Job ID = 1294394 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,702,372 reads read : 12,702,372 reads written : 12,702,372 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: 00:05:37 12702372 reads; of these: 12702372 (100.00%) were unpaired; of these: 793341 (6.25%) aligned 0 times 7906943 (62.25%) aligned exactly 1 time 4002088 (31.51%) aligned >1 times 93.75% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:37 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] 1664481 / 11909031 = 0.1398 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 07:24:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.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 07:24:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:24:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:24:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.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 07:24:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:24:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:24:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.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 07:24:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:24:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:24:24: 1000000 INFO @ Mon, 03 Jun 2019 07:24:26: 1000000 INFO @ Mon, 03 Jun 2019 07:24:26: 1000000 INFO @ Mon, 03 Jun 2019 07:24:31: 2000000 INFO @ Mon, 03 Jun 2019 07:24:35: 2000000 INFO @ Mon, 03 Jun 2019 07:24:36: 2000000 INFO @ Mon, 03 Jun 2019 07:24:38: 3000000 INFO @ Mon, 03 Jun 2019 07:24:44: 3000000 INFO @ Mon, 03 Jun 2019 07:24:45: 4000000 INFO @ Mon, 03 Jun 2019 07:24:45: 3000000 INFO @ Mon, 03 Jun 2019 07:24:52: 5000000 INFO @ Mon, 03 Jun 2019 07:24:53: 4000000 INFO @ Mon, 03 Jun 2019 07:24:54: 4000000 INFO @ Mon, 03 Jun 2019 07:24:58: 6000000 INFO @ Mon, 03 Jun 2019 07:25:01: 5000000 INFO @ Mon, 03 Jun 2019 07:25:03: 5000000 INFO @ Mon, 03 Jun 2019 07:25:05: 7000000 INFO @ Mon, 03 Jun 2019 07:25:10: 6000000 INFO @ Mon, 03 Jun 2019 07:25:12: 6000000 INFO @ Mon, 03 Jun 2019 07:25:12: 8000000 INFO @ Mon, 03 Jun 2019 07:25:18: 7000000 INFO @ Mon, 03 Jun 2019 07:25:19: 9000000 INFO @ Mon, 03 Jun 2019 07:25:20: 7000000 INFO @ Mon, 03 Jun 2019 07:25:26: 10000000 INFO @ Mon, 03 Jun 2019 07:25:26: 8000000 INFO @ Mon, 03 Jun 2019 07:25:28: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:25:28: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:25:28: #1 total tags in treatment: 10244550 INFO @ Mon, 03 Jun 2019 07:25:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:25:28: #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 07:25:28: #1 tags after filtering in treatment: 10244550 INFO @ Mon, 03 Jun 2019 07:25:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:25:28: #1 finished! INFO @ Mon, 03 Jun 2019 07:25:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:25:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:25:29: 8000000 INFO @ Mon, 03 Jun 2019 07:25:29: #2 number of paired peaks: 459 WARNING @ Mon, 03 Jun 2019 07:25:29: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Mon, 03 Jun 2019 07:25:29: start model_add_line... INFO @ Mon, 03 Jun 2019 07:25:29: start X-correlation... INFO @ Mon, 03 Jun 2019 07:25:29: end of X-cor INFO @ Mon, 03 Jun 2019 07:25:29: #2 finished! INFO @ Mon, 03 Jun 2019 07:25:29: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 07:25:29: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 07:25:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.10_model.r WARNING @ Mon, 03 Jun 2019 07:25:29: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:25:29: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 07:25:29: #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 07:25:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:25:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:25:35: 9000000 INFO @ Mon, 03 Jun 2019 07:25:38: 9000000 INFO @ Mon, 03 Jun 2019 07:25:43: 10000000 INFO @ Mon, 03 Jun 2019 07:25:45: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:25:45: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:25:45: #1 total tags in treatment: 10244550 INFO @ Mon, 03 Jun 2019 07:25:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:25:45: #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 07:25:45: #1 tags after filtering in treatment: 10244550 INFO @ Mon, 03 Jun 2019 07:25:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:25:45: #1 finished! INFO @ Mon, 03 Jun 2019 07:25:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:25:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:25:46: 10000000 INFO @ Mon, 03 Jun 2019 07:25:46: #2 number of paired peaks: 459 WARNING @ Mon, 03 Jun 2019 07:25:46: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Mon, 03 Jun 2019 07:25:46: start model_add_line... INFO @ Mon, 03 Jun 2019 07:25:46: start X-correlation... INFO @ Mon, 03 Jun 2019 07:25:47: end of X-cor INFO @ Mon, 03 Jun 2019 07:25:47: #2 finished! INFO @ Mon, 03 Jun 2019 07:25:47: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 07:25:47: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 07:25:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.20_model.r WARNING @ Mon, 03 Jun 2019 07:25:47: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:25:47: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 07:25:47: #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 07:25:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:25:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:25:48: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:25:48: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:25:48: #1 total tags in treatment: 10244550 INFO @ Mon, 03 Jun 2019 07:25:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:25:48: #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 07:25:48: #1 tags after filtering in treatment: 10244550 INFO @ Mon, 03 Jun 2019 07:25:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:25:48: #1 finished! INFO @ Mon, 03 Jun 2019 07:25:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:25:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:25:49: #2 number of paired peaks: 459 WARNING @ Mon, 03 Jun 2019 07:25:49: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Mon, 03 Jun 2019 07:25:49: start model_add_line... INFO @ Mon, 03 Jun 2019 07:25:49: start X-correlation... INFO @ Mon, 03 Jun 2019 07:25:49: end of X-cor INFO @ Mon, 03 Jun 2019 07:25:49: #2 finished! INFO @ Mon, 03 Jun 2019 07:25:49: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 07:25:49: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 07:25:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.05_model.r WARNING @ Mon, 03 Jun 2019 07:25:49: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:25:49: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 07:25:49: #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 07:25:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:25:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:25:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:26:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:26:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:26:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.10_summits.bed INFO @ Mon, 03 Jun 2019 07:26:11: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1610 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:26:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:26:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:26:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:26:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:26:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.20_summits.bed INFO @ Mon, 03 Jun 2019 07:26:29: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (1199 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:26:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.05_peaks.xls INFO @ Mon, 03 Jun 2019 07:26:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:26:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287571/SRX287571.05_summits.bed INFO @ Mon, 03 Jun 2019 07:26:32: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1831 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。