Job ID = 1294934 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,240,980 reads read : 19,240,980 reads written : 19,240,980 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: 00:09:17 19240980 reads; of these: 19240980 (100.00%) were unpaired; of these: 903615 (4.70%) aligned 0 times 12171546 (63.26%) aligned exactly 1 time 6165819 (32.05%) aligned >1 times 95.30% overall alignment rate Time searching: 00:09:17 Overall time: 00:09:17 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] 2075538 / 18337365 = 0.1132 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 11:09:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.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 11:09:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:09:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:09:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.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 11:09:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:09:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:09:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.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 11:09:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:09:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:09:16: 1000000 INFO @ Mon, 03 Jun 2019 11:09:18: 1000000 INFO @ Mon, 03 Jun 2019 11:09:18: 1000000 INFO @ Mon, 03 Jun 2019 11:09:24: 2000000 INFO @ Mon, 03 Jun 2019 11:09:29: 2000000 INFO @ Mon, 03 Jun 2019 11:09:29: 2000000 INFO @ Mon, 03 Jun 2019 11:09:31: 3000000 INFO @ Mon, 03 Jun 2019 11:09:39: 4000000 INFO @ Mon, 03 Jun 2019 11:09:39: 3000000 INFO @ Mon, 03 Jun 2019 11:09:40: 3000000 INFO @ Mon, 03 Jun 2019 11:09:47: 5000000 INFO @ Mon, 03 Jun 2019 11:09:50: 4000000 INFO @ Mon, 03 Jun 2019 11:09:51: 4000000 INFO @ Mon, 03 Jun 2019 11:09:54: 6000000 INFO @ Mon, 03 Jun 2019 11:10:01: 5000000 INFO @ Mon, 03 Jun 2019 11:10:01: 5000000 INFO @ Mon, 03 Jun 2019 11:10:03: 7000000 INFO @ Mon, 03 Jun 2019 11:10:11: 6000000 INFO @ Mon, 03 Jun 2019 11:10:11: 8000000 INFO @ Mon, 03 Jun 2019 11:10:12: 6000000 INFO @ Mon, 03 Jun 2019 11:10:19: 9000000 INFO @ Mon, 03 Jun 2019 11:10:21: 7000000 INFO @ Mon, 03 Jun 2019 11:10:22: 7000000 INFO @ Mon, 03 Jun 2019 11:10:26: 10000000 INFO @ Mon, 03 Jun 2019 11:10:31: 8000000 INFO @ Mon, 03 Jun 2019 11:10:33: 8000000 INFO @ Mon, 03 Jun 2019 11:10:34: 11000000 INFO @ Mon, 03 Jun 2019 11:10:41: 12000000 INFO @ Mon, 03 Jun 2019 11:10:42: 9000000 INFO @ Mon, 03 Jun 2019 11:10:43: 9000000 INFO @ Mon, 03 Jun 2019 11:10:49: 13000000 INFO @ Mon, 03 Jun 2019 11:10:52: 10000000 INFO @ Mon, 03 Jun 2019 11:10:53: 10000000 INFO @ Mon, 03 Jun 2019 11:10:57: 14000000 INFO @ Mon, 03 Jun 2019 11:11:02: 11000000 INFO @ Mon, 03 Jun 2019 11:11:03: 11000000 INFO @ Mon, 03 Jun 2019 11:11:05: 15000000 INFO @ Mon, 03 Jun 2019 11:11:12: 12000000 INFO @ Mon, 03 Jun 2019 11:11:13: 16000000 INFO @ Mon, 03 Jun 2019 11:11:14: 12000000 INFO @ Mon, 03 Jun 2019 11:11:16: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:11:16: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:11:16: #1 total tags in treatment: 16261827 INFO @ Mon, 03 Jun 2019 11:11:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:11:16: #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 11:11:16: #1 tags after filtering in treatment: 16261827 INFO @ Mon, 03 Jun 2019 11:11:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:11:16: #1 finished! INFO @ Mon, 03 Jun 2019 11:11:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:11:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:11:18: #2 number of paired peaks: 251 WARNING @ Mon, 03 Jun 2019 11:11:18: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Mon, 03 Jun 2019 11:11:18: start model_add_line... INFO @ Mon, 03 Jun 2019 11:11:18: start X-correlation... INFO @ Mon, 03 Jun 2019 11:11:18: end of X-cor INFO @ Mon, 03 Jun 2019 11:11:18: #2 finished! INFO @ Mon, 03 Jun 2019 11:11:18: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 11:11:18: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 11:11:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.10_model.r WARNING @ Mon, 03 Jun 2019 11:11:18: #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, 03 Jun 2019 11:11:18: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 11:11:18: #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 11:11:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:11:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:11:23: 13000000 INFO @ Mon, 03 