Job ID = 1293929 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,481,092 reads read : 22,481,092 reads written : 22,481,092 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: 00:08:50 22481092 reads; of these: 22481092 (100.00%) were unpaired; of these: 936963 (4.17%) aligned 0 times 13583185 (60.42%) aligned exactly 1 time 7960944 (35.41%) aligned >1 times 95.83% overall alignment rate Time searching: 00:08:50 Overall time: 00:08:50 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] 4209101 / 21544129 = 0.1954 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 03:36:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.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 03:36:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:36:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:36:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.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 03:36:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:36:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:36:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.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 03:36:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:36:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:36:48: 1000000 INFO @ Mon, 03 Jun 2019 03:36:49: 1000000 INFO @ Mon, 03 Jun 2019 03:36:49: 1000000 INFO @ Mon, 03 Jun 2019 03:36:56: 2000000 INFO @ Mon, 03 Jun 2019 03:36:56: 2000000 INFO @ Mon, 03 Jun 2019 03:36:58: 2000000 INFO @ Mon, 03 Jun 2019 03:37:03: 3000000 INFO @ Mon, 03 Jun 2019 03:37:03: 3000000 INFO @ Mon, 03 Jun 2019 03:37:06: 3000000 INFO @ Mon, 03 Jun 2019 03:37:10: 4000000 INFO @ Mon, 03 Jun 2019 03:37:11: 4000000 INFO @ Mon, 03 Jun 2019 03:37:15: 4000000 INFO @ Mon, 03 Jun 2019 03:37:18: 5000000 INFO @ Mon, 03 Jun 2019 03:37:18: 5000000 INFO @ Mon, 03 Jun 2019 03:37:23: 5000000 INFO @ Mon, 03 Jun 2019 03:37:25: 6000000 INFO @ Mon, 03 Jun 2019 03:37:26: 6000000 INFO @ Mon, 03 Jun 2019 03:37:31: 6000000 INFO @ Mon, 03 Jun 2019 03:37:33: 7000000 INFO @ Mon, 03 Jun 2019 03:37:33: 7000000 INFO @ Mon, 03 Jun 2019 03:37:40: 8000000 INFO @ Mon, 03 Jun 2019 03:37:40: 7000000 INFO @ Mon, 03 Jun 2019 03:37:41: 8000000 INFO @ Mon, 03 Jun 2019 03:37:47: 9000000 INFO @ Mon, 03 Jun 2019 03:37:48: 8000000 INFO @ Mon, 03 Jun 2019 03:37:49: 9000000 INFO @ Mon, 03 Jun 2019 03:37:54: 10000000 INFO @ Mon, 03 Jun 2019 03:37:56: 10000000 INFO @ Mon, 03 Jun 2019 03:37:57: 9000000 INFO @ Mon, 03 Jun 2019 03:38:02: 11000000 INFO @ Mon, 03 Jun 2019 03:38:03: 11000000 INFO @ Mon, 03 Jun 2019 03:38:05: 10000000 INFO @ Mon, 03 Jun 2019 03:38:09: 12000000 INFO @ Mon, 03 Jun 2019 03:38:11: 12000000 INFO @ Mon, 03 Jun 2019 03:38:14: 11000000 INFO @ Mon, 03 Jun 2019 03:38:16: 13000000 INFO @ Mon, 03 Jun 2019 03:38:18: 13000000 INFO @ Mon, 03 Jun 2019 03:38:22: 12000000 INFO @ Mon, 03 Jun 2019 03:38:24: 14000000 INFO @ Mon, 03 Jun 2019 03:38:25: 14000000 INFO @ Mon, 03 Jun 2019 03:38:30: 13000000 INFO @ Mon, 03 Jun 2019 03:38:31: 15000000 INFO @ Mon, 03 Jun 2019 03:38:33: 15000000 INFO @ Mon, 03 Jun 2019 03:38:38: 16000000 INFO @ Mon, 03 Jun 2019 03:38:39: 14000000 INFO @ Mon, 03 Jun 2019 03:38:40: 16000000 INFO @ Mon, 03 Jun 2019 03:38:46: 17000000 INFO @ Mon, 03 Jun 2019 03:38:47: 17000000 INFO @ Mon, 03 Jun 2019 03:38:47: 15000000 INFO @ Mon, 03 Jun 2019 03:38:48: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 03:38:48: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 03:38:48: #1 total tags in treatment: 17335028 INFO @ Mon, 03 Jun 2019 03:38:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:38:48: #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 03:38:49: #1 tags after filtering in treatment: 17335028 INFO @ Mon, 03 Jun 2019 03:38:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:38:49: #1 finished! INFO @ Mon, 03 Jun 2019 03:38:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:38:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:38:50: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 03:38:50: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 03:38:50: #1 total tags in treatment: 17335028 INFO @ Mon, 03 Jun 2019 03:38:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:38:50: #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 03:38:50: #2 number of paired peaks: 526 WARNING @ Mon, 03 Jun 2019 03:38:50: Fewer paired peaks (526) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 526 pairs to build model! INFO @ Mon, 03 Jun 2019 03:38:50: start model_add_line... INFO @ Mon, 03 Jun 2019 03:38:50: start X-correlation... INFO @ Mon, 03 Jun 2019 03:38:50: end of X-cor INFO @ Mon, 03 Jun 2019 03:38:50: #2 finished! INFO @ Mon, 03 Jun 2019 03:38:50: #2 predicted fragment length is 39 bps INFO @ Mon, 03 Jun 