Job ID = 1294985 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,494,133 reads read : 21,494,133 reads written : 21,494,133 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: 00:09:43 21494133 reads; of these: 21494133 (100.00%) were unpaired; of these: 1285136 (5.98%) aligned 0 times 13473051 (62.68%) aligned exactly 1 time 6735946 (31.34%) aligned >1 times 94.02% overall alignment rate Time searching: 00:09:43 Overall time: 00:09:43 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] 3043046 / 20208997 = 0.1506 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 11:29:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.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 11:29:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:29:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:29:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.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 11:29:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:29:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:29:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.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 11:29:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:29:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:29:20: 1000000 INFO @ Mon, 03 Jun 2019 11:29:20: 1000000 INFO @ Mon, 03 Jun 2019 11:29:21: 1000000 INFO @ Mon, 03 Jun 2019 11:29:31: 2000000 INFO @ Mon, 03 Jun 2019 11:29:31: 2000000 INFO @ Mon, 03 Jun 2019 11:29:32: 2000000 INFO @ Mon, 03 Jun 2019 11:29:41: 3000000 INFO @ Mon, 03 Jun 2019 11:29:43: 3000000 INFO @ Mon, 03 Jun 2019 11:29:43: 3000000 INFO @ Mon, 03 Jun 2019 11:29:51: 4000000 INFO @ Mon, 03 Jun 2019 11:29:54: 4000000 INFO @ Mon, 03 Jun 2019 11:29:55: 4000000 INFO @ Mon, 03 Jun 2019 11:30:01: 5000000 INFO @ Mon, 03 Jun 2019 11:30:06: 5000000 INFO @ Mon, 03 Jun 2019 11:30:06: 5000000 INFO @ Mon, 03 Jun 2019 11:30:10: 6000000 INFO @ Mon, 03 Jun 2019 11:30:18: 6000000 INFO @ Mon, 03 Jun 2019 11:30:18: 6000000 INFO @ Mon, 03 Jun 2019 11:30:20: 7000000 INFO @ Mon, 03 Jun 2019 11:30:29: 8000000 INFO @ Mon, 03 Jun 2019 11:30:29: 7000000 INFO @ Mon, 03 Jun 2019 11:30:30: 7000000 INFO @ Mon, 03 Jun 2019 11:30:38: 9000000 INFO @ Mon, 03 Jun 2019 11:30:40: 8000000 INFO @ Mon, 03 Jun 2019 11:30:41: 8000000 INFO @ Mon, 03 Jun 2019 11:30:48: 10000000 INFO @ Mon, 03 Jun 2019 11:30:51: 9000000 INFO @ Mon, 03 Jun 2019 11:30:52: 9000000 INFO @ Mon, 03 Jun 2019 11:30:58: 11000000 INFO @ Mon, 03 Jun 2019 11:31:02: 10000000 INFO @ Mon, 03 Jun 2019 11:31:03: 10000000 INFO @ Mon, 03 Jun 2019 11:31:07: 12000000 INFO @ Mon, 03 Jun 2019 11:31:14: 11000000 INFO @ Mon, 03 Jun 2019 11:31:14: 11000000 INFO @ Mon, 03 Jun 2019 11:31:16: 13000000 INFO @ Mon, 03 Jun 2019 11:31:25: 12000000 INFO @ Mon, 03 Jun 2019 11:31:25: 14000000 INFO @ Mon, 03 Jun 2019 11:31:25: 12000000 INFO @ Mon, 03 Jun 2019 11:31:34: 15000000 INFO @ Mon, 03 Jun 2019 11:31:36: 13000000 INFO @ Mon, 03 Jun 2019 11:31:37: 13000000 INFO @ Mon, 03 Jun 2019 11:31:43: 16000000 INFO @ Mon, 03 Jun 2019 11:31:47: 14000000 INFO @ Mon, 03 Jun 2019 11:31:48: 14000000 INFO @ Mon, 03 Jun 2019 11:31:53: 17000000 INFO @ Mon, 03 Jun 2019 11:31:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:31:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:31:55: #1 total tags in treatment: 17165951 INFO @ Mon, 03 Jun 2019 11:31:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:31:55: #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 11:31:55: #1 tags after filtering in treatment: 17165951 INFO @ Mon, 03 Jun 2019 11:31:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:31:55: #1 finished! INFO @ Mon, 03 Jun 2019 11:31:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:31:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:31:57: #2 number of paired peaks: 208 WARNING @ Mon, 03 Jun 2019 11:31:57: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Mon, 03 Jun 2019 11:31:57: start model_add_line... INFO @ Mon, 03 Jun 2019 11:31:57: start X-correlation... INFO @ Mon, 03 Jun 2019 11:31:57: end of X-cor INFO @ Mon, 03 Jun 2019 11:31:57: #2 finished! INFO @ Mon, 03 Jun 2019 11:31:57: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 11:31:57: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 11:31:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.20_model.r WARNING @ Mon, 03 Jun 2019 11:31:57: #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 11:31:57: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 11:31:57: #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 