Job ID = 2590640 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,643,933 reads read : 17,643,933 reads written : 17,643,933 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1198802.sra.cache’: 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: 00:08:29 17643933 reads; of these: 17643933 (100.00%) were unpaired; of these: 997731 (5.65%) aligned 0 times 11037626 (62.56%) aligned exactly 1 time 5608576 (31.79%) aligned >1 times 94.35% overall alignment rate Time searching: 00:08:29 Overall time: 00:08:29 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] 3433221 / 16646202 = 0.2062 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 23:04:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.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 23:04:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:04:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:04:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.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 23:04:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:04:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:04:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.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 23:04:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:04:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:04:45: 1000000 INFO @ Mon, 12 Aug 2019 23:04:45: 1000000 INFO @ Mon, 12 Aug 2019 23:04:46: 1000000 INFO @ Mon, 12 Aug 2019 23:04:53: 2000000 INFO @ Mon, 12 Aug 2019 23:04:53: 2000000 INFO @ Mon, 12 Aug 2019 23:04:55: 2000000 INFO @ Mon, 12 Aug 2019 23:05:01: 3000000 INFO @ Mon, 12 Aug 2019 23:05:02: 3000000 INFO @ Mon, 12 Aug 2019 23:05:06: 3000000 INFO @ Mon, 12 Aug 2019 23:05:09: 4000000 INFO @ Mon, 12 Aug 2019 23:05:11: 4000000 INFO @ Mon, 12 Aug 2019 23:05:16: 4000000 INFO @ Mon, 12 Aug 2019 23:05:17: 5000000 INFO @ Mon, 12 Aug 2019 23:05:20: 5000000 INFO @ Mon, 12 Aug 2019 23:05:25: 6000000 INFO @ Mon, 12 Aug 2019 23:05:27: 5000000 INFO @ Mon, 12 Aug 2019 23:05:29: 6000000 INFO @ Mon, 12 Aug 2019 23:05:32: 7000000 INFO @ Mon, 12 Aug 2019 23:05:37: 6000000 INFO @ Mon, 12 Aug 2019 23:05:37: 7000000 INFO @ Mon, 12 Aug 2019 23:05:40: 8000000 INFO @ Mon, 12 Aug 2019 23:05:46: 8000000 INFO @ Mon, 12 Aug 2019 23:05:47: 7000000 INFO @ Mon, 12 Aug 2019 23:05:47: 9000000 INFO @ Mon, 12 Aug 2019 23:05:54: 9000000 INFO @ Mon, 12 Aug 2019 23:05:55: 10000000 INFO @ Mon, 12 Aug 2019 23:05:56: 8000000 INFO @ Mon, 12 Aug 2019 23:06:02: 11000000 INFO @ Mon, 12 Aug 2019 23:06:03: 10000000 INFO @ Mon, 12 Aug 2019 23:06:06: 9000000 INFO @ Mon, 12 Aug 2019 23:06:10: 12000000 INFO @ Mon, 12 Aug 2019 23:06:11: 11000000 INFO @ Mon, 12 Aug 2019 23:06:16: 10000000 INFO @ Mon, 12 Aug 2019 23:06:17: 13000000 INFO @ Mon, 12 Aug 2019 23:06:19: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:06:19: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:06:19: #1 total tags in treatment: 13212981 INFO @ Mon, 12 Aug 2019 23:06:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:06:19: #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 23:06:19: #1 tags after filtering in treatment: 13212981 INFO @ Mon, 12 Aug 2019 23:06:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:06:19: #1 finished! INFO @ Mon, 12 Aug 2019 23:06:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:06:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:06:19: 12000000 INFO @ Mon, 12 Aug 2019 23:06:20: #2 number of paired peaks: 118 WARNING @ Mon, 12 Aug 2019 23:06:20: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Mon, 12 Aug 2019 23:06:20: start model_add_line... INFO @ Mon, 12 Aug 2019 23:06:21: start X-correlation... INFO @ Mon, 12 Aug 2019 23:06:21: end of X-cor INFO @ Mon, 12 Aug 2019 23:06:21: #2 finished! INFO @ Mon, 12 Aug 2019 23:06:21: #2 predicted fragment length is 52 bps INFO @ Mon, 12 Aug 2019 23:06:21: #2 alternative fragment length(s) may be 3,52,507,512,561 bps INFO @ Mon, 12 Aug 2019 23:06:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.20_model.r WARNING @ Mon, 12 Aug 2019 23:06:21: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:06:21: #2 You may need to consider one of the other alternative d(s): 3,52,507,512,561 WARNING @ Mon, 12 Aug 2019 23:06:21: #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 23:06:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:06:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:06:25: 11000000 INFO @ Mon, 12 Aug 2019 23:06:28: 13000000 INFO @ Mon, 12 Aug 2019 23:06:30: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:06:30: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:06:30: #1 total tags in treatment: 13212981 INFO @ Mon, 12 Aug 2019 23:06:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:06:30: #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 23:06:30: #1 tags after filtering in treatment: 13212981 INFO @ Mon, 12 Aug 2019 23:06:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:06:30: #1 finished! INFO @ Mon, 12 Aug 2019 23:06:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:06:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:06:31: #2 number of paired peaks: 118 WARNING @ Mon, 12 Aug 2019 23:06:31: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Mon, 12 Aug 2019 23:06:31: start model_add_line... INFO @ Mon, 12 Aug 2019 23:06:31: start X-correlation... INFO @ Mon, 12 Aug 2019 23:06:31: end of X-cor INFO @ Mon, 12 Aug 2019 23:06:31: #2 finished! INFO @ Mon, 12 Aug 2019 23:06:31: #2 predicted fragment length is 52 bps INFO @ Mon, 12 Aug 2019 23:06:31: #2 alternative fragment length(s) may be 3,52,507,512,561 bps INFO @ Mon, 12 Aug 2019 23:06:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.10_model.r WARNING @ Mon, 12 Aug 2019 23:06:31: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:06:31: #2 You may need to consider one of the other alternative d(s): 3,52,507,512,561 WARNING @ Mon, 12 Aug 2019 23:06:31: #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 23:06:31: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:06:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:06:35: 12000000 INFO @ Mon, 12 Aug 2019 23:06:45: 13000000 INFO @ Mon, 12 Aug 2019 23:06:47: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:06:47: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:06:47: #1 total tags in treatment: 13212981 INFO @ Mon, 12 Aug 2019 23:06:47: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:06:47: #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 23:06:47: #1 tags after filtering in treatment: 13212981 INFO @ Mon, 12 Aug 2019 23:06:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:06:47: #1 finished! INFO @ Mon, 12 Aug 2019 23:06:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:06:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:06:48: #2 number of paired peaks: 118 WARNING @ Mon, 12 Aug 2019 23:06:48: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Mon, 12 Aug 2019 23:06:48: start model_add_line... INFO @ Mon, 12 Aug 2019 23:06:48: start X-correlation... INFO @ Mon, 12 Aug 2019 23:06:48: end of X-cor INFO @ Mon, 12 Aug 2019 23:06:48: #2 finished! INFO @ Mon, 12 Aug 2019 23:06:48: #2 predicted fragment length is 52 bps INFO @ Mon, 12 Aug 2019 23:06:48: #2 alternative fragment length(s) may be 3,52,507,512,561 bps INFO @ Mon, 12 Aug 2019 23:06:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.05_model.r WARNING @ Mon, 12 Aug 2019 23:06:48: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:06:48: #2 You may need to consider one of the other alternative d(s): 3,52,507,512,561 WARNING @ Mon, 12 Aug 2019 23:06:48: #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 23:06:48: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:06:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:06:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:07:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:07:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:07:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:07:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.20_summits.bed INFO @ Mon, 12 Aug 2019 23:07:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (457 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:07:25: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:07:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:07:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:07:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.10_summits.bed INFO @ Mon, 12 Aug 2019 23:07:27: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (931 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:07:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:07:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:07:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495297/SRX495297.05_summits.bed INFO @ Mon, 12 Aug 2019 23:07:42: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1314 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。