Job ID = 1294850 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,653,541 reads read : 19,653,541 reads written : 19,653,541 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: 00:11:48 19653541 reads; of these: 19653541 (100.00%) were unpaired; of these: 1806757 (9.19%) aligned 0 times 6719674 (34.19%) aligned exactly 1 time 11127110 (56.62%) aligned >1 times 90.81% overall alignment rate Time searching: 00:11:48 Overall time: 00:11:48 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] 3772926 / 17846784 = 0.2114 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 10:50:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.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 10:50:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:50:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:50:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.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 10:50:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:50:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:50:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.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 10:50:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:50:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:50:30: 1000000 INFO @ Mon, 03 Jun 2019 10:50:31: 1000000 INFO @ Mon, 03 Jun 2019 10:50:31: 1000000 INFO @ Mon, 03 Jun 2019 10:50:40: 2000000 INFO @ Mon, 03 Jun 2019 10:50:40: 2000000 INFO @ Mon, 03 Jun 2019 10:50:41: 2000000 INFO @ Mon, 03 Jun 2019 10:50:49: 3000000 INFO @ Mon, 03 Jun 2019 10:50:50: 3000000 INFO @ Mon, 03 Jun 2019 10:50:51: 3000000 INFO @ Mon, 03 Jun 2019 10:50:58: 4000000 INFO @ Mon, 03 Jun 2019 10:50:59: 4000000 INFO @ Mon, 03 Jun 2019 10:51:01: 4000000 INFO @ Mon, 03 Jun 2019 10:51:07: 5000000 INFO @ Mon, 03 Jun 2019 10:51:08: 5000000 INFO @ Mon, 03 Jun 2019 10:51:11: 5000000 INFO @ Mon, 03 Jun 2019 10:51:17: 6000000 INFO @ Mon, 03 Jun 2019 10:51:18: 6000000 INFO @ Mon, 03 Jun 2019 10:51:22: 6000000 INFO @ Mon, 03 Jun 2019 10:51:28: 7000000 INFO @ Mon, 03 Jun 2019 10:51:30: 7000000 INFO @ Mon, 03 Jun 2019 10:51:33: 7000000 INFO @ Mon, 03 Jun 2019 10:51:37: 8000000 INFO @ Mon, 03 Jun 2019 10:51:39: 8000000 INFO @ Mon, 03 Jun 2019 10:51:43: 8000000 INFO @ Mon, 03 Jun 2019 10:51:46: 9000000 INFO @ Mon, 03 Jun 2019 10:51:49: 9000000 INFO @ Mon, 03 Jun 2019 10:51:54: 9000000 INFO @ Mon, 03 Jun 2019 10:51:55: 10000000 INFO @ Mon, 03 Jun 2019 10:51:58: 10000000 INFO @ Mon, 03 Jun 2019 10:52:04: 11000000 INFO @ Mon, 03 Jun 2019 10:52:05: 10000000 INFO @ Mon, 03 Jun 2019 10:52:08: 11000000 INFO @ Mon, 03 Jun 2019 10:52:13: 12000000 INFO @ Mon, 03 Jun 2019 10:52:15: 11000000 INFO @ Mon, 03 Jun 2019 10:52:18: 12000000 INFO @ Mon, 03 Jun 2019 10:52:22: 13000000 INFO @ Mon, 03 Jun 2019 10:52:26: 12000000 INFO @ Mon, 03 Jun 2019 10:52:28: 13000000 INFO @ Mon, 03 Jun 2019 10:52:31: 14000000 INFO @ Mon, 03 Jun 2019 10:52:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:52:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:52:31: #1 total tags in treatment: 14073858 INFO @ Mon, 03 Jun 2019 10:52:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:52:31: #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 10:52:32: #1 tags after filtering in treatment: 14073858 INFO @ Mon, 03 Jun 2019 10:52:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:52:32: #1 finished! INFO @ Mon, 03 Jun 2019 10:52:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:52:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:52:33: #2 number of paired peaks: 921 WARNING @ Mon, 03 Jun 2019 10:52:33: Fewer paired peaks (921) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 921 pairs to build model! INFO @ Mon, 03 Jun 2019 10:52:33: start model_add_line... INFO @ Mon, 03 Jun 2019 10:52:33: start X-correlation... INFO @ Mon, 03 Jun 2019 10:52:33: end of X-cor INFO @ Mon, 03 Jun 2019 10:52:33: #2 finished! INFO @ Mon, 03 Jun 2019 10:52:33: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 10:52:33: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 10:52:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.05_model.r WARNING @ Mon, 03 Jun 2019 10:52:33: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:52:33: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 10:52:33: #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 10:52:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:52:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:52:36: 13000000 INFO @ Mon, 03 Jun 2019 10:52:37: 14000000 INFO @ Mon, 03 Jun 2019 10:52:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:52:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:52:37: #1 total tags in treatment: 14073858 INFO @ Mon, 03 Jun 2019 10:52:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:52:37: #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 10:52:38: #1 tags after filtering in treatment: 14073858 INFO @ Mon, 03 Jun 2019 10:52:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:52:38: #1 finished! INFO @ Mon, 03 Jun 2019 10:52:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:52:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:52:39: #2 number of paired peaks: 921 WARNING @ Mon, 03 Jun 2019 10:52:39: Fewer paired peaks (921) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 921 pairs to build model! INFO @ Mon, 03 Jun 2019 10:52:39: start model_add_line... INFO @ Mon, 03 Jun 2019 10:52:39: start X-correlation... INFO @ Mon, 03 Jun 2019 10:52:39: end of X-cor INFO @ Mon, 03 Jun 2019 10:52:39: #2 finished! INFO @ Mon, 03 Jun 2019 10:52:39: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 10:52:39: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 10:52:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.20_model.r WARNING @ Mon, 03 Jun 2019 10:52:39: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:52:39: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 10:52:39: #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 10:52:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:52:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:52:47: 14000000 INFO @ Mon, 03 Jun 2019 10:52:48: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:52:48: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:52:48: #1 total tags in treatment: 14073858 INFO @ Mon, 03 Jun 2019 10:52:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:52:48: #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 10:52:48: #1 tags after filtering in treatment: 14073858 INFO @ Mon, 03 Jun 2019 10:52:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:52:48: #1 finished! INFO @ Mon, 03 Jun 2019 10:52:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:52:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:52:49: #2 number of paired peaks: 921 WARNING @ Mon, 03 Jun 2019 10:52:49: Fewer paired peaks (921) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 921 pairs to build model! INFO @ Mon, 03 Jun 2019 10:52:49: start model_add_line... INFO @ Mon, 03 Jun 2019 10:52:49: start X-correlation... INFO @ Mon, 03 Jun 2019 10:52:49: end of X-cor INFO @ Mon, 03 Jun 2019 10:52:49: #2 finished! INFO @ Mon, 03 Jun 2019 10:52:49: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 10:52:49: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 10:52:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.10_model.r WARNING @ Mon, 03 Jun 2019 10:52:49: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:52:49: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 10:52:49: #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 10:52:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:52:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:53:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:53:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:53:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:53:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:53:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:53:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.05_summits.bed INFO @ Mon, 03 Jun 2019 10:53:37: Done! pass1 - making usageList (14 chroms): 6 millis pass2 - checking and writing primary data (12275 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:53:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:53:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:53:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.20_summits.bed INFO @ Mon, 03 Jun 2019 10:53:42: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1582 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:53:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:53:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:53:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287944/SRX287944.10_summits.bed INFO @ Mon, 03 Jun 2019 10:53:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4394 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。