Job ID = 2590281 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,249,589 reads read : 18,249,589 reads written : 18,249,589 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:02 18249589 reads; of these: 18249589 (100.00%) were unpaired; of these: 976546 (5.35%) aligned 0 times 13034920 (71.43%) aligned exactly 1 time 4238123 (23.22%) aligned >1 times 94.65% overall alignment rate Time searching: 00:07:02 Overall time: 00:07:02 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] 1666049 / 17273043 = 0.0965 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, 12 Aug 2019 20:47:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.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, 12 Aug 2019 20:47:09: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:47:09: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:47:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.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, 12 Aug 2019 20:47:10: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:47:10: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:47:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.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, 12 Aug 2019 20:47:11: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:47:11: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:47:20: 1000000 INFO @ Mon, 12 Aug 2019 20:47:20: 1000000 INFO @ Mon, 12 Aug 2019 20:47:22: 1000000 INFO @ Mon, 12 Aug 2019 20:47:29: 2000000 INFO @ Mon, 12 Aug 2019 20:47:32: 2000000 INFO @ Mon, 12 Aug 2019 20:47:33: 2000000 INFO @ Mon, 12 Aug 2019 20:47:38: 3000000 INFO @ Mon, 12 Aug 2019 20:47:44: 3000000 INFO @ Mon, 12 Aug 2019 20:47:45: 3000000 INFO @ Mon, 12 Aug 2019 20:47:47: 4000000 INFO @ Mon, 12 Aug 2019 20:47:55: 5000000 INFO @ Mon, 12 Aug 2019 20:47:56: 4000000 INFO @ Mon, 12 Aug 2019 20:47:57: 4000000 INFO @ Mon, 12 Aug 2019 20:48:04: 6000000 INFO @ Mon, 12 Aug 2019 20:48:07: 5000000 INFO @ Mon, 12 Aug 2019 20:48:09: 5000000 INFO @ Mon, 12 Aug 2019 20:48:13: 7000000 INFO @ Mon, 12 Aug 2019 20:48:19: 6000000 INFO @ Mon, 12 Aug 2019 20:48:20: 6000000 INFO @ Mon, 12 Aug 2019 20:48:21: 8000000 INFO @ Mon, 12 Aug 2019 20:48:30: 9000000 INFO @ Mon, 12 Aug 2019 20:48:30: 7000000 INFO @ Mon, 12 Aug 2019 20:48:32: 7000000 INFO @ Mon, 12 Aug 2019 20:48:39: 10000000 INFO @ Mon, 12 Aug 2019 20:48:42: 8000000 INFO @ Mon, 12 Aug 2019 20:48:43: 8000000 INFO @ Mon, 12 Aug 2019 20:48:47: 11000000 INFO @ Mon, 12 Aug 2019 20:48:53: 9000000 INFO @ Mon, 12 Aug 2019 20:48:54: 9000000 INFO @ Mon, 12 Aug 2019 20:48:56: 12000000 INFO @ Mon, 12 Aug 2019 20:49:02: 10000000 INFO @ Mon, 12 Aug 2019 20:49:04: 10000000 INFO @ Mon, 12 Aug 2019 20:49:05: 13000000 INFO @ Mon, 12 Aug 2019 20:49:14: 11000000 INFO @ Mon, 12 Aug 2019 20:49:14: 14000000 INFO @ Mon, 12 Aug 2019 20:49:15: 11000000 INFO @ Mon, 12 Aug 2019 20:49:23: 15000000 INFO @ Mon, 12 Aug 2019 20:49:25: 12000000 INFO @ Mon, 12 Aug 2019 20:49:26: 12000000 INFO @ Mon, 12 Aug 2019 20:49:28: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:49:28: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:49:28: #1 total tags in treatment: 15606994 INFO @ Mon, 12 Aug 2019 20:49:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:49:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:49:28: #1 tags after filtering in treatment: 15606994 INFO @ Mon, 12 Aug 2019 20:49:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:49:28: #1 finished! INFO @ Mon, 12 Aug 2019 20:49:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:49:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:49:30: #2 number of paired peaks: 146 WARNING @ Mon, 12 Aug 2019 20:49:30: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Mon, 12 Aug 2019 20:49:30: start model_add_line... INFO @ Mon, 12 Aug 2019 20:49:30: start X-correlation... INFO @ Mon, 12 Aug 2019 20:49:30: end of X-cor INFO @ Mon, 12 Aug 2019 20:49:30: #2 finished! INFO @ Mon, 12 Aug 2019 20:49:30: #2 predicted fragment length is 46 bps INFO @ Mon, 12 Aug 2019 20:49:30: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 12 Aug 2019 20:49:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.20_model.r WARNING @ Mon, 12 Aug 2019 20:49:30: #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, 12 Aug 2019 20:49:30: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 12 Aug 2019 20:49:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:49:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:49:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:49:36: 