Job ID = 2001152 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,752,351 reads read : 26,752,351 reads written : 26,752,351 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:37 26752351 reads; of these: 26752351 (100.00%) were unpaired; of these: 602398 (2.25%) aligned 0 times 19614667 (73.32%) aligned exactly 1 time 6535286 (24.43%) aligned >1 times 97.75% overall alignment rate Time searching: 00:11:38 Overall time: 00:11:38 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] 1818200 / 26149953 = 0.0695 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 04:06:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.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 04:06:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:06:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:06:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.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 04:06:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:06:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:06:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.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 04:06:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:06:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:07:06: 1000000 INFO @ Fri, 05 Jul 2019 04:07:07: 1000000 INFO @ Fri, 05 Jul 2019 04:07:09: 1000000 INFO @ Fri, 05 Jul 2019 04:07:14: 2000000 INFO @ Fri, 05 Jul 2019 04:07:16: 2000000 INFO @ Fri, 05 Jul 2019 04:07:17: 2000000 INFO @ Fri, 05 Jul 2019 04:07:22: 3000000 INFO @ Fri, 05 Jul 2019 04:07:24: 3000000 INFO @ Fri, 05 Jul 2019 04:07:26: 3000000 INFO @ Fri, 05 Jul 2019 04:07:30: 4000000 INFO @ Fri, 05 Jul 2019 04:07:33: 4000000 INFO @ Fri, 05 Jul 2019 04:07:34: 4000000 INFO @ Fri, 05 Jul 2019 04:07:38: 5000000 INFO @ Fri, 05 Jul 2019 04:07:42: 5000000 INFO @ Fri, 05 Jul 2019 04:07:43: 5000000 INFO @ Fri, 05 Jul 2019 04:07:46: 6000000 INFO @ Fri, 05 Jul 2019 04:07:50: 6000000 INFO @ Fri, 05 Jul 2019 04:07:51: 6000000 INFO @ Fri, 05 Jul 2019 04:07:54: 7000000 INFO @ Fri, 05 Jul 2019 04:07:58: 7000000 INFO @ Fri, 05 Jul 2019 04:07:59: 7000000 INFO @ Fri, 05 Jul 2019 04:08:02: 8000000 INFO @ Fri, 05 Jul 2019 04:08:06: 8000000 INFO @ Fri, 05 Jul 2019 04:08:07: 8000000 INFO @ Fri, 05 Jul 2019 04:08:10: 9000000 INFO @ Fri, 05 Jul 2019 04:08:15: 9000000 INFO @ Fri, 05 Jul 2019 04:08:15: 9000000 INFO @ Fri, 05 Jul 2019 04:08:18: 10000000 INFO @ Fri, 05 Jul 2019 04:08:23: 10000000 INFO @ Fri, 05 Jul 2019 04:08:23: 10000000 INFO @ Fri, 05 Jul 2019 04:08:25: 11000000 INFO @ Fri, 05 Jul 2019 04:08:31: 11000000 INFO @ Fri, 05 Jul 2019 04:08:32: 11000000 INFO @ Fri, 05 Jul 2019 04:08:33: 12000000 INFO @ Fri, 05 Jul 2019 04:08:39: 12000000 INFO @ Fri, 05 Jul 2019 04:08:40: 12000000 INFO @ Fri, 05 Jul 2019 04:08:41: 13000000 INFO @ Fri, 05 Jul 2019 04:08:47: 13000000 INFO @ Fri, 05 Jul 2019 04:08:48: 13000000 INFO @ Fri, 05 Jul 2019 04:08:49: 14000000 INFO @ Fri, 05 Jul 2019 04:08:55: 14000000 INFO @ Fri, 05 Jul 2019 04:08:56: 14000000 INFO @ Fri, 05 Jul 2019 04:08:56: 15000000 INFO @ Fri, 05 Jul 2019 04:09:03: 15000000 INFO @ Fri, 05 Jul 2019 04:09:04: 16000000 INFO @ Fri, 05 Jul 2019 04:09:05: 15000000 INFO @ Fri, 05 Jul 2019 04:09:12: 16000000 INFO @ Fri, 05 Jul 2019 04:09:12: 17000000 INFO @ Fri, 05 Jul 2019 04:09:13: 16000000 INFO @ Fri, 05 Jul 2019 04:09:20: 18000000 INFO @ Fri, 05 Jul 2019 04:09:21: 17000000 INFO @ Fri, 05 Jul 2019 04:09:21: 17000000 INFO @ Fri, 05 Jul 2019 04:09:28: 19000000 INFO @ Fri, 05 Jul 2019 04:09:29: 18000000 INFO @ Fri, 05 Jul 2019 04:09:29: 18000000 INFO @ Fri, 05 Jul 2019 04:09:35: 20000000 INFO @ Fri, 05 Jul 2019 04:09:37: 19000000 INFO @ Fri, 05 Jul 2019 04:09:37: 19000000 INFO @ Fri, 05 Jul 2019 04:09:43: 21000000 INFO @ Fri, 05 Jul 2019 04:09:45: 20000000 INFO @ Fri, 05 Jul 2019 04:09:45: 20000000 INFO @ Fri, 05 Jul 2019 04:09:51: 22000000 INFO @ Fri, 05 Jul 2019 04:09:53: 21000000 INFO @ Fri, 05 Jul 2019 04:09:54: 21000000 INFO @ Fri, 05 Jul 2019 04:09:58: 23000000 INFO @ Fri, 05 Jul 2019 04:10:01: 22000000 INFO @ Fri, 05 Jul 2019 04:10:02: 22000000 INFO @ Fri, 05 Jul 2019 04:10:07: 24000000 INFO @ Fri, 05 Jul 2019 04:10:09: 23000000 INFO @ Fri, 05 Jul 2019 04:10:10: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:10:10: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:10:10: #1 total tags in treatment: 24331753 INFO @ Fri, 05 Jul 2019 04:10:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:10:10: #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 04:10:10: 23000000 INFO @ Fri, 05 Jul 2019 04:10:10: #1 tags after filtering in treatment: 24331610 INFO @ Fri, 05 Jul 2019 04:10:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:10:10: #1 finished! INFO @ Fri, 05 Jul 2019 04:10:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:10:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:10:16: #2 number of paired peaks: 59204 INFO @ Fri, 05 Jul 2019 04:10:16: start model_add_line... INFO @ Fri, 05 Jul 2019 04:10:16: start X-correlation... INFO @ Fri, 05 Jul 2019 04:10:16: end of X-cor INFO @ Fri, 05 Jul 2019 04:10:16: #2 finished! INFO @ Fri, 05 Jul 2019 04:10:16: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 04:10:16: #2 alternative fragment length(s) may be 3,131,504 bps INFO @ Fri, 05 Jul 2019 04:10:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.05_model.r INFO @ Fri, 05 Jul 2019 04:10:16: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:10:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:10:17: 24000000 INFO @ Fri, 05 Jul 2019 04:10:18: 24000000 INFO @ Fri, 05 Jul 2019 04:10:20: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:10:20: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:10:20: #1 total tags in treatment: 24331753 INFO @ Fri, 05 Jul 2019 04:10:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:10:20: #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 04:10:21: #1 tags after filtering in treatment: 24331610 INFO @ Fri, 05 Jul 2019 04:10:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:10:21: #1 finished! INFO @ Fri, 05 Jul 2019 04:10:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:10:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:10:21: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:10:21: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:10:21: #1 total tags in treatment: 24331753 INFO @ Fri, 05 Jul 2019 04:10:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:10:21: #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 04:10:22: #1 tags after filtering in treatment: 24331610 INFO @ Fri, 05 Jul 2019 04:10:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:10:22: #1 finished! INFO @ Fri, 05 Jul 2019 04:10:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:10:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:10:26: #2 number of paired peaks: 59204 INFO @ Fri, 05 Jul 2019 04:10:26: start model_add_line... INFO @ Fri, 05 Jul 2019 04:10:27: start X-correlation... INFO @ Fri, 05 Jul 2019 04:10:27: end of X-cor INFO @ Fri, 05 Jul 2019 04:10:27: #2 finished! INFO @ Fri, 05 Jul 2019 04:10:27: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 04:10:27: #2 alternative fragment length(s) may be 3,131,504 bps INFO @ Fri, 05 Jul 2019 04:10:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.20_model.r INFO @ Fri, 05 Jul 2019 04:10:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:10:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:10:27: #2 number of paired peaks: 59204 INFO @ Fri, 05 Jul 2019 04:10:27: start model_add_line... INFO @ Fri, 05 Jul 2019 04:10:28: start X-correlation... INFO @ Fri, 05 Jul 2019 04:10:28: end of X-cor INFO @ Fri, 05 Jul 2019 04:10:28: #2 finished! INFO @ Fri, 05 Jul 2019 04:10:28: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 04:10:28: #2 alternative fragment length(s) may be 3,131,504 bps INFO @ Fri, 05 Jul 2019 04:10:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.10_model.r INFO @ Fri, 05 Jul 2019 04:10:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:10:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:11:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:11:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:11:57: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:12:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:12:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:12:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.05_summits.bed INFO @ Fri, 05 Jul 2019 04:12:31: Done! pass1 - making usageList (77 chroms): 4 millis pass2 - checking and writing primary data (6377 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:12:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:12:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:12:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.20_summits.bed INFO @ Fri, 05 Jul 2019 04:12:39: Done! pass1 - making usageList (31 chroms): 2 millis pass2 - checking and writing primary data (183 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:12:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:12:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:12:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101842/ERX101842.10_summits.bed INFO @ Fri, 05 Jul 2019 04:12:44: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (1419 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。