Job ID = 1295197 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,493,128 reads read : 18,493,128 reads written : 18,493,128 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: 00:07:15 18493128 reads; of these: 18493128 (100.00%) were unpaired; of these: 1125004 (6.08%) aligned 0 times 13121027 (70.95%) aligned exactly 1 time 4247097 (22.97%) aligned >1 times 93.92% overall alignment rate Time searching: 00:07:15 Overall time: 00:07:15 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] 1482536 / 17368124 = 0.0854 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 12:49:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.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 12:49:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:49:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:49:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.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 12:49:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:49:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:49:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.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 12:49:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:49:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:50:07: 1000000 INFO @ Mon, 03 Jun 2019 12:50:07: 1000000 INFO @ Mon, 03 Jun 2019 12:50:09: 1000000 INFO @ Mon, 03 Jun 2019 12:50:16: 2000000 INFO @ Mon, 03 Jun 2019 12:50:16: 2000000 INFO @ Mon, 03 Jun 2019 12:50:19: 2000000 INFO @ Mon, 03 Jun 2019 12:50:25: 3000000 INFO @ Mon, 03 Jun 2019 12:50:25: 3000000 INFO @ Mon, 03 Jun 2019 12:50:29: 3000000 INFO @ Mon, 03 Jun 2019 12:50:34: 4000000 INFO @ Mon, 03 Jun 2019 12:50:34: 4000000 INFO @ Mon, 03 Jun 2019 12:50:40: 4000000 INFO @ Mon, 03 Jun 2019 12:50:41: 5000000 INFO @ Mon, 03 Jun 2019 12:50:43: 5000000 INFO @ Mon, 03 Jun 2019 12:50:49: 6000000 INFO @ Mon, 03 Jun 2019 12:50:50: 5000000 INFO @ Mon, 03 Jun 2019 12:50:51: 6000000 INFO @ Mon, 03 Jun 2019 12:50:57: 7000000 INFO @ Mon, 03 Jun 2019 12:51:00: 7000000 INFO @ Mon, 03 Jun 2019 12:51:01: 6000000 INFO @ Mon, 03 Jun 2019 12:51:05: 8000000 INFO @ Mon, 03 Jun 2019 12:51:09: 8000000 INFO @ Mon, 03 Jun 2019 12:51:12: 7000000 INFO @ Mon, 03 Jun 2019 12:51:14: 9000000 INFO @ Mon, 03 Jun 2019 12:51:18: 9000000 INFO @ Mon, 03 Jun 2019 12:51:21: 10000000 INFO @ Mon, 03 Jun 2019 12:51:23: 8000000 INFO @ Mon, 03 Jun 2019 12:51:26: 10000000 INFO @ Mon, 03 Jun 2019 12:51:29: 11000000 INFO @ Mon, 03 Jun 2019 12:51:33: 9000000 INFO @ Mon, 03 Jun 2019 12:51:35: 11000000 INFO @ Mon, 03 Jun 2019 12:51:37: 12000000 INFO @ Mon, 03 Jun 2019 12:51:43: 12000000 INFO @ Mon, 03 Jun 2019 12:51:43: 10000000 INFO @ Mon, 03 Jun 2019 12:51:44: 13000000 INFO @ Mon, 03 Jun 2019 12:51:51: 13000000 INFO @ Mon, 03 Jun 2019 12:51:52: 14000000 INFO @ Mon, 03 Jun 2019 12:51:53: 11000000 INFO @ Mon, 03 Jun 2019 12:52:00: 15000000 INFO @ Mon, 03 Jun 2019 12:52:00: 14000000 INFO @ Mon, 03 Jun 2019 12:52:03: 12000000 INFO @ Mon, 03 Jun 2019 12:52:07: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:52:07: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:52:07: #1 total tags in treatment: 15885588 INFO @ Mon, 03 Jun 2019 12:52:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:52:07: #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 12:52:07: #1 tags after filtering in treatment: 15885588 INFO @ Mon, 03 Jun 2019 12:52:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:52:07: #1 finished! INFO @ Mon, 03 Jun 2019 12:52:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:52:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:52:08: 15000000 INFO @ Mon, 03 Jun 2019 12:52:08: #2 number of paired peaks: 181 WARNING @ Mon, 03 Jun 2019 12:52:08: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Mon, 03 Jun 2019 12:52:08: start model_add_line... INFO @ Mon, 03 Jun 2019 12:52:09: start X-correlation... INFO @ Mon, 03 Jun 2019 12:52:09: end of X-cor INFO @ Mon, 03 Jun 2019 12:52:09: #2 finished! INFO @ Mon, 03 Jun 2019 12:52:09: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 12:52:09: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 12:52:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.10_model.r WARNING @ Mon, 03 Jun 2019 12:52:09: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:52:09: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 12:52:09: #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 12:52:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:52:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:52:14: 13000000 INFO @ Mon, 03 Jun 2019 12:52:16: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:52:16: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:52:16: #1 total tags in treatment: 15885588 INFO @ Mon, 03 Jun 2019 12:52:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:52:16: #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 12:52:16: #1 tags after filtering in treatment: 15885588 INFO @ Mon, 03 Jun 2019 12:52:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:52:16: #1 finished! INFO @ Mon, 03 Jun 2019 12:52:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:52:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:52:18: #2 number of paired peaks: 181 WARNING @ Mon, 03 Jun 2019 12:52:18: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Mon, 03 Jun 2019 12:52:18: start model_add_line... INFO @ Mon, 03 Jun 2019 12:52:18: start X-correlation... INFO @ Mon, 03 Jun 2019 12:52:18: end of X-cor INFO @ Mon, 03 Jun 2019 12:52:18: #2 finished! INFO @ Mon, 03 Jun 2019 12:52:18: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 12:52:18: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 12:52:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.20_model.r WARNING @ Mon, 03 Jun 2019 12:52:18: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:52:18: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 12:52:18: #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 12:52:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:52:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:52:24: 14000000 INFO @ Mon, 03 Jun 2019 12:52:36: 15000000 INFO @ Mon, 03 Jun 2019 12:52:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:52:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:52:46: #1 total tags in treatment: 15885588 INFO @ Mon, 03 Jun 2019 12:52:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:52:46: #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 12:52:46: #1 tags after filtering in treatment: 15885588 INFO @ Mon, 03 Jun 2019 12:52:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:52:46: #1 finished! INFO @ Mon, 03 Jun 2019 12:52:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:52:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:52:47: #2 number of paired peaks: 181 WARNING @ Mon, 03 Jun 2019 12:52:47: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Mon, 03 Jun 2019 12:52:47: start model_add_line... INFO @ Mon, 03 Jun 2019 12:52:47: start X-correlation... INFO @ Mon, 03 Jun 2019 12:52:47: end of X-cor INFO @ Mon, 03 Jun 2019 12:52:47: #2 finished! INFO @ Mon, 03 Jun 2019 12:52:47: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 12:52:47: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 12:52:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.05_model.r WARNING @ Mon, 03 Jun 2019 12:52:47: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:52:47: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 12:52:47: #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 12:52:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:52:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:52:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:52:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:53:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:53:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:53:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.10_summits.bed INFO @ Mon, 03 Jun 2019 12:53:10: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1606 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:53:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:53:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:53:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.20_summits.bed INFO @ Mon, 03 Jun 2019 12:53:19: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1060 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:53:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:53:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:53:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:53:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331381/SRX331381.05_summits.bed INFO @ Mon, 03 Jun 2019 12:53:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1952 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。