Job ID = 2001705 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,153,712 reads read : 28,153,712 reads written : 28,153,712 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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:05:02 28153712 reads; of these: 28153712 (100.00%) were unpaired; of these: 708611 (2.52%) aligned 0 times 24799321 (88.09%) aligned exactly 1 time 2645780 (9.40%) aligned >1 times 97.48% overall alignment rate Time searching: 00:05:03 Overall time: 00:05:03 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] 14263299 / 27445101 = 0.5197 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 09:40:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.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 09:40:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:40:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:40:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.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 09:40:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:40:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:40:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.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 09:40:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:40:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:40:12: 1000000 INFO @ Fri, 05 Jul 2019 09:40:13: 1000000 INFO @ Fri, 05 Jul 2019 09:40:15: 1000000 INFO @ Fri, 05 Jul 2019 09:40:19: 2000000 INFO @ Fri, 05 Jul 2019 09:40:19: 2000000 INFO @ Fri, 05 Jul 2019 09:40:23: 2000000 INFO @ Fri, 05 Jul 2019 09:40:26: 3000000 INFO @ Fri, 05 Jul 2019 09:40:26: 3000000 INFO @ Fri, 05 Jul 2019 09:40:30: 3000000 INFO @ Fri, 05 Jul 2019 09:40:32: 4000000 INFO @ Fri, 05 Jul 2019 09:40:33: 4000000 INFO @ Fri, 05 Jul 2019 09:40:37: 4000000 INFO @ Fri, 05 Jul 2019 09:40:39: 5000000 INFO @ Fri, 05 Jul 2019 09:40:39: 5000000 INFO @ Fri, 05 Jul 2019 09:40:44: 5000000 INFO @ Fri, 05 Jul 2019 09:40:45: 6000000 INFO @ Fri, 05 Jul 2019 09:40:45: 6000000 INFO @ Fri, 05 Jul 2019 09:40:51: 6000000 INFO @ Fri, 05 Jul 2019 09:40:52: 7000000 INFO @ Fri, 05 Jul 2019 09:40:52: 7000000 INFO @ Fri, 05 Jul 2019 09:40:58: 7000000 INFO @ Fri, 05 Jul 2019 09:40:58: 8000000 INFO @ Fri, 05 Jul 2019 09:40:59: 8000000 INFO @ Fri, 05 Jul 2019 09:41:05: 9000000 INFO @ Fri, 05 Jul 2019 09:41:05: 8000000 INFO @ Fri, 05 Jul 2019 09:41:05: 9000000 INFO @ Fri, 05 Jul 2019 09:41:11: 10000000 INFO @ Fri, 05 Jul 2019 09:41:12: 9000000 INFO @ Fri, 05 Jul 2019 09:41:12: 10000000 INFO @ Fri, 05 Jul 2019 09:41:17: 11000000 INFO @ Fri, 05 Jul 2019 09:41:19: 11000000 INFO @ Fri, 05 Jul 2019 09:41:19: 10000000 INFO @ Fri, 05 Jul 2019 09:41:23: 12000000 INFO @ Fri, 05 Jul 2019 09:41:25: 12000000 INFO @ Fri, 05 Jul 2019 09:41:25: 11000000 INFO @ Fri, 05 Jul 2019 09:41:30: 13000000 INFO @ Fri, 05 Jul 2019 09:41:31: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:41:31: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:41:31: #1 total tags in treatment: 13181802 INFO @ Fri, 05 Jul 2019 09:41:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:41:31: #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 09:41:31: #1 tags after filtering in treatment: 13181536 INFO @ Fri, 05 Jul 2019 09:41:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:41:31: #1 finished! INFO @ Fri, 05 Jul 2019 09:41:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:41:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:41:32: 13000000 INFO @ Fri, 05 Jul 2019 09:41:32: 12000000 INFO @ Fri, 05 Jul 2019 09:41:33: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:41:33: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:41:33: #1 total tags in treatment: 13181802 INFO @ Fri, 05 Jul 2019 09:41:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:41:33: #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 09:41:33: #1 tags after filtering in treatment: 13181536 INFO @ Fri, 05 Jul 2019 09:41:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:41:33: #1 finished! INFO @ Fri, 05 Jul 2019 09:41:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:41:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:41:35: #2 number of paired peaks: 46301 INFO @ Fri, 05 Jul 2019 09:41:35: start model_add_line... INFO @ Fri, 05 Jul 2019 09:41:35: start X-correlation... INFO @ Fri, 05 Jul 2019 09:41:35: end of X-cor INFO @ Fri, 05 Jul 2019 09:41:35: #2 finished! INFO @ Fri, 05 Jul 2019 09:41:35: #2 predicted fragment length is 138 bps INFO @ Fri, 05 Jul 2019 09:41:35: #2 alternative fragment length(s) may be 4,138 bps INFO @ Fri, 05 Jul 2019 09:41:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.05_model.r INFO @ Fri, 05 Jul 2019 09:41:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:41:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:41:37: #2 number of paired peaks: 46301 INFO @ Fri, 05 Jul 2019 09:41:37: start model_add_line... INFO @ Fri, 05 Jul 2019 09:41:37: start X-correlation... INFO @ Fri, 05 Jul 2019 09:41:37: end of X-cor INFO @ Fri, 05 Jul 2019 09:41:37: #2 finished! INFO @ Fri, 05 Jul 2019 09:41:37: #2 predicted fragment length is 138 bps INFO @ Fri, 05 Jul 2019 09:41:37: #2 alternative fragment length(s) may be 4,138 bps INFO @ Fri, 05 Jul 2019 09:41:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.10_model.r INFO @ Fri, 05 Jul 2019 09:41:37: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:41:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:41:39: 13000000 INFO @ Fri, 05 Jul 2019 09:41:40: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:41:40: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:41:40: #1 total tags in treatment: 13181802 INFO @ Fri, 05 Jul 2019 09:41:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:41:40: #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 09:41:41: #1 tags after filtering in treatment: 13181536 INFO @ Fri, 05 Jul 2019 09:41:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:41:41: #1 finished! INFO @ Fri, 05 Jul 2019 09:41:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:41:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:41:44: #2 number of paired peaks: 46301 INFO @ Fri, 05 Jul 2019 09:41:44: start model_add_line... INFO @ Fri, 05 Jul 2019 09:41:44: start X-correlation... INFO @ Fri, 05 Jul 2019 09:41:44: end of X-cor INFO @ Fri, 05 Jul 2019 09:41:44: #2 finished! INFO @ Fri, 05 Jul 2019 09:41:44: #2 predicted fragment length is 138 bps INFO @ Fri, 05 Jul 2019 09:41:44: #2 alternative fragment length(s) may be 4,138 bps INFO @ Fri, 05 Jul 2019 09:41:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.20_model.r INFO @ Fri, 05 Jul 2019 09:41:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:41:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:42:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:42:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:42:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:42:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.05_peaks.xls INFO @ Fri, 05 Jul 2019 09:42:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:42:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.05_summits.bed INFO @ Fri, 05 Jul 2019 09:42:36: Done! pass1 - making usageList (136 chroms): 9 millis pass2 - checking and writing primary data (45488 records, 4 fields): 62 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:42:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.10_peaks.xls INFO @ Fri, 05 Jul 2019 09:42:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:42:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.10_summits.bed INFO @ Fri, 05 Jul 2019 09:42:40: Done! pass1 - making usageList (115 chroms): 12 millis pass2 - checking and writing primary data (36566 records, 4 fields): 51 millis INFO @ Fri, 05 Jul 2019 09:42:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.20_peaks.xls CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:42:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:42:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102015/ERX102015.20_summits.bed INFO @ Fri, 05 Jul 2019 09:42:45: Done! pass1 - making usageList (88 chroms): 6 millis pass2 - checking and writing primary data (26008 records, 4 fields): 38 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。