Job ID = 2001597 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,310,275 reads read : 23,310,275 reads written : 23,310,275 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:54 23310275 reads; of these: 23310275 (100.00%) were unpaired; of these: 489482 (2.10%) aligned 0 times 20579891 (88.29%) aligned exactly 1 time 2240902 (9.61%) aligned >1 times 97.90% overall alignment rate Time searching: 00:04:57 Overall time: 00:04:57 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] 10800273 / 22820793 = 0.4733 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 05:52:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.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 05:52:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:52:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:52:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.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 05:52:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:52:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:52:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.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 05:52:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:52:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:52:23: 1000000 INFO @ Fri, 05 Jul 2019 05:52:24: 1000000 INFO @ Fri, 05 Jul 2019 05:52:25: 1000000 INFO @ Fri, 05 Jul 2019 05:52:30: 2000000 INFO @ Fri, 05 Jul 2019 05:52:30: 2000000 INFO @ Fri, 05 Jul 2019 05:52:33: 2000000 INFO @ Fri, 05 Jul 2019 05:52:37: 3000000 INFO @ Fri, 05 Jul 2019 05:52:37: 3000000 INFO @ Fri, 05 Jul 2019 05:52:41: 3000000 INFO @ Fri, 05 Jul 2019 05:52:43: 4000000 INFO @ Fri, 05 Jul 2019 05:52:44: 4000000 INFO @ Fri, 05 Jul 2019 05:52:49: 5000000 INFO @ Fri, 05 Jul 2019 05:52:49: 4000000 INFO @ Fri, 05 Jul 2019 05:52:51: 5000000 INFO @ Fri, 05 Jul 2019 05:52:55: 6000000 INFO @ Fri, 05 Jul 2019 05:52:57: 5000000 INFO @ Fri, 05 Jul 2019 05:52:58: 6000000 INFO @ Fri, 05 Jul 2019 05:53:02: 7000000 INFO @ Fri, 05 Jul 2019 05:53:05: 7000000 INFO @ Fri, 05 Jul 2019 05:53:05: 6000000 INFO @ Fri, 05 Jul 2019 05:53:08: 8000000 INFO @ Fri, 05 Jul 2019 05:53:12: 8000000 INFO @ Fri, 05 Jul 2019 05:53:13: 7000000 INFO @ Fri, 05 Jul 2019 05:53:16: 9000000 INFO @ Fri, 05 Jul 2019 05:53:19: 9000000 INFO @ Fri, 05 Jul 2019 05:53:23: 8000000 INFO @ Fri, 05 Jul 2019 05:53:25: 10000000 INFO @ Fri, 05 Jul 2019 05:53:26: 10000000 INFO @ Fri, 05 Jul 2019 05:53:32: 9000000 INFO @ Fri, 05 Jul 2019 05:53:32: 11000000 INFO @ Fri, 05 Jul 2019 05:53:36: 11000000 INFO @ Fri, 05 Jul 2019 05:53:39: 12000000 INFO @ Fri, 05 Jul 2019 05:53:40: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:53:40: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:53:40: #1 total tags in treatment: 12020520 INFO @ Fri, 05 Jul 2019 05:53:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:53:40: #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 05:53:40: #1 tags after filtering in treatment: 12020219 INFO @ Fri, 05 Jul 2019 05:53:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:53:40: #1 finished! INFO @ Fri, 05 Jul 2019 05:53:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:53:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:53:41: 10000000 INFO @ Fri, 05 Jul 2019 05:53:43: #2 number of paired peaks: 43894 INFO @ Fri, 05 Jul 2019 05:53:43: start model_add_line... INFO @ Fri, 05 Jul 2019 05:53:43: start X-correlation... INFO @ Fri, 05 Jul 2019 05:53:43: end of X-cor INFO @ Fri, 05 Jul 2019 05:53:43: #2 finished! INFO @ Fri, 05 Jul 2019 05:53:43: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 05:53:43: #2 alternative fragment length(s) may be 3,136 bps INFO @ Fri, 05 Jul 2019 05:53:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.05_model.r INFO @ Fri, 05 Jul 2019 05:53:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:53:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:53:46: 12000000 INFO @ Fri, 05 Jul 2019 05:53:46: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:53:46: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:53:46: #1 total tags in treatment: 12020520 INFO @ Fri, 05 Jul 2019 05:53:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:53:46: #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 05:53:46: #1 tags after filtering in treatment: 12020219 INFO @ Fri, 05 Jul 2019 05:53:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:53:46: #1 finished! INFO @ Fri, 05 Jul 2019 05:53:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:53:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:53:49: #2 number of paired peaks: 43894 INFO @ Fri, 05 Jul 2019 05:53:49: start model_add_line... INFO @ Fri, 05 Jul 2019 05:53:50: 11000000 INFO @ Fri, 05 Jul 2019 05:53:50: start X-correlation... INFO @ Fri, 05 Jul 2019 05:53:50: end of X-cor INFO @ Fri, 05 Jul 2019 05:53:50: #2 finished! INFO @ Fri, 05 Jul 2019 05:53:50: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 05:53:50: #2 alternative fragment length(s) may be 3,136 bps INFO @ Fri, 05 Jul 2019 05:53:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.20_model.r INFO @ Fri, 05 Jul 2019 05:53:50: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:53:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:53:57: 12000000 INFO @ Fri, 05 Jul 2019 05:53:58: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:53:58: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:53:58: #1 total tags in treatment: 12020520 INFO @ Fri, 05 Jul 2019 05:53:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:53:58: #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 05:53:58: #1 tags after filtering in treatment: 12020219 INFO @ Fri, 05 Jul 2019 05:53:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:53:58: #1 finished! INFO @ Fri, 05 Jul 2019 05:53:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:53:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:54:01: #2 number of paired peaks: 43894 INFO @ Fri, 05 Jul 2019 05:54:01: start model_add_line... INFO @ Fri, 05 Jul 2019 05:54:01: start X-correlation... INFO @ Fri, 05 Jul 2019 05:54:01: end of X-cor INFO @ Fri, 05 Jul 2019 05:54:01: #2 finished! INFO @ Fri, 05 Jul 2019 05:54:01: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 05:54:01: #2 alternative fragment length(s) may be 3,136 bps INFO @ Fri, 05 Jul 2019 05:54:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.10_model.r INFO @ Fri, 05 Jul 2019 05:54:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:54:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:54:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:54:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:54:37: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:54:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.05_peaks.xls INFO @ Fri, 05 Jul 2019 05:54:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:54:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.05_summits.bed INFO @ Fri, 05 Jul 2019 05:54:40: Done! pass1 - making usageList (129 chroms): 13 millis pass2 - checking and writing primary data (42130 records, 4 fields): 61 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:54:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.20_peaks.xls INFO @ Fri, 05 Jul 2019 05:54:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:54:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.20_summits.bed INFO @ Fri, 05 Jul 2019 05:54:49: Done! pass1 - making usageList (82 chroms): 10 millis pass2 - checking and writing primary data (24143 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:54:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.10_peaks.xls INFO @ Fri, 05 Jul 2019 05:54:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:54:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101925/ERX101925.10_summits.bed INFO @ Fri, 05 Jul 2019 05:54:58: Done! pass1 - making usageList (109 chroms): 9 millis pass2 - checking and writing primary data (34249 records, 4 fields): 47 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。