Job ID = 1293317 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,802,445 reads read : 24,802,445 reads written : 24,802,445 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:00:00 Multiseed full-index search: 00:07:27 24802445 reads; of these: 24802445 (100.00%) were unpaired; of these: 2590594 (10.44%) aligned 0 times 20959968 (84.51%) aligned exactly 1 time 1251883 (5.05%) aligned >1 times 89.56% overall alignment rate Time searching: 00:07:27 Overall time: 00:07:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 10374016 / 22211851 = 0.4670 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 @ Sun, 02 Jun 2019 23:04:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 02 Jun 2019 23:04:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:04:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:04:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 02 Jun 2019 23:04:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:04:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:04:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 02 Jun 2019 23:04:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:04:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:04:13: 1000000 INFO @ Sun, 02 Jun 2019 23:04:15: 1000000 INFO @ Sun, 02 Jun 2019 23:04:15: 1000000 INFO @ Sun, 02 Jun 2019 23:04:21: 2000000 INFO @ Sun, 02 Jun 2019 23:04:24: 2000000 INFO @ Sun, 02 Jun 2019 23:04:24: 2000000 INFO @ Sun, 02 Jun 2019 23:04:29: 3000000 INFO @ Sun, 02 Jun 2019 23:04:32: 3000000 INFO @ Sun, 02 Jun 2019 23:04:33: 3000000 INFO @ Sun, 02 Jun 2019 23:04:36: 4000000 INFO @ Sun, 02 Jun 2019 23:04:40: 4000000 INFO @ Sun, 02 Jun 2019 23:04:41: 4000000 INFO @ Sun, 02 Jun 2019 23:04:44: 5000000 INFO @ Sun, 02 Jun 2019 23:04:49: 5000000 INFO @ Sun, 02 Jun 2019 23:04:50: 5000000 INFO @ Sun, 02 Jun 2019 23:04:52: 6000000 INFO @ Sun, 02 Jun 2019 23:04:57: 6000000 INFO @ Sun, 02 Jun 2019 23:04:58: 6000000 INFO @ Sun, 02 Jun 2019 23:04:59: 7000000 INFO @ Sun, 02 Jun 2019 23:05:06: 7000000 INFO @ Sun, 02 Jun 2019 23:05:07: 7000000 INFO @ Sun, 02 Jun 2019 23:05:07: 8000000 INFO @ Sun, 02 Jun 2019 23:05:15: 8000000 INFO @ Sun, 02 Jun 2019 23:05:15: 9000000 INFO @ Sun, 02 Jun 2019 23:05:15: 8000000 INFO @ Sun, 02 Jun 2019 23:05:23: 10000000 INFO @ Sun, 02 Jun 2019 23:05:23: 9000000 INFO @ Sun, 02 Jun 2019 23:05:24: 9000000 INFO @ Sun, 02 Jun 2019 23:05:30: 11000000 INFO @ Sun, 02 Jun 2019 23:05:31: 10000000 INFO @ Sun, 02 Jun 2019 23:05:32: 10000000 INFO @ Sun, 02 Jun 2019 23:05:36: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 23:05:36: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 23:05:36: #1 total tags in treatment: 11837835 INFO @ Sun, 02 Jun 2019 23:05:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:05:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:05:36: #1 tags after filtering in treatment: 11837835 INFO @ Sun, 02 Jun 2019 23:05:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:05:36: #1 finished! INFO @ Sun, 02 Jun 2019 23:05:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:05:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:05:38: #2 number of paired peaks: 6539 INFO @ Sun, 02 Jun 2019 23:05:38: start model_add_line... INFO @ Sun, 02 Jun 2019 23:05:38: start X-correlation... INFO @ Sun, 02 Jun 2019 23:05:38: end of X-cor INFO @ Sun, 02 Jun 2019 23:05:38: #2 finished! INFO @ Sun, 02 Jun 2019 23:05:38: #2 predicted fragment length is 147 bps INFO @ Sun, 02 Jun 2019 23:05:38: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 02 Jun 2019 23:05:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.05_model.r WARNING @ Sun, 02 Jun 2019 23:05:38: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:05:38: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sun, 02 Jun 2019 23:05:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:05:38: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:05:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:05:40: 11000000 INFO @ Sun, 02 Jun 2019 23:05:41: 11000000 INFO @ Sun, 02 Jun 2019 23:05:46: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 23:05:46: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 23:05:46: #1 total tags in treatment: 11837835 INFO @ Sun, 02 Jun 2019 23:05:46: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:05:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:05:47: #1 tags after filtering in treatment: 11837835 INFO @ Sun, 02 Jun 2019 23:05:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:05:47: #1 finished! INFO @ Sun, 02 Jun 2019 23:05:47: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:05:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:05:48: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 23:05:48: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 23:05:48: #1 total tags in treatment: 11837835 INFO @ Sun, 02 Jun 2019 23:05:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:05:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:05:48: #1 tags after filtering in treatment: 11837835 INFO @ Sun, 02 Jun 2019 23:05:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:05:48: #1 finished! INFO @ Sun, 02 Jun 2019 23:05:48: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:05:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:05:48: #2 number of paired peaks: 6539 INFO @ Sun, 02 Jun 2019 23:05:48: start model_add_line... INFO @ Sun, 02 Jun 2019 23:05:49: start X-correlation... INFO @ Sun, 02 Jun 2019 23:05:49: end of X-cor INFO @ Sun, 02 Jun 2019 23:05:49: #2 finished! INFO @ Sun, 02 Jun 2019 23:05:49: #2 predicted fragment length is 147 bps INFO @ Sun, 02 Jun 2019 23:05:49: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 02 Jun 2019 23:05:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.10_model.r WARNING @ Sun, 02 Jun 2019 23:05:49: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:05:49: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sun, 02 Jun 2019 23:05:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:05:49: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:05:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:05:50: #2 number of paired peaks: 6539 INFO @ Sun, 02 Jun 2019 23:05:50: start model_add_line... INFO @ Sun, 02 Jun 2019 23:05:50: start X-correlation... INFO @ Sun, 02 Jun 2019 23:05:50: end of X-cor INFO @ Sun, 02 Jun 2019 23:05:50: #2 finished! INFO @ Sun, 02 Jun 2019 23:05:50: #2 predicted fragment length is 147 bps INFO @ Sun, 02 Jun 2019 23:05:50: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 02 Jun 2019 23:05:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.20_model.r WARNING @ Sun, 02 Jun 2019 23:05:50: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:05:50: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sun, 02 Jun 2019 23:05:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:05:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:05:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:06:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:06:29: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:06:30: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:06:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:06:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:06:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.05_summits.bed INFO @ Sun, 02 Jun 2019 23:06:36: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (10816 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:06:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:06:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:06:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.10_summits.bed INFO @ Sun, 02 Jun 2019 23:06:46: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (8542 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:06:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:06:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:06:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX102368/ERX102368.20_summits.bed INFO @ Sun, 02 Jun 2019 23:06:48: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (6508 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。