Job ID = 2590478 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,992,334 reads read : 13,984,668 reads written : 6,992,334 reads 0-length : 6,992,334 spots read : 6,984,932 reads read : 13,969,864 reads written : 6,984,932 reads 0-length : 6,984,932 spots read : 7,012,666 reads read : 14,025,332 reads written : 7,012,666 reads 0-length : 7,012,666 spots read : 7,044,895 reads read : 14,089,790 reads written : 7,044,895 reads 0-length : 7,044,895 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: 00:10:35 28034827 reads; of these: 28034827 (100.00%) were unpaired; of these: 830732 (2.96%) aligned 0 times 20845519 (74.36%) aligned exactly 1 time 6358576 (22.68%) aligned >1 times 97.04% overall alignment rate Time searching: 00:10:35 Overall time: 00:10:35 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] 4204024 / 27204095 = 0.1545 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 22:19:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.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 22:19:06: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:19:06: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:19:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.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 22:19:07: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:19:07: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:19:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.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 22:19:08: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:19:08: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:19:14: 1000000 INFO @ Mon, 12 Aug 2019 22:19:16: 1000000 INFO @ Mon, 12 Aug 2019 22:19:17: 1000000 INFO @ Mon, 12 Aug 2019 22:19:20: 2000000 INFO @ Mon, 12 Aug 2019 22:19:24: 2000000 INFO @ Mon, 12 Aug 2019 22:19:25: 2000000 INFO @ Mon, 12 Aug 2019 22:19:26: 3000000 INFO @ Mon, 12 Aug 2019 22:19:32: 3000000 INFO @ Mon, 12 Aug 2019 22:19:32: 4000000 INFO @ Mon, 12 Aug 2019 22:19:33: 3000000 INFO @ Mon, 12 Aug 2019 22:19:38: 5000000 INFO @ Mon, 12 Aug 2019 22:19:40: 4000000 INFO @ Mon, 12 Aug 2019 22:19:41: 4000000 INFO @ Mon, 12 Aug 2019 22:19:44: 6000000 INFO @ Mon, 12 Aug 2019 22:19:48: 5000000 INFO @ Mon, 12 Aug 2019 22:19:49: 5000000 INFO @ Mon, 12 Aug 2019 22:19:50: 7000000 INFO @ Mon, 12 Aug 2019 22:19:56: 6000000 INFO @ Mon, 12 Aug 2019 22:19:56: 8000000 INFO @ Mon, 12 Aug 2019 22:19:57: 6000000 INFO @ Mon, 12 Aug 2019 22:20:02: 9000000 INFO @ Mon, 12 Aug 2019 22:20:03: 7000000 INFO @ Mon, 12 Aug 2019 22:20:04: 7000000 INFO @ Mon, 12 Aug 2019 22:20:08: 10000000 INFO @ Mon, 12 Aug 2019 22:20:11: 8000000 INFO @ Mon, 12 Aug 2019 22:20:12: 8000000 INFO @ Mon, 12 Aug 2019 22:20:14: 11000000 INFO @ Mon, 12 Aug 2019 22:20:19: 9000000 INFO @ Mon, 12 Aug 2019 22:20:20: 9000000 INFO @ Mon, 12 Aug 2019 22:20:21: 12000000 INFO @ Mon, 12 Aug 2019 22:20:27: 13000000 INFO @ Mon, 12 Aug 2019 22:20:27: 10000000 INFO @ Mon, 12 Aug 2019 22:20:28: 10000000 INFO @ Mon, 12 Aug 2019 22:20:33: 14000000 INFO @ Mon, 12 Aug 2019 22:20:34: 11000000 INFO @ Mon, 12 Aug 2019 22:20:35: 11000000 INFO @ Mon, 12 Aug 2019 22:20:39: 15000000 INFO @ Mon, 12 Aug 2019 22:20:42: 12000000 INFO @ Mon, 12 Aug 2019 22:20:43: 12000000 INFO @ Mon, 12 Aug 2019 22:20:45: 16000000 INFO @ Mon, 12 Aug 2019 22:20:50: 13000000 INFO @ Mon, 12 Aug 2019 22:20:51: 17000000 INFO @ Mon, 12 Aug 2019 22:20:51: 13000000 INFO @ Mon, 12 Aug 2019 22:20:57: 18000000 INFO @ Mon, 12 Aug 2019 22:20:58: 14000000 INFO @ Mon, 12 Aug 2019 22:20:58: 14000000 INFO @ Mon, 12 Aug 2019 22:21:03: 19000000 INFO @ Mon, 12 Aug 2019 22:21:05: 15000000 INFO @ Mon, 12 Aug 2019 22:21:06: 15000000 INFO @ Mon, 12 Aug 2019 22:21:09: 20000000 INFO @ Mon, 12 Aug 2019 22:21:13: 16000000 INFO @ Mon, 12 Aug 2019 22:21:14: 16000000 INFO @ Mon, 12 Aug 2019 22:21:15: 21000000 INFO @ Mon, 12 Aug 2019 22:21:21: 17000000 INFO @ Mon, 12 Aug 2019 22:21:21: 22000000 INFO @ Mon, 12 Aug 2019 22:21:22: 17000000 INFO @ Mon, 12 Aug 2019 22:21:27: 23000000 INFO @ Mon, 12 Aug 2019 22:21:27: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:21:27: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:21:27: #1 total tags in treatment: 23000071 INFO @ Mon, 12 Aug 2019 22:21:27: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:21:27: #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 22:21:28: #1 tags after filtering in treatment: 23000071 INFO @ Mon, 12 Aug 2019 22:21:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:21:28: #1 finished! INFO @ Mon, 12 Aug 2019 22:21:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:21:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:21:29: 18000000 INFO @ Mon, 12 Aug 2019 22:21:29: 18000000 INFO @ Mon, 12 Aug 2019 22:21:30: #2 number of paired peaks: 252 WARNING @ Mon, 12 Aug 2019 22:21:30: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Mon, 12 Aug 2019 22:21:30: start model_add_line... INFO @ Mon, 12 Aug 2019 22:21:30: start X-correlation... INFO @ Mon, 12 Aug 2019 22:21:30: end of X-cor INFO @ Mon, 12 Aug 2019 22:21:30: #2 finished! INFO @ Mon, 12 Aug 2019 22:21:30: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 22:21:30: #2 alternative fragment length(s) may be 3,43 