Jun 2019 11:11:25: 13000000 INFO @ Mon, 03 Jun 2019 11:11:33: 14000000 INFO @ Mon, 03 Jun 2019 11:11:36: 14000000 INFO @ Mon, 03 Jun 2019 11:11:43: 15000000 INFO @ Mon, 03 Jun 2019 11:11:46: 15000000 INFO @ Mon, 03 Jun 2019 11:11:54: 16000000 INFO @ Mon, 03 Jun 2019 11:11:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:11:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:11:56: #1 total tags in treatment: 16261827 INFO @ Mon, 03 Jun 2019 11:11:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:11:56: #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 11:11:57: #1 tags after filtering in treatment: 16261827 INFO @ Mon, 03 Jun 2019 11:11:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:11:57: #1 finished! INFO @ Mon, 03 Jun 2019 11:11:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:11:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:11:57: 16000000 INFO @ Mon, 03 Jun 2019 11:11:58: #2 number of paired peaks: 251 WARNING @ Mon, 03 Jun 2019 11:11:58: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Mon, 03 Jun 2019 11:11:58: start model_add_line... INFO @ Mon, 03 Jun 2019 11:11:58: start X-correlation... INFO @ Mon, 03 Jun 2019 11:11:58: end of X-cor INFO @ Mon, 03 Jun 2019 11:11:58: #2 finished! INFO @ Mon, 03 Jun 2019 11:11:58: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 11:11:58: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 11:11:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.05_model.r WARNING @ Mon, 03 Jun 2019 11:11:58: #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, 03 Jun 2019 11:11:58: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 11:11:58: #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 11:11:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:11:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:11:59: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:11:59: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:11:59: #1 total tags in treatment: 16261827 INFO @ Mon, 03 Jun 2019 11:11:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:11:59: #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 11:12:00: #1 tags after filtering in treatment: 16261827 INFO @ Mon, 03 Jun 2019 11:12:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:12:00: #1 finished! INFO @ Mon, 03 Jun 2019 11:12:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:12:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:12:01: #2 number of paired peaks: 251 WARNING @ Mon, 03 Jun 2019 11:12:01: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Mon, 03 Jun 2019 11:12:01: start model_add_line... INFO @ Mon, 03 Jun 2019 11:12:01: start X-correlation... INFO @ Mon, 03 Jun 2019 11:12:01: end of X-cor INFO @ Mon, 03 Jun 2019 11:12:01: #2 finished! INFO @ Mon, 03 Jun 2019 11:12:01: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 11:12:01: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 11:12:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.20_model.r WARNING @ Mon, 03 Jun 2019 11:12:01: #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, 03 Jun 2019 11:12:01: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 11:12:01: #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 11:12:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:12:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:12:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:12:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:12:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:12:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.10_summits.bed INFO @ Mon, 03 Jun 2019 11:12:24: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1780 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:12:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:12:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:13:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:13:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:13:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.05_summits.bed INFO @ Mon, 03 Jun 2019 11:13:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2138 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:13:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:13:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:13:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287999/SRX287999.20_summits.bed INFO @ Mon, 03 Jun 2019 11:13:07: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1353 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。