Job ID = 1295525 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,015,255 reads read : 28,015,255 reads written : 28,015,255 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: 00:12:31 28015255 reads; of these: 28015255 (100.00%) were unpaired; of these: 7564530 (27.00%) aligned 0 times 15246937 (54.42%) aligned exactly 1 time 5203788 (18.57%) aligned >1 times 73.00% overall alignment rate Time searching: 00:12:31 Overall time: 00:12:31 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] 2962010 / 20450725 = 0.1448 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 14:28:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.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 14:28:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:28:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:28:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.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 14:28:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:28:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:29:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.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 14:29:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:29:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:29:13: 1000000 INFO @ Mon, 03 Jun 2019 14:29:13: 1000000 INFO @ Mon, 03 Jun 2019 14:29:14: 1000000 INFO @ Mon, 03 Jun 2019 14:29:26: 2000000 INFO @ Mon, 03 Jun 2019 14:29:27: 2000000 INFO @ Mon, 03 Jun 2019 14:29:27: 2000000 INFO @ Mon, 03 Jun 2019 14:29:39: 3000000 INFO @ Mon, 03 Jun 2019 14:29:40: 3000000 INFO @ Mon, 03 Jun 2019 14:29:41: 3000000 INFO @ Mon, 03 Jun 2019 14:29:51: 4000000 INFO @ Mon, 03 Jun 2019 14:29:53: 4000000 INFO @ Mon, 03 Jun 2019 14:29:54: 4000000 INFO @ Mon, 03 Jun 2019 14:30:03: 5000000 INFO @ Mon, 03 Jun 2019 14:30:07: 5000000 INFO @ Mon, 03 Jun 2019 14:30:07: 5000000 INFO @ Mon, 03 Jun 2019 14:30:16: 6000000 INFO @ Mon, 03 Jun 2019 14:30:20: 6000000 INFO @ Mon, 03 Jun 2019 14:30:21: 6000000 INFO @ Mon, 03 Jun 2019 14:30:29: 7000000 INFO @ Mon, 03 Jun 2019 14:30:33: 7000000 INFO @ Mon, 03 Jun 2019 14:30:35: 7000000 INFO @ Mon, 03 Jun 2019 14:30:41: 8000000 INFO @ Mon, 03 Jun 2019 14:30:46: 8000000 INFO @ Mon, 03 Jun 2019 14:30:48: 8000000 INFO @ Mon, 03 Jun 2019 14:30:54: 9000000 INFO @ Mon, 03 Jun 2019 14:30:59: 9000000 INFO @ Mon, 03 Jun 2019 14:31:02: 9000000 INFO @ Mon, 03 Jun 2019 14:31:06: 10000000 INFO @ Mon, 03 Jun 2019 14:31:12: 10000000 INFO @ Mon, 03 Jun 2019 14:31:15: 10000000 INFO @ Mon, 03 Jun 2019 14:31:19: 11000000 INFO @ Mon, 03 Jun 2019 14:31:25: 11000000 INFO @ Mon, 03 Jun 2019 14:31:28: 11000000 INFO @ Mon, 03 Jun 2019 14:31:31: 12000000 INFO @ Mon, 03 Jun 2019 14:31:39: 12000000 INFO @ Mon, 03 Jun 2019 14:31:42: 12000000 INFO @ Mon, 03 Jun 2019 14:31:44: 13000000 INFO @ Mon, 03 Jun 2019 14:31:53: 13000000 INFO @ Mon, 03 Jun 2019 14:31:56: 13000000 INFO @ Mon, 03 Jun 2019 14:31:57: 14000000 INFO @ Mon, 03 Jun 2019 14:32:06: 14000000 INFO @ Mon, 03 Jun 2019 14:32:09: 14000000 INFO @ Mon, 03 Jun 2019 14:32:11: 15000000 INFO @ Mon, 03 Jun 2019 14:32:19: 15000000 INFO @ Mon, 03 Jun 2019 14:32:21: 15000000 INFO @ Mon, 03 Jun 2019 14:32:23: 16000000 INFO @ Mon, 03 Jun 2019 14:32:32: 16000000 INFO @ Mon, 03 Jun 2019 14:32:34: 16000000 INFO @ Mon, 03 Jun 2019 14:32:36: 17000000 INFO @ Mon, 03 Jun 2019 14:32:43: #1 tag size is determined as 46 bps INFO @ Mon, 03 Jun 2019 14:32:43: #1 tag size = 46 INFO @ Mon, 03 Jun 2019 14:32:43: #1 total tags in treatment: 17488715 INFO @ Mon, 03 Jun 2019 14:32:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:32:43: #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 14:32:43: #1 tags after filtering in treatment: 17488715 INFO @ Mon, 03 Jun 2019 14:32:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:32:43: #1 finished! INFO @ Mon, 03 Jun 2019 14:32:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:32:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:32:45: 17000000 INFO @ Mon, 03 Jun 2019 14:32:45: #2 number of paired peaks: 344 WARNING @ Mon, 03 Jun 2019 14:32:45: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Mon, 03 Jun 2019 14:32:45: start model_add_line... INFO @ Mon, 03 Jun 2019 14:32:46: start X-correlation... INFO @ Mon, 03 Jun 2019 14:32:46: end of X-cor INFO @ Mon, 03 Jun 2019 14:32:46: #2 finished! INFO @ Mon, 03 Jun 2019 14:32:46: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 14:32:46: #2 alternative fragment length(s) may be 4,48 bps INFO @ Mon, 03 Jun 2019 14:32:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.05_model.r WARNING @ Mon, 03 Jun 2019 