Job ID = 1294819 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,856,264 reads read : 16,856,264 reads written : 16,856,264 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: 00:06:59 16856264 reads; of these: 16856264 (100.00%) were unpaired; of these: 886547 (5.26%) aligned 0 times 11886624 (70.52%) aligned exactly 1 time 4083093 (24.22%) aligned >1 times 94.74% overall alignment rate Time searching: 00:06:59 Overall time: 00:06:59 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] 1505787 / 15969717 = 0.0943 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 10:34:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.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 10:34:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:34:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:34:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.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 10:34:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:34:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:34:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.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 10:34:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:34:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:34:17: 1000000 INFO @ Mon, 03 Jun 2019 10:34:18: 1000000 INFO @ Mon, 03 Jun 2019 10:34:20: 1000000 INFO @ Mon, 03 Jun 2019 10:34:24: 2000000 INFO @ Mon, 03 Jun 2019 10:34:26: 2000000 INFO @ Mon, 03 Jun 2019 10:34:28: 2000000 INFO @ Mon, 03 Jun 2019 10:34:32: 3000000 INFO @ Mon, 03 Jun 2019 10:34:34: 3000000 INFO @ Mon, 03 Jun 2019 10:34:37: 3000000 INFO @ Mon, 03 Jun 2019 10:34:39: 4000000 INFO @ Mon, 03 Jun 2019 10:34:41: 4000000 INFO @ Mon, 03 Jun 2019 10:34:45: 4000000 INFO @ Mon, 03 Jun 2019 10:34:46: 5000000 INFO @ Mon, 03 Jun 2019 10:34:49: 5000000 INFO @ Mon, 03 Jun 2019 10:34:53: 6000000 INFO @ Mon, 03 Jun 2019 10:34:54: 5000000 INFO @ Mon, 03 Jun 2019 10:34:57: 6000000 INFO @ Mon, 03 Jun 2019 10:35:00: 7000000 INFO @ Mon, 03 Jun 2019 10:35:03: 6000000 INFO @ Mon, 03 Jun 2019 10:35:04: 7000000 INFO @ Mon, 03 Jun 2019 10:35:07: 8000000 INFO @ Mon, 03 Jun 2019 10:35:11: 7000000 INFO @ Mon, 03 Jun 2019 10:35:12: 8000000 INFO @ Mon, 03 Jun 2019 10:35:14: 9000000 INFO @ Mon, 03 Jun 2019 10:35:19: 9000000 INFO @ Mon, 03 Jun 2019 10:35:20: 8000000 INFO @ Mon, 03 Jun 2019 10:35:21: 10000000 INFO @ Mon, 03 Jun 2019 10:35:27: 10000000 INFO @ Mon, 03 Jun 2019 10:35:28: 9000000 INFO @ Mon, 03 Jun 2019 10:35:28: 11000000 INFO @ Mon, 03 Jun 2019 10:35:35: 11000000 INFO @ Mon, 03 Jun 2019 10:35:36: 12000000 INFO @ Mon, 03 Jun 2019 10:35:37: 10000000 INFO @ Mon, 03 Jun 2019 10:35:42: 12000000 INFO @ Mon, 03 Jun 2019 10:35:43: 13000000 INFO @ Mon, 03 Jun 2019 10:35:45: 11000000 INFO @ Mon, 03 Jun 2019 10:35:50: 14000000 INFO @ Mon, 03 Jun 2019 10:35:50: 13000000 INFO @ Mon, 03 Jun 2019 10:35:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:35:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:35:53: #1 total tags in treatment: 14463930 INFO @ Mon, 03 Jun 2019 10:35:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:35:53: #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 10:35:53: #1 tags after filtering in treatment: 14463930 INFO @ Mon, 03 Jun 2019 10:35:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:35:53: #1 finished! INFO @ Mon, 03 Jun 2019 10:35:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:35:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:35:54: 12000000 INFO @ Mon, 03 Jun 2019 10:35:55: #2 number of paired peaks: 126 WARNING @ Mon, 03 Jun 2019 10:35:55: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Mon, 03 Jun 2019 10:35:55: start model_add_line... INFO @ Mon, 03 Jun 2019 10:35:55: start X-correlation... INFO @ Mon, 03 Jun 2019 10:35:55: end of X-cor INFO @ Mon, 03 Jun 2019 10:35:55: #2 finished! INFO @ Mon, 03 Jun 2019 10:35:55: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 10:35:55: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 10:35:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.10_model.r WARNING @ Mon, 03 Jun 2019 10:35:55: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:35:55: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 10:35:55: #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 10:35:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:35:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:35:57: 14000000 INFO @ Mon, 03 Jun 2019 10:36:01: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:36:01: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:36:01: #1 total tags in treatment: 14463930 INFO @ Mon, 03 Jun 2019 10:36:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:36:01: #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 10:36:01: #1 tags after filtering in treatment: 14463930 INFO @ Mon, 03 Jun 2019 10:36:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:36:01: #1 finished! INFO @ Mon, 03 Jun 2019 10:36:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:36:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:36:02: 13000000 INFO @ Mon, 03 Jun 2019 10:36:03: #2 number of paired peaks: 126 WARNING @ Mon, 03 Jun 2019 10:36:03: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Mon, 03 Jun 2019 10:36:03: start model_add_line... INFO @ Mon, 03 Jun 2019 10:36:03: start X-correlation... INFO @ Mon, 03 Jun 2019 10:36:03: end of X-cor INFO @ Mon, 03 Jun 2019 10:36:03: #2 finished! INFO @ Mon, 03 Jun 2019 10:36:03: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 10:36:03: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 10:36:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.05_model.r WARNING @ Mon, 03 Jun 2019 10:36:03: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:36:03: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 10:36:03: #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 10:36:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:36:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:36:11: 14000000 INFO @ Mon, 03 Jun 2019 10:36:15: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:36:15: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:36:15: #1 total tags in treatment: 14463930 INFO @ Mon, 03 Jun 2019 10:36:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:36:15: #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 10:36:15: #1 tags after filtering in treatment: 14463930 INFO @ Mon, 03 Jun 2019 10:36:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:36:15: #1 finished! INFO @ Mon, 03 Jun 2019 10:36:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:36:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:36:16: #2 number of paired peaks: 126 WARNING @ Mon, 03 Jun 2019 10:36:16: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Mon, 03 Jun 2019 10:36:16: start model_add_line... INFO @ Mon, 03 Jun 2019 10:36:16: start X-correlation... INFO @ Mon, 03 Jun 2019 10:36:16: end of X-cor INFO @ Mon, 03 Jun 2019 10:36:16: #2 finished! INFO @ Mon, 03 Jun 2019 10:36:16: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 10:36:16: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 10:36:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.20_model.r WARNING @ Mon, 03 Jun 2019 10:36:16: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:36:16: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 10:36:16: #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 10:36:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:36:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:36:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:36:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:36:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:36:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:36:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.10_summits.bed INFO @ Mon, 03 Jun 2019 10:36:52: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1642 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:36:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:37:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:37:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:37:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.05_summits.bed INFO @ Mon, 03 Jun 2019 10:37:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1938 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:37:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:37:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:37:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287918/SRX287918.20_summits.bed INFO @ Mon, 03 Jun 2019 10:37:13: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1191 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。