Job ID = 2001708 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,468,337 reads read : 22,468,337 reads written : 22,468,337 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: 00:00:01 Multiseed full-index search: 00:06:20 22468337 reads; of these: 22468337 (100.00%) were unpaired; of these: 419617 (1.87%) aligned 0 times 19871926 (88.44%) aligned exactly 1 time 2176794 (9.69%) aligned >1 times 98.13% overall alignment rate Time searching: 00:06:23 Overall time: 00:06:23 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] 11488196 / 22048720 = 0.5210 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 09:36:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.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 09:36:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:36:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:36:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.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 09:36:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:36:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:36:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.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 09:36:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:36:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:36:38: 1000000 INFO @ Fri, 05 Jul 2019 09:36:39: 1000000 INFO @ Fri, 05 Jul 2019 09:36:40: 1000000 INFO @ Fri, 05 Jul 2019 09:36:46: 2000000 INFO @ Fri, 05 Jul 2019 09:36:47: 2000000 INFO @ Fri, 05 Jul 2019 09:36:49: 2000000 INFO @ Fri, 05 Jul 2019 09:36:53: 3000000 INFO @ Fri, 05 Jul 2019 09:36:56: 3000000 INFO @ Fri, 05 Jul 2019 09:36:58: 3000000 INFO @ Fri, 05 Jul 2019 09:37:01: 4000000 INFO @ Fri, 05 Jul 2019 09:37:04: 4000000 INFO @ Fri, 05 Jul 2019 09:37:07: 4000000 INFO @ Fri, 05 Jul 2019 09:37:09: 5000000 INFO @ Fri, 05 Jul 2019 09:37:12: 5000000 INFO @ Fri, 05 Jul 2019 09:37:16: 5000000 INFO @ Fri, 05 Jul 2019 09:37:17: 6000000 INFO @ Fri, 05 Jul 2019 09:37:19: 6000000 INFO @ Fri, 05 Jul 2019 09:37:24: 7000000 INFO @ Fri, 05 Jul 2019 09:37:25: 6000000 INFO @ Fri, 05 Jul 2019 09:37:26: 7000000 INFO @ Fri, 05 Jul 2019 09:37:33: 8000000 INFO @ Fri, 05 Jul 2019 09:37:34: 8000000 INFO @ Fri, 05 Jul 2019 09:37:35: 7000000 INFO @ Fri, 05 Jul 2019 09:37:41: 9000000 INFO @ Fri, 05 Jul 2019 09:37:41: 9000000 INFO @ Fri, 05 Jul 2019 09:37:43: 8000000 INFO @ Fri, 05 Jul 2019 09:37:47: 10000000 INFO @ Fri, 05 Jul 2019 09:37:48: 10000000 INFO @ Fri, 05 Jul 2019 09:37:51: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:37:51: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:37:51: #1 total tags in treatment: 10560524 INFO @ Fri, 05 Jul 2019 09:37:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:37:51: #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 09:37:52: #1 tags after filtering in treatment: 10560233 INFO @ Fri, 05 Jul 2019 09:37:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:37:52: #1 finished! INFO @ Fri, 05 Jul 2019 09:37:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:37:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:37:52: 9000000 INFO @ Fri, 05 Jul 2019 09:37:52: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:37:52: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:37:52: #1 total tags in treatment: 10560524 INFO @ Fri, 05 Jul 2019 09:37:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:37:52: #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 09:37:53: #1 tags after filtering in treatment: 10560233 INFO @ Fri, 05 Jul 2019 09:37:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:37:53: #1 finished! INFO @ Fri, 05 Jul 2019 09:37:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:37:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:37:55: #2 number of paired peaks: 51167 INFO @ Fri, 05 Jul 2019 09:37:55: start model_add_line... INFO @ Fri, 05 Jul 2019 09:37:55: start X-correlation... INFO @ Fri, 05 Jul 2019 09:37:55: end of X-cor INFO @ Fri, 05 Jul 2019 09:37:55: #2 finished! INFO @ Fri, 05 Jul 2019 09:37:55: #2 predicted fragment length is 141 bps INFO @ Fri, 05 Jul 2019 09:37:55: #2 alternative fragment length(s) may be 3,141 bps INFO @ Fri, 05 Jul 2019 09:37:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.20_model.r INFO @ Fri, 05 Jul 2019 09:37:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:37:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:37:56: #2 number of paired peaks: 51167 INFO @ Fri, 05 Jul 2019 09:37:56: start model_add_line... INFO @ Fri, 05 Jul 2019 09:37:56: start X-correlation... INFO @ Fri, 05 Jul 2019 09:37:56: end of X-cor INFO @ Fri, 05 Jul 2019 09:37:56: #2 finished! INFO @ Fri, 05 Jul 2019 09:37:56: #2 predicted fragment length is 141 bps INFO @ Fri, 05 Jul 2019 09:37:56: #2 alternative fragment length(s) may be 3,141 bps INFO @ Fri, 05 Jul 2019 09:37:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.05_model.r INFO @ Fri, 05 Jul 2019 09:37:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:37:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:38:01: 10000000 INFO @ Fri, 05 Jul 2019 09:38:06: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:38:06: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:38:06: #1 total tags in treatment: 10560524 INFO @ Fri, 05 Jul 2019 09:38:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:38:06: #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 09:38:06: #1 tags after filtering in treatment: 10560233 INFO @ Fri, 05 Jul 2019 09:38:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:38:06: #1 finished! INFO @ Fri, 05 Jul 2019 09:38:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:38:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:38:09: #2 number of paired peaks: 51167 INFO @ Fri, 05 Jul 2019 09:38:09: start model_add_line... INFO @ Fri, 05 Jul 2019 09:38:09: start X-correlation... INFO @ Fri, 05 Jul 2019 09:38:09: end of X-cor INFO @ Fri, 05 Jul 2019 09:38:09: #2 finished! INFO @ Fri, 05 Jul 2019 09:38:09: #2 predicted fragment length is 141 bps INFO @ Fri, 05 Jul 2019 09:38:09: #2 alternative fragment length(s) may be 3,141 bps INFO @ Fri, 05 Jul 2019 09:38:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.10_model.r INFO @ Fri, 05 Jul 2019 09:38:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:38:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:38:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:38:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:38:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:38:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.20_peaks.xls INFO @ Fri, 05 Jul 2019 09:38:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:38:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.20_summits.bed INFO @ Fri, 05 Jul 2019 09:38:45: Done! pass1 - making usageList (75 chroms): 7 millis pass2 - checking and writing primary data (19661 records, 4 fields): 34 millis INFO @ Fri, 05 Jul 2019 09:38:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.05_peaks.xls INFO @ Fri, 05 Jul 2019 09:38:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:38:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.05_summits.bed INFO @ Fri, 05 Jul 2019 09:38:47: Done! pass1 - making usageList (134 chroms): 14 millis pass2 - checking and writing primary data (43636 records, 4 fields): 60 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:38:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.10_peaks.xls INFO @ Fri, 05 Jul 2019 09:38:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:39:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102016/ERX102016.10_summits.bed INFO @ Fri, 05 Jul 2019 09:39:00: Done! pass1 - making usageList (104 chroms): 8 millis pass2 - checking and writing primary data (32474 records, 4 fields): 271 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。