13000000 INFO @ Mon, 12 Aug 2019 20:49:38: 13000000 INFO @ Mon, 12 Aug 2019 20:49:48: 14000000 INFO @ Mon, 12 Aug 2019 20:49:50: 14000000 INFO @ Mon, 12 Aug 2019 20:49:59: 15000000 INFO @ Mon, 12 Aug 2019 20:50:01: 15000000 INFO @ Mon, 12 Aug 2019 20:50:07: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:50:07: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:50:07: #1 total tags in treatment: 15606994 INFO @ Mon, 12 Aug 2019 20:50:07: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:50:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:50:07: #1 tags after filtering in treatment: 15606994 INFO @ Mon, 12 Aug 2019 20:50:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:50:07: #1 finished! INFO @ Mon, 12 Aug 2019 20:50:07: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:50:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:50:08: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:50:08: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:50:08: #1 total tags in treatment: 15606994 INFO @ Mon, 12 Aug 2019 20:50:08: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:50:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:50:08: #2 number of paired peaks: 146 WARNING @ Mon, 12 Aug 2019 20:50:08: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Mon, 12 Aug 2019 20:50:08: start model_add_line... INFO @ Mon, 12 Aug 2019 20:50:08: start X-correlation... INFO @ Mon, 12 Aug 2019 20:50:08: end of X-cor INFO @ Mon, 12 Aug 2019 20:50:08: #2 finished! INFO @ Mon, 12 Aug 2019 20:50:08: #2 predicted fragment length is 46 bps INFO @ Mon, 12 Aug 2019 20:50:08: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 12 Aug 2019 20:50:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.05_model.r WARNING @ Mon, 12 Aug 2019 20:50:08: #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, 12 Aug 2019 20:50:08: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 12 Aug 2019 20:50:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:50:08: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:50:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:50:09: #1 tags after filtering in treatment: 15606994 INFO @ Mon, 12 Aug 2019 20:50:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:50:09: #1 finished! INFO @ Mon, 12 Aug 2019 20:50:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:50:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:50:10: #2 number of paired peaks: 146 WARNING @ Mon, 12 Aug 2019 20:50:10: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Mon, 12 Aug 2019 20:50:10: start model_add_line... INFO @ Mon, 12 Aug 2019 20:50:10: start X-correlation... INFO @ Mon, 12 Aug 2019 20:50:10: end of X-cor INFO @ Mon, 12 Aug 2019 20:50:10: #2 finished! INFO @ Mon, 12 Aug 2019 20:50:10: #2 predicted fragment length is 46 bps INFO @ Mon, 12 Aug 2019 20:50:10: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 12 Aug 2019 20:50:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.10_model.r WARNING @ Mon, 12 Aug 2019 20:50:10: #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, 12 Aug 2019 20:50:10: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 12 Aug 2019 20:50:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:50:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:50:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:50:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:50:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:50:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:50:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.20_summits.bed INFO @ Mon, 12 Aug 2019 20:50:33: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1146 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:50:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:50:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:51:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:51:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:51:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.05_summits.bed INFO @ Mon, 12 Aug 2019 20:51:11: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1896 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:51:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:51:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:51:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287678/SRX287678.10_summits.bed INFO @ Mon, 12 Aug 2019 20:51:13: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1612 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。