14:32:46: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:32:46: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Mon, 03 Jun 2019 14:32:46: #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 14:32:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:32:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:32:47: 17000000 INFO @ Mon, 03 Jun 2019 14:32:51: #1 tag size is determined as 46 bps INFO @ Mon, 03 Jun 2019 14:32:51: #1 tag size = 46 INFO @ Mon, 03 Jun 2019 14:32:51: #1 total tags in treatment: 17488715 INFO @ Mon, 03 Jun 2019 14:32:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:32:51: #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 14:32:52: #1 tags after filtering in treatment: 17488715 INFO @ Mon, 03 Jun 2019 14:32:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:32:52: #1 finished! INFO @ Mon, 03 Jun 2019 14:32:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:32:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:32:53: #1 tag size is determined as 46 bps INFO @ Mon, 03 Jun 2019 14:32:53: #1 tag size = 46 INFO @ Mon, 03 Jun 2019 14:32:53: #1 total tags in treatment: 17488715 INFO @ Mon, 03 Jun 2019 14:32:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:32:53: #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 14:32:54: #2 number of paired peaks: 344 WARNING @ Mon, 03 Jun 2019 14:32:54: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Mon, 03 Jun 2019 14:32:54: start model_add_line... INFO @ Mon, 03 Jun 2019 14:32:54: #1 tags after filtering in treatment: 17488715 INFO @ Mon, 03 Jun 2019 14:32:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:32:54: #1 finished! INFO @ Mon, 03 Jun 2019 14:32:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:32:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:32:54: start X-correlation... INFO @ Mon, 03 Jun 2019 14:32:54: end of X-cor INFO @ Mon, 03 Jun 2019 14:32:54: #2 finished! INFO @ Mon, 03 Jun 2019 14:32:54: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 14:32:54: #2 alternative fragment length(s) may be 4,48 bps INFO @ Mon, 03 Jun 2019 14:32:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.20_model.r WARNING @ Mon, 03 Jun 2019 14:32:54: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:32:54: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Mon, 03 Jun 2019 14:32:54: #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 14:32:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:32:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:32:56: #2 number of paired peaks: 344 WARNING @ Mon, 03 Jun 2019 14:32:56: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Mon, 03 Jun 2019 14:32:56: start model_add_line... INFO @ Mon, 03 Jun 2019 14:32:56: start X-correlation... INFO @ Mon, 03 Jun 2019 14:32:56: end of X-cor INFO @ Mon, 03 Jun 2019 14:32:56: #2 finished! INFO @ Mon, 03 Jun 2019 14:32:56: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 14:32:56: #2 alternative fragment length(s) may be 4,48 bps INFO @ Mon, 03 Jun 2019 14:32:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.10_model.r WARNING @ Mon, 03 Jun 2019 14:32:56: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:32:56: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Mon, 03 Jun 2019 14:32:56: #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 14:32:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:32:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:33:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:34:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:34:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:34:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:34:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:34:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.05_summits.bed INFO @ Mon, 03 Jun 2019 14:34:20: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3926 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:34:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:34:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:34:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.10_summits.bed INFO @ Mon, 03 Jun 2019 14:34:31: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2183 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:34:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:34:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:34:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX359798/SRX359798.20_summits.bed INFO @ Mon, 03 Jun 2019 14:34:32: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1037 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。