Job ID = 2001537 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,264,465 reads read : 27,264,465 reads written : 27,264,465 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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:28 27264465 reads; of these: 27264465 (100.00%) were unpaired; of these: 548647 (2.01%) aligned 0 times 23417720 (85.89%) aligned exactly 1 time 3298098 (12.10%) aligned >1 times 97.99% overall alignment rate Time searching: 00:06:30 Overall time: 00:06:30 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 8 files... [bam_rmdupse_core] 10942100 / 26715818 = 0.4096 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 04:44:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.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 @ Fri, 05 Jul 2019 04:44:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:44:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:44:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.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 @ Fri, 05 Jul 2019 04:44:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:44:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:44:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.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 @ Fri, 05 Jul 2019 04:44:03: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:44:03: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:44:08: 1000000 INFO @ Fri, 05 Jul 2019 04:44:11: 1000000 INFO @ Fri, 05 Jul 2019 04:44:11: 1000000 INFO @ Fri, 05 Jul 2019 04:44:14: 2000000 INFO @ Fri, 05 Jul 2019 04:44:18: 2000000 INFO @ Fri, 05 Jul 2019 04:44:18: 2000000 INFO @ Fri, 05 Jul 2019 04:44:20: 3000000 INFO @ Fri, 05 Jul 2019 04:44:25: 3000000 INFO @ Fri, 05 Jul 2019 04:44:26: 3000000 INFO @ Fri, 05 Jul 2019 04:44:27: 4000000 INFO @ Fri, 05 Jul 2019 04:44:32: 4000000 INFO @ Fri, 05 Jul 2019 04:44:33: 5000000 INFO @ Fri, 05 Jul 2019 04:44:33: 4000000 INFO @ Fri, 05 Jul 2019 04:44:39: 6000000 INFO @ Fri, 05 Jul 2019 04:44:39: 5000000 INFO @ Fri, 05 Jul 2019 04:44:41: 5000000 INFO @ Fri, 05 Jul 2019 04:44:45: 7000000 INFO @ Fri, 05 Jul 2019 04:44:46: 6000000 INFO @ Fri, 05 Jul 2019 04:44:49: 6000000 INFO @ Fri, 05 Jul 2019 04:44:51: 8000000 INFO @ Fri, 05 Jul 2019 04:44:53: 7000000 INFO @ Fri, 05 Jul 2019 04:44:56: 7000000 INFO @ Fri, 05 Jul 2019 04:44:58: 9000000 INFO @ Fri, 05 Jul 2019 04:45:00: 8000000 INFO @ Fri, 05 Jul 2019 04:45:04: 8000000 INFO @ Fri, 05 Jul 2019 04:45:04: 10000000 INFO @ Fri, 05 Jul 2019 04:45:07: 9000000 INFO @ Fri, 05 Jul 2019 04:45:10: 11000000 INFO @ Fri, 05 Jul 2019 04:45:11: 9000000 INFO @ Fri, 05 Jul 2019 04:45:15: 10000000 INFO @ Fri, 05 Jul 2019 04:45:16: 12000000 INFO @ Fri, 05 Jul 2019 04:45:19: 10000000 INFO @ Fri, 05 Jul 2019 04:45:22: 11000000 INFO @ Fri, 05 Jul 2019 04:45:23: 13000000 INFO @ Fri, 05 Jul 2019 04:45:27: 11000000 INFO @ Fri, 05 Jul 2019 04:45:29: 12000000 INFO @ Fri, 05 Jul 2019 04:45:29: 14000000 INFO @ Fri, 05 Jul 2019 04:45:34: 12000000 INFO @ Fri, 05 Jul 2019 04:45:35: 15000000 INFO @ Fri, 05 Jul 2019 04:45:36: 13000000 INFO @ Fri, 05 Jul 2019 04:45:40: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:45:40: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:45:40: #1 total tags in treatment: 15773718 INFO @ Fri, 05 Jul 2019 04:45:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:45:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 04:45:41: #1 tags after filtering in treatment: 15773479 INFO @ Fri, 05 Jul 2019 04:45:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:45:41: #1 finished! INFO @ Fri, 05 Jul 2019 04:45:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:45:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:45:42: 13000000 INFO @ Fri, 05 Jul 2019 04:45:43: 14000000 INFO @ Fri, 05 Jul 2019 04:45:45: #2 number of paired peaks: 51259 INFO @ Fri, 05 Jul 2019 04:45:45: start model_add_line... INFO @ Fri, 05 Jul 2019 04:45:45: start X-correlation... INFO @ Fri, 05 Jul 2019 04:45:45: end of X-cor INFO @ Fri, 05 Jul 2019 04:45:45: #2 finished! INFO @ Fri, 05 Jul 2019 04:45:45: #2 predicted fragment length is 139 bps INFO @ Fri, 05 Jul 2019 04:45:45: #2 alternative fragment length(s) may be 4,139 bps INFO @ Fri, 05 Jul 