bps INFO @ Mon, 12 Aug 2019 22:21:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.05_model.r WARNING @ Mon, 12 Aug 2019 22:21:30: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:21:30: #2 You may need to consider one of the other alternative d(s): 3,43 WARNING @ Mon, 12 Aug 2019 22:21:30: #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 22:21:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:21:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:21:36: 19000000 INFO @ Mon, 12 Aug 2019 22:21:37: 19000000 INFO @ Mon, 12 Aug 2019 22:21:44: 20000000 INFO @ Mon, 12 Aug 2019 22:21:45: 20000000 INFO @ Mon, 12 Aug 2019 22:21:52: 21000000 INFO @ Mon, 12 Aug 2019 22:21:53: 21000000 INFO @ Mon, 12 Aug 2019 22:22:00: 22000000 INFO @ Mon, 12 Aug 2019 22:22:00: 22000000 INFO @ Mon, 12 Aug 2019 22:22:07: 23000000 INFO @ Mon, 12 Aug 2019 22:22:08: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:22:08: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:22:08: #1 total tags in treatment: 23000071 INFO @ Mon, 12 Aug 2019 22:22:08: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:22:08: #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 22:22:08: #1 tags after filtering in treatment: 23000071 INFO @ Mon, 12 Aug 2019 22:22:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:22:08: #1 finished! INFO @ Mon, 12 Aug 2019 22:22:08: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:22:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:22:08: 23000000 INFO @ Mon, 12 Aug 2019 22:22:08: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:22:08: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:22:08: #1 total tags in treatment: 23000071 INFO @ Mon, 12 Aug 2019 22:22:08: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:22:08: #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 22:22:09: #1 tags after filtering in treatment: 23000071 INFO @ Mon, 12 Aug 2019 22:22:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:22:09: #1 finished! INFO @ Mon, 12 Aug 2019 22:22:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:22:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:22:10: #2 number of paired peaks: 252 WARNING @ Mon, 12 Aug 2019 22:22:10: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Mon, 12 Aug 2019 22:22:10: start model_add_line... INFO @ Mon, 12 Aug 2019 22:22:10: start X-correlation... INFO @ Mon, 12 Aug 2019 22:22:10: end of X-cor INFO @ Mon, 12 Aug 2019 22:22:10: #2 finished! INFO @ Mon, 12 Aug 2019 22:22:10: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 22:22:10: #2 alternative fragment length(s) may be 3,43 bps INFO @ Mon, 12 Aug 2019 22:22:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.10_model.r WARNING @ Mon, 12 Aug 2019 22:22:10: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:22:10: #2 You may need to consider one of the other alternative d(s): 3,43 WARNING @ Mon, 12 Aug 2019 22:22:10: #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 22:22:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:22:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:22:11: #2 number of paired peaks: 252 WARNING @ Mon, 12 Aug 2019 22:22:11: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Mon, 12 Aug 2019 22:22:11: start model_add_line... INFO @ Mon, 12 Aug 2019 22:22:11: start X-correlation... INFO @ Mon, 12 Aug 2019 22:22:11: end of X-cor INFO @ Mon, 12 Aug 2019 22:22:11: #2 finished! INFO @ Mon, 12 Aug 2019 22:22:11: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 22:22:11: #2 alternative fragment length(s) may be 3,43 bps INFO @ Mon, 12 Aug 2019 22:22:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.20_model.r WARNING @ Mon, 12 Aug 2019 22:22:11: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:22:11: #2 You may need to consider one of the other alternative d(s): 3,43 WARNING @ Mon, 12 Aug 2019 22:22:11: #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 22:22:11: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:22:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:22:25: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:22:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:22:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:22:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.05_summits.bed INFO @ Mon, 12 Aug 2019 22:22:52: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3011 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:23:05: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:23:06: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:23:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:23:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:23:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.10_summits.bed INFO @ Mon, 12 Aug 2019 22:23:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1311 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:23:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:23:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:23:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981708/SRX3981708.20_summits.bed INFO @ Mon, 12 Aug 2019 22:23:32: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (464 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。