2019 03:38:50: #2 alternative fragment length(s) may be 2,39,597 bps INFO @ Mon, 03 Jun 2019 03:38:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.05_model.r WARNING @ Mon, 03 Jun 2019 03:38:50: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:38:50: #2 You may need to consider one of the other alternative d(s): 2,39,597 WARNING @ Mon, 03 Jun 2019 03:38:50: #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 03:38:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:38:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:38:50: #1 tags after filtering in treatment: 17335028 INFO @ Mon, 03 Jun 2019 03:38:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:38:50: #1 finished! INFO @ Mon, 03 Jun 2019 03:38:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:38:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:38:52: #2 number of paired peaks: 526 WARNING @ Mon, 03 Jun 2019 03:38:52: Fewer paired peaks (526) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 526 pairs to build model! INFO @ Mon, 03 Jun 2019 03:38:52: start model_add_line... INFO @ Mon, 03 Jun 2019 03:38:52: start X-correlation... INFO @ Mon, 03 Jun 2019 03:38:52: end of X-cor INFO @ Mon, 03 Jun 2019 03:38:52: #2 finished! INFO @ Mon, 03 Jun 2019 03:38:52: #2 predicted fragment length is 39 bps INFO @ Mon, 03 Jun 2019 03:38:52: #2 alternative fragment length(s) may be 2,39,597 bps INFO @ Mon, 03 Jun 2019 03:38:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.20_model.r WARNING @ Mon, 03 Jun 2019 03:38:52: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:38:52: #2 You may need to consider one of the other alternative d(s): 2,39,597 WARNING @ Mon, 03 Jun 2019 03:38:52: #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 03:38:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:38:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:38:56: 16000000 INFO @ Mon, 03 Jun 2019 03:39:04: 17000000 INFO @ Mon, 03 Jun 2019 03:39:07: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 03:39:07: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 03:39:07: #1 total tags in treatment: 17335028 INFO @ Mon, 03 Jun 2019 03:39:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:39:07: #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 03:39:07: #1 tags after filtering in treatment: 17335028 INFO @ Mon, 03 Jun 2019 03:39:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:39:07: #1 finished! INFO @ Mon, 03 Jun 2019 03:39:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:39:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:39:09: #2 number of paired peaks: 526 WARNING @ Mon, 03 Jun 2019 03:39:09: Fewer paired peaks (526) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 526 pairs to build model! INFO @ Mon, 03 Jun 2019 03:39:09: start model_add_line... INFO @ Mon, 03 Jun 2019 03:39:09: start X-correlation... INFO @ Mon, 03 Jun 2019 03:39:09: end of X-cor INFO @ Mon, 03 Jun 2019 03:39:09: #2 finished! INFO @ Mon, 03 Jun 2019 03:39:09: #2 predicted fragment length is 39 bps INFO @ Mon, 03 Jun 2019 03:39:09: #2 alternative fragment length(s) may be 2,39,597 bps INFO @ Mon, 03 Jun 2019 03:39:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.10_model.r WARNING @ Mon, 03 Jun 2019 03:39:09: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:39:09: #2 You may need to consider one of the other alternative d(s): 2,39,597 WARNING @ Mon, 03 Jun 2019 03:39:09: #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 03:39:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:39:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:39:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:39:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:39:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:39:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:39:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:39:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.05_summits.bed INFO @ Mon, 03 Jun 2019 03:39:56: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3985 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:39:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:39:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:39:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.20_summits.bed INFO @ Mon, 03 Jun 2019 03:39:58: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (738 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:40:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:40:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:40:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX149200/SRX149200.10_summits.bed INFO @ Mon, 03 Jun 2019 03:40:14: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2448 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。