time 9023951 (20.06%) aligned >1 times 85.63% overall alignment rate Time searching: 00:14:28 Overall time: 00:14:28 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 12 files... [bam_rmdupse_core] 6254933 / 38512630 = 0.1624 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 06:17:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.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 06:17:34: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:17:34: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:17:39: 1000000 INFO @ Wed, 22 Apr 2020 06:17:44: 2000000 INFO @ Wed, 22 Apr 2020 06:17:49: 3000000 INFO @ Wed, 22 Apr 2020 06:17:54: 4000000 INFO @ Wed, 22 Apr 2020 06:17:59: 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 @ Wed, 22 Apr 2020 06:18:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.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 06:18:04: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:18:04: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:18:04: 6000000 INFO @ Wed, 22 Apr 2020 06:18:10: 7000000 INFO @ Wed, 22 Apr 2020 06:18:10: 1000000 INFO @ Wed, 22 Apr 2020 06:18:15: 8000000 INFO @ Wed, 22 Apr 2020 06:18:15: 2000000 INFO @ Wed, 22 Apr 2020 06:18:21: 9000000 INFO @ Wed, 22 Apr 2020 06:18:21: 3000000 INFO @ Wed, 22 Apr 2020 06:18:26: 10000000 INFO @ Wed, 22 Apr 2020 06:18:27: 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 @ Wed, 22 Apr 2020 06:18:32: 11000000 INFO @ Wed, 22 Apr 2020 06:18:32: 5000000 INFO @ Wed, 22 Apr 2020 06:18:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.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 06:18:34: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:18:34: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:18:38: 12000000 INFO @ Wed, 22 Apr 2020 06:18:38: 6000000 INFO @ Wed, 22 Apr 2020 06:18:39: 1000000 INFO @ Wed, 22 Apr 2020 06:18:43: 13000000 INFO @ Wed, 22 Apr 2020 06:18:44: 7000000 INFO @ Wed, 22 Apr 2020 06:18:45: 2000000 INFO @ Wed, 22 Apr 2020 06:18:49: 14000000 INFO @ Wed, 22 Apr 2020 06:18:49: 8000000 INFO @ Wed, 22 Apr 2020 06:18:51: 3000000 INFO @ Wed, 22 Apr 2020 06:18:54: 15000000 INFO @ Wed, 22 Apr 2020 06:18:55: 9000000 INFO @ Wed, 22 Apr 2020 06:18:56: 4000000 INFO @ Wed, 22 Apr 2020 06:19:00: 16000000 INFO @ Wed, 22 Apr 2020 06:19:01: 10000000 INFO @ Wed, 22 Apr 2020 06:19:02: 5000000 INFO @ Wed, 22 Apr 2020 06:19:06: 17000000 INFO @ Wed, 22 Apr 2020 06:19:07: 11000000 INFO @ Wed, 22 Apr 2020 06:19:08: 6000000 INFO @ Wed, 22 Apr 2020 06:19:11: 18000000 INFO @ Wed, 22 Apr 2020 06:19:12: 12000000 INFO @ Wed, 22 Apr 2020 06:19:13: 7000000 INFO @ Wed, 22 Apr 2020 06:19:17: 19000000 INFO @ Wed, 22 Apr 2020 06:19:18: 13000000 INFO @ Wed, 22 Apr 2020 06:19:19: 8000000 INFO @ Wed, 22 Apr 2020 06:19:22: 20000000 INFO @ Wed, 22 Apr 2020 06:19:24: 14000000 INFO @ Wed, 22 Apr 2020 06:19:25: 9000000 INFO @ Wed, 22 Apr 2020 06:19:28: 21000000 INFO @ Wed, 22 Apr 2020 06:19:29: 15000000 INFO @ Wed, 22 Apr 2020 06:19:30: 10000000 INFO @ Wed, 22 Apr 2020 06:19:34: 22000000 INFO @ Wed, 22 Apr 2020 06:19:35: 16000000 INFO @ Wed, 22 Apr 2020 06:19:36: 11000000 INFO @ Wed, 22 Apr 2020 06:19:39: 23000000 INFO @ Wed, 22 Apr 2020 06:19:41: 17000000 INFO @ Wed, 22 Apr 2020 06:19:42: 12000000 INFO @ Wed, 22 Apr 2020 06:19:45: 24000000 INFO @ Wed, 22 Apr 2020 06:19:46: 18000000 INFO @ Wed, 22 Apr 2020 06:19:47: 13000000 INFO @ Wed, 22 Apr 2020 06:19:50: 25000000 INFO @ Wed, 22 Apr 2020 06:19:52: 19000000 INFO @ Wed, 22 Apr 2020 06:19:53: 14000000 INFO @ Wed, 22 Apr 2020 06:19:56: 26000000 INFO @ Wed, 22 Apr 2020 06:19:57: 20000000 INFO @ Wed, 22 Apr 2020 06:19:58: 15000000 INFO @ Wed, 22 Apr 2020 06:20:01: 27000000 INFO @ Wed, 22 Apr 2020 06:20:03: 21000000 INFO @ Wed, 22 Apr 2020 06:20:04: 16000000 INFO @ Wed, 22 Apr 2020 06:20:07: 28000000 INFO @ Wed, 22 Apr 2020 06:20:08: 22000000 INFO @ Wed, 22 Apr 2020 06:20:09: 17000000 INFO @ Wed, 22 Apr 2020 06:20:12: 29000000 INFO @ Wed, 22 Apr 2020 06:20:14: 23000000 INFO @ Wed, 22 Apr 2020 06:20:15: 18000000 INFO @ Wed, 22 Apr 2020 06:20:18: 30000000 INFO @ Wed, 22 Apr 2020 06:20:19: 24000000 INFO @ Wed, 22 Apr 2020 06:20:20: 19000000 INFO @ Wed, 22 Apr 2020 06:20:23: 31000000 INFO @ Wed, 22 Apr 2020 06:20:25: 25000000 INFO @ Wed, 22 Apr 2020 06:20:26: 20000000 INFO @ Wed, 22 Apr 2020 06:20:29: 32000000 INFO @ Wed, 22 Apr 2020 06:20:30: 26000000 INFO @ Wed, 22 Apr 2020 06:20:31: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:20:31: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:20:31: #1 total tags in treatment: 32257697 INFO @ Wed, 22 Apr 2020 06:20:31: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:20:31: #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 06:20:31: #1 tags after filtering in treatment: 32257593 INFO @ Wed, 22 Apr 2020 06:20:31: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:20:31: #1 finished! INFO @ Wed, 22 Apr 2020 06:20:31: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:20:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:20:31: 21000000 INFO @ Wed, 22 Apr 2020 06:20:36: 27000000 INFO @ Wed, 22 Apr 2020 06:20:36: #2 number of paired peaks: 58703 INFO @ Wed, 22 Apr 2020 06:20:36: start model_add_line... INFO @ Wed, 22 Apr 2020 06:20:36: start X-correlation... INFO @ Wed, 22 Apr 2020 06:20:36: end of X-cor INFO @ Wed, 22 Apr 2020 06:20:36: #2 finished! INFO @ Wed, 22 Apr 2020 06:20:36: #2 predicted fragment length is 182 bps INFO @ Wed, 22 Apr 2020 06:20:36: #2 alternative fragment length(s) may be 182 bps INFO @ Wed, 22 Apr 2020 06:20:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.05_model.r INFO @ Wed, 22 Apr 2020 06:20:36: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:20:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:20:37: 22000000 INFO @ Wed, 22 Apr 2020 06:20:41: 28000000 INFO @ Wed, 22 Apr 2020 06:20:42: 23000000 INFO @ Wed, 22 Apr 2020 06:20:47: 29000000 INFO @ Wed, 22 Apr 2020 06:20:48: 24000000 INFO @ Wed, 22 Apr 2020 06:20:52: 30000000 INFO @ Wed, 22 Apr 2020 06:20:53: 25000000 INFO @ Wed, 22 Apr 2020 06:20:57: 31000000 INFO @ Wed, 22 Apr 2020 06:20:59: 26000000 INFO @ Wed, 22 Apr 2020 06:21:03: 32000000 INFO @ Wed, 22 Apr 2020 06:21:04: 27000000 INFO @ Wed, 22 Apr 2020 06:21:05: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:21:05: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:21:05: #1 total tags in treatment: 32257697 INFO @ Wed, 22 Apr 2020 06:21:05: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:21:05: #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 06:21:05: #1 tags after filtering in treatment: 32257593 INFO @ Wed, 22 Apr 2020 06:21:05: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:21:05: #1 finished! INFO @ Wed, 22 Apr 2020 06:21:05: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:21:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:21:10: 28000000 INFO @ Wed, 22 Apr 2020 06:21:10: #2 number of paired peaks: 58703 INFO @ Wed, 22 Apr 2020 06:21:10: start model_add_line... INFO @ Wed, 22 Apr 2020 06:21:10: start X-correlation... INFO @ Wed, 22 Apr 2020 06:21:10: end of X-cor INFO @ Wed, 22 Apr 2020 06:21:10: #2 finished! INFO @ Wed, 22 Apr 2020 06:21:10: #2 predicted fragment length is 182 bps INFO @ Wed, 22 Apr 2020 06:21:10: #2 alternative fragment length(s) may be 182 bps INFO @ Wed, 22 Apr 2020 06:21:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.10_model.r INFO @ Wed, 22 Apr 2020 06:21:10: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:21:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:21:15: 29000000 INFO @ Wed, 22 Apr 2020 06:21:21: 30000000 INFO @ Wed, 22 Apr 2020 06:21:26: 31000000 INFO @ Wed, 22 Apr 2020 06:21:31: 32000000 INFO @ Wed, 22 Apr 2020 06:21:33: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:21:33: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:21:33: #1 total tags in treatment: 32257697 INFO @ Wed, 22 Apr 2020 06:21:33: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:21:33: #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 06:21:33: #1 tags after filtering in treatment: 32257593 INFO @ Wed, 22 Apr 2020 06:21:33: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:21:33: #1 finished! INFO @ Wed, 22 Apr 2020 06:21:33: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:21:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:21:38: #2 number of paired peaks: 58703 INFO @ Wed, 22 Apr 2020 06:21:38: start model_add_line... INFO @ Wed, 22 Apr 2020 06:21:38: start X-correlation... INFO @ Wed, 22 Apr 2020 06:21:38: end of X-cor INFO @ Wed, 22 Apr 2020 06:21:38: #2 finished! INFO @ Wed, 22 Apr 2020 06:21:38: #2 predicted fragment length is 182 bps INFO @ Wed, 22 Apr 2020 06:21:38: #2 alternative fragment length(s) may be 182 bps INFO @ Wed, 22 Apr 2020 06:21:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.20_model.r INFO @ Wed, 22 Apr 2020 06:21:38: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:21:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:21:50: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:22:24: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:22:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:22:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:22:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.05_summits.bed INFO @ Wed, 22 Apr 2020 06:22:31: Done! pass1 - making usageList (134 chroms): 5 millis pass2 - checking and writing primary data (33934 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:22:59: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:23:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:23:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:23:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.10_summits.bed INFO @ Wed, 22 Apr 2020 06:23:05: Done! pass1 - making usageList (101 chroms): 3 millis pass2 - checking and writing primary data (20094 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:23:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:23:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:23:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761709/SRX5761709.20_summits.bed INFO @ Wed, 22 Apr 2020 06:23:41: Done! pass1 - making usageList (71 chroms): 2 millis pass2 - checking and writing primary data (12643 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。