11:31:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:31:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:31:58: 15000000 INFO @ Mon, 03 Jun 2019 11:31:58: 15000000 INFO @ Mon, 03 Jun 2019 11:32:10: 16000000 INFO @ Mon, 03 Jun 2019 11:32:10: 16000000 INFO @ Mon, 03 Jun 2019 11:32:22: 17000000 INFO @ Mon, 03 Jun 2019 11:32:22: 17000000 INFO @ Mon, 03 Jun 2019 11:32:24: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:32:24: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:32:24: #1 total tags in treatment: 17165951 INFO @ Mon, 03 Jun 2019 11:32:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:32:24: #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 11:32:24: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:32:24: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:32:24: #1 total tags in treatment: 17165951 INFO @ Mon, 03 Jun 2019 11:32:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:32:24: #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 11:32:24: #1 tags after filtering in treatment: 17165951 INFO @ Mon, 03 Jun 2019 11:32:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:32:24: #1 finished! INFO @ Mon, 03 Jun 2019 11:32:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:32:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:32:24: #1 tags after filtering in treatment: 17165951 INFO @ Mon, 03 Jun 2019 11:32:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:32:24: #1 finished! INFO @ Mon, 03 Jun 2019 11:32:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:32:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:32:26: #2 number of paired peaks: 208 WARNING @ Mon, 03 Jun 2019 11:32:26: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Mon, 03 Jun 2019 11:32:26: start model_add_line... INFO @ Mon, 03 Jun 2019 11:32:26: start X-correlation... INFO @ Mon, 03 Jun 2019 11:32:26: end of X-cor INFO @ Mon, 03 Jun 2019 11:32:26: #2 finished! INFO @ Mon, 03 Jun 2019 11:32:26: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 11:32:26: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 11:32:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.05_model.r WARNING @ Mon, 03 Jun 2019 11:32:26: #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 11:32:26: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 11:32:26: #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 11:32:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:32:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:32:26: #2 number of paired peaks: 208 WARNING @ Mon, 03 Jun 2019 11:32:26: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Mon, 03 Jun 2019 11:32:26: start model_add_line... INFO @ Mon, 03 Jun 2019 11:32:26: start X-correlation... INFO @ Mon, 03 Jun 2019 11:32:26: end of X-cor INFO @ Mon, 03 Jun 2019 11:32:26: #2 finished! INFO @ Mon, 03 Jun 2019 11:32:26: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 11:32:26: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 11:32:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.10_model.r WARNING @ Mon, 03 Jun 2019 11:32:26: #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 11:32:26: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 11:32:26: #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 11:32:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:32:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:32:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:33:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:33:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:33:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.20_summits.bed INFO @ Mon, 03 Jun 2019 11:33:04: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1325 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:33:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:33:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:33:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:33:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:33:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.10_summits.bed INFO @ Mon, 03 Jun 2019 11:33:33: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1789 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:33:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:33:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:33:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288040/SRX288040.05_summits.bed INFO @ Mon, 03 Jun 2019 11:33:33: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2227 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。