2019 04:45:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.05_model.r INFO @ Fri, 05 Jul 2019 04:45:45: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:45:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:45:49: 14000000 INFO @ Fri, 05 Jul 2019 04:45:50: 15000000 INFO @ Fri, 05 Jul 2019 04:45:55: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:45:55: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:45:55: #1 total tags in treatment: 15773718 INFO @ Fri, 05 Jul 2019 04:45:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:45:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 04:45:56: #1 tags after filtering in treatment: 15773479 INFO @ Fri, 05 Jul 2019 04:45:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:45:56: #1 finished! INFO @ Fri, 05 Jul 2019 04:45:56: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:45:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:45:57: 15000000 INFO @ Fri, 05 Jul 2019 04:46:00: #2 number of paired peaks: 51259 INFO @ Fri, 05 Jul 2019 04:46:00: start model_add_line... INFO @ Fri, 05 Jul 2019 04:46:00: start X-correlation... INFO @ Fri, 05 Jul 2019 04:46:00: end of X-cor INFO @ Fri, 05 Jul 2019 04:46:00: #2 finished! INFO @ Fri, 05 Jul 2019 04:46:00: #2 predicted fragment length is 139 bps INFO @ Fri, 05 Jul 2019 04:46:00: #2 alternative fragment length(s) may be 4,139 bps INFO @ Fri, 05 Jul 2019 04:46:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.20_model.r INFO @ Fri, 05 Jul 2019 04:46:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:46:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:46:03: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:46:03: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:46:03: #1 total tags in treatment: 15773718 INFO @ Fri, 05 Jul 2019 04:46:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:46:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 04:46:03: #1 tags after filtering in treatment: 15773479 INFO @ Fri, 05 Jul 2019 04:46:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:46:03: #1 finished! INFO @ Fri, 05 Jul 2019 04:46:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:46:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:46:07: #2 number of paired peaks: 51259 INFO @ Fri, 05 Jul 2019 04:46:07: start model_add_line... INFO @ Fri, 05 Jul 2019 04:46:08: start X-correlation... INFO @ Fri, 05 Jul 2019 04:46:08: end of X-cor INFO @ Fri, 05 Jul 2019 04:46:08: #2 finished! INFO @ Fri, 05 Jul 2019 04:46:08: #2 predicted fragment length is 139 bps INFO @ Fri, 05 Jul 2019 04:46:08: #2 alternative fragment length(s) may be 4,139 bps INFO @ Fri, 05 Jul 2019 04:46:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.10_model.r INFO @ Fri, 05 Jul 2019 04:46:08: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:46:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:46:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:46:52: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:46:59: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:46:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:47:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:47:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.05_summits.bed INFO @ Fri, 05 Jul 2019 04:47:00: Done! pass1 - making usageList (132 chroms): 13 millis pass2 - checking and writing primary data (42829 records, 4 fields): 58 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:47:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:47:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:47:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.20_summits.bed INFO @ Fri, 05 Jul 2019 04:47:19: Done! pass1 - making usageList (83 chroms): 6 millis pass2 - checking and writing primary data (22269 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:47:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:47:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:47:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101880/ERX101880.10_summits.bed INFO @ Fri, 05 Jul 2019 04:47:27: Done! pass1 - making usageList (109 chroms): 10 millis pass2 - checking and writing primary data (33711 records, 4 fields): 46 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。