Job ID = 1294969 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,953,572 reads read : 18,953,572 reads written : 18,953,572 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: 00:09:28 18953572 reads; of these: 18953572 (100.00%) were unpaired; of these: 973846 (5.14%) aligned 0 times 11627644 (61.35%) aligned exactly 1 time 6352082 (33.51%) aligned >1 times 94.86% overall alignment rate Time searching: 00:09:28 Overall time: 00:09:28 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 8 files... [bam_rmdupse_core] 3038821 / 17979726 = 0.1690 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 @ Mon, 03 Jun 2019 11:21:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.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 @ Mon, 03 Jun 2019 11:21:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:21:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:21:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.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 @ Mon, 03 Jun 2019 11:21:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:21:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:21:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.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 @ Mon, 03 Jun 2019 11:21:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:21:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:21:39: 1000000 INFO @ Mon, 03 Jun 2019 11:21:40: 1000000 INFO @ Mon, 03 Jun 2019 11:21:41: 1000000 INFO @ Mon, 03 Jun 2019 11:21:48: 2000000 INFO @ Mon, 03 Jun 2019 11:21:49: 2000000 INFO @ Mon, 03 Jun 2019 11:21:51: 2000000 INFO @ Mon, 03 Jun 2019 11:21:57: 3000000 INFO @ Mon, 03 Jun 2019 11:21:58: 3000000 INFO @ Mon, 03 Jun 2019 11:22:01: 3000000 INFO @ Mon, 03 Jun 2019 11:22:06: 4000000 INFO @ Mon, 03 Jun 2019 11:22:08: 4000000 INFO @ Mon, 03 Jun 2019 11:22:12: 4000000 INFO @ Mon, 03 Jun 2019 11:22:16: 5000000 INFO @ Mon, 03 Jun 2019 11:22:17: 5000000 INFO @ Mon, 03 Jun 2019 11:22:22: 5000000 INFO @ Mon, 03 Jun 2019 11:22:26: 6000000 INFO @ Mon, 03 Jun 2019 11:22:27: 6000000 INFO @ Mon, 03 Jun 2019 11:22:32: 6000000 INFO @ Mon, 03 Jun 2019 11:22:36: 7000000 INFO @ Mon, 03 Jun 2019 11:22:37: 7000000 INFO @ Mon, 03 Jun 2019 11:22:42: 7000000 INFO @ Mon, 03 Jun 2019 11:22:45: 8000000 INFO @ Mon, 03 Jun 2019 11:22:46: 8000000 INFO @ Mon, 03 Jun 2019 11:22:52: 8000000 INFO @ Mon, 03 Jun 2019 11:22:55: 9000000 INFO @ Mon, 03 Jun 2019 11:22:56: 9000000 INFO @ Mon, 03 Jun 2019 11:23:02: 9000000 INFO @ Mon, 03 Jun 2019 11:23:04: 10000000 INFO @ Mon, 03 Jun 2019 11:23:05: 10000000 INFO @ Mon, 03 Jun 2019 11:23:12: 10000000 INFO @ Mon, 03 Jun 2019 11:23:13: 11000000 INFO @ Mon, 03 Jun 2019 11:23:14: 11000000 INFO @ Mon, 03 Jun 2019 11:23:23: 12000000 INFO @ Mon, 03 Jun 2019 11:23:23: 11000000 INFO @ Mon, 03 Jun 2019 11:23:24: 12000000 INFO @ Mon, 03 Jun 2019 11:23:32: 13000000 INFO @ Mon, 03 Jun 2019 11:23:33: 13000000 INFO @ Mon, 03 Jun 2019 11:23:33: 12000000 INFO @ Mon, 03 Jun 2019 11:23:40: 14000000 INFO @ Mon, 03 Jun 2019 11:23:42: 14000000 INFO @ Mon, 03 Jun 2019 11:23:44: 13000000 INFO @ Mon, 03 Jun 2019 11:23:48: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:23:48: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:23:48: #1 total tags in treatment: 14940905 INFO @ Mon, 03 Jun 2019 11:23:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:23:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 11:23:49: #1 tags after filtering in treatment: 14940905 INFO @ Mon, 03 Jun 2019 11:23:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:23:49: #1 finished! INFO @ Mon, 03 Jun 2019 11:23:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:23:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:23:50: #2 number of paired peaks: 442 WARNING @ Mon, 03 Jun 2019 11:23:50: Fewer paired peaks (442) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 442 pairs to build model! INFO @ Mon, 03 Jun 2019 11:23:50: start model_add_line... INFO @ Mon, 03 Jun 2019 11:23:50: start X-correlation... INFO @ Mon, 03 Jun 2019 11:23:50: end of X-cor INFO @ Mon, 03 Jun 2019 11:23:50: #2 finished! INFO @ Mon, 03 Jun 2019 11:23:50: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 11:23:50: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 11:23:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.20_model.r WARNING @ Mon, 03 Jun 2019 11:23:50: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:23:50: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 11:23:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 11:23:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:23:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:23:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:23:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:23:50: #1 total tags in treatment: 14940905 INFO @ Mon, 03 Jun 2019 11:23:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:23:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 11:23:51: #1 tags after filtering in treatment: 14940905 INFO @ Mon, 03 Jun 2019 11:23:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:23:51: #1 finished! INFO @ Mon, 03 Jun 2019 11:23:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:23:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:23:52: #2 number of paired peaks: 442 WARNING @ Mon, 03 Jun 2019 11:23:52: Fewer paired peaks (442) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 442 pairs to build model! INFO @ Mon, 03 Jun 2019 11:23:52: start model_add_line... INFO @ Mon, 03 Jun 2019 11:23:52: start X-correlation... INFO @ Mon, 03 Jun 2019 11:23:52: end of X-cor INFO @ Mon, 03 Jun 2019 11:23:52: #2 finished! INFO @ Mon, 03 Jun 2019 11:23:52: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 11:23:52: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 11:23:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.10_model.r WARNING @ Mon, 03 Jun 2019 11:23:52: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:23:52: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 11:23:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 11:23:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:23:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:23:54: 14000000 INFO @ Mon, 03 Jun 2019 11:24:03: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:24:03: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:24:03: #1 total tags in treatment: 14940905 INFO @ Mon, 03 Jun 2019 11:24:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:24:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 11:24:03: #1 tags after filtering in treatment: 14940905 INFO @ Mon, 03 Jun 2019 11:24:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:24:03: #1 finished! INFO @ Mon, 03 Jun 2019 11:24:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:24:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:24:05: #2 number of paired peaks: 442 WARNING @ Mon, 03 Jun 2019 11:24:05: Fewer paired peaks (442) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 442 pairs to build model! INFO @ Mon, 03 Jun 2019 11:24:05: start model_add_line... INFO @ Mon, 03 Jun 2019 11:24:05: start X-correlation... INFO @ Mon, 03 Jun 2019 11:24:05: end of X-cor INFO @ Mon, 03 Jun 2019 11:24:05: #2 finished! INFO @ Mon, 03 Jun 2019 11:24:05: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 11:24:05: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 11:24:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.05_model.r WARNING @ Mon, 03 Jun 2019 11:24:05: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:24:05: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 11:24:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 11:24:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:24:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:24:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:24:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:24:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:24:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:24:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:24:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.20_summits.bed INFO @ Mon, 03 Jun 2019 11:24:49: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1537 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:24:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:24:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:24:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.10_summits.bed INFO @ Mon, 03 Jun 2019 11:24:52: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1950 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:25:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:25:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:25:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288028/SRX288028.05_summits.bed INFO @ Mon, 03 Jun 2019 11:25:04: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2201 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。