Job ID = 2002189 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,054,746 reads read : 12,054,746 reads written : 12,054,746 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: 00:25:58 12054746 reads; of these: 12054746 (100.00%) were unpaired; of these: 1750379 (14.52%) aligned 0 times 6735296 (55.87%) aligned exactly 1 time 3569071 (29.61%) aligned >1 times 85.48% overall alignment rate Time searching: 00:26:01 Overall time: 00:26:01 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] 636067 / 10304367 = 0.0617 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 11:43:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.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 11:43:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:43:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:43:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.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 11:43:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:43:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:43:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.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 11:43:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:43:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:44:07: 1000000 INFO @ Fri, 05 Jul 2019 11:44:07: 1000000 INFO @ Fri, 05 Jul 2019 11:44:08: 1000000 INFO @ Fri, 05 Jul 2019 11:44:18: 2000000 INFO @ Fri, 05 Jul 2019 11:44:18: 2000000 INFO @ Fri, 05 Jul 2019 11:44:18: 2000000 INFO @ Fri, 05 Jul 2019 11:44:28: 3000000 INFO @ Fri, 05 Jul 2019 11:44:28: 3000000 INFO @ Fri, 05 Jul 2019 11:44:28: 3000000 INFO @ Fri, 05 Jul 2019 11:44:38: 4000000 INFO @ Fri, 05 Jul 2019 11:44:39: 4000000 INFO @ Fri, 05 Jul 2019 11:44:39: 4000000 INFO @ Fri, 05 Jul 2019 11:44:48: 5000000 INFO @ Fri, 05 Jul 2019 11:44:49: 5000000 INFO @ Fri, 05 Jul 2019 11:44:49: 5000000 INFO @ Fri, 05 Jul 2019 11:44:58: 6000000 INFO @ Fri, 05 Jul 2019 11:44:59: 6000000 INFO @ Fri, 05 Jul 2019 11:44:59: 6000000 INFO @ Fri, 05 Jul 2019 11:45:08: 7000000 INFO @ Fri, 05 Jul 2019 11:45:10: 7000000 INFO @ Fri, 05 Jul 2019 11:45:10: 7000000 INFO @ Fri, 05 Jul 2019 11:45:18: 8000000 INFO @ Fri, 05 Jul 2019 11:45:20: 8000000 INFO @ Fri, 05 Jul 2019 11:45:20: 8000000 INFO @ Fri, 05 Jul 2019 11:45:28: 9000000 INFO @ Fri, 05 Jul 2019 11:45:31: 9000000 INFO @ Fri, 05 Jul 2019 11:45:31: 9000000 INFO @ Fri, 05 Jul 2019 11:45:35: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:45:35: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:45:35: #1 total tags in treatment: 9668300 INFO @ Fri, 05 Jul 2019 11:45:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:45:35: #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 11:45:35: #1 tags after filtering in treatment: 9668092 INFO @ Fri, 05 Jul 2019 11:45:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:45:35: #1 finished! INFO @ Fri, 05 Jul 2019 11:45:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:45:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:45:37: #2 number of paired peaks: 18011 INFO @ Fri, 05 Jul 2019 11:45:37: start model_add_line... INFO @ Fri, 05 Jul 2019 11:45:37: start X-correlation... INFO @ Fri, 05 Jul 2019 11:45:37: end of X-cor INFO @ Fri, 05 Jul 2019 11:45:37: #2 finished! INFO @ Fri, 05 Jul 2019 11:45:37: #2 predicted fragment length is 98 bps INFO @ Fri, 05 Jul 2019 11:45:37: #2 alternative fragment length(s) may be 98 bps INFO @ Fri, 05 Jul 2019 11:45:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.05_model.r WARNING @ Fri, 05 Jul 2019 11:45:37: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 11:45:37: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Fri, 05 Jul 2019 11:45:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 11:45:37: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:45:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:45:38: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:45:38: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:45:38: #1 total tags in treatment: 9668300 INFO @ Fri, 05 Jul 2019 11:45:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:45:38: #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 11:45:38: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:45:38: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:45:38: #1 total tags in treatment: 9668300 INFO @ Fri, 05 Jul 2019 11:45:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:45:38: #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 11:45:38: #1 tags after filtering in treatment: 9668092 INFO @ Fri, 05 Jul 2019 11:45:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:45:38: #1 finished! INFO @ Fri, 05 Jul 2019 11:45:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:45:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:45:38: #1 tags after filtering in treatment: 9668092 INFO @ Fri, 05 Jul 2019 11:45:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:45:38: #1 finished! INFO @ Fri, 05 Jul 2019 11:45:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:45:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:45:40: #2 number of paired peaks: 18011 INFO @ Fri, 05 Jul 2019 11:45:40: start model_add_line... INFO @ Fri, 05 Jul 2019 11:45:40: #2 number of paired peaks: 18011 INFO @ Fri, 05 Jul 2019 11:45:40: start model_add_line... INFO @ Fri, 05 Jul 2019 11:45:41: start X-correlation... INFO @ Fri, 05 Jul 2019 11:45:41: end of X-cor INFO @ Fri, 05 Jul 2019 11:45:41: #2 finished! INFO @ Fri, 05 Jul 2019 11:45:41: #2 predicted fragment length is 98 bps INFO @ Fri, 05 Jul 2019 11:45:41: #2 alternative fragment length(s) may be 98 bps INFO @ Fri, 05 Jul 2019 11:45:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.10_model.r WARNING @ Fri, 05 Jul 2019 11:45:41: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 11:45:41: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Fri, 05 Jul 2019 11:45:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 11:45:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:45:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:45:41: start X-correlation... INFO @ Fri, 05 Jul 2019 11:45:41: end of X-cor INFO @ Fri, 05 Jul 2019 11:45:41: #2 finished! INFO @ Fri, 05 Jul 2019 11:45:41: #2 predicted fragment length is 98 bps INFO @ Fri, 05 Jul 2019 11:45:41: #2 alternative fragment length(s) may be 98 bps INFO @ Fri, 05 Jul 2019 11:45:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.20_model.r WARNING @ Fri, 05 Jul 2019 11:45:41: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 11:45:41: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Fri, 05 Jul 2019 11:45:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 11:45:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:45:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:46:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:46:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:46:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:46:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:46:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:46:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.05_summits.bed INFO @ Fri, 05 Jul 2019 11:46:23: Done! pass1 - making usageList (60 chroms): 3 millis pass2 - checking and writing primary data (4207 records, 4 fields): 16 millis INFO @ Fri, 05 Jul 2019 11:46:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:46:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:46:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.20_summits.bed INFO @ Fri, 05 Jul 2019 11:46:26: Done! INFO @ Fri, 05 Jul 2019 11:46:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.10_peaks.xls INFO @ Fri, 05 Jul 2019 11:46:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:46:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2250258/ERX2250258.10_summits.bed INFO @ Fri, 05 Jul 2019 11:46:26: Done! pass1 - making usageList (27 chroms): 2 millis pass2 - checking and writing primary data (278 records, 4 fields): 3 millis pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (937 records, 4 fields): 4 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。