Job ID = 1294796 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,355,751 reads read : 17,355,751 reads written : 17,355,751 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: 00:09:01 17355751 reads; of these: 17355751 (100.00%) were unpaired; of these: 1036274 (5.97%) aligned 0 times 10819920 (62.34%) aligned exactly 1 time 5499557 (31.69%) aligned >1 times 94.03% overall alignment rate Time searching: 00:09:01 Overall time: 00:09:01 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] 2522112 / 16319477 = 0.1545 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 10:27:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.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 10:27:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:27:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:27:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.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 10:27:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:27:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:27:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.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 10:27:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:27:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:27:40: 1000000 INFO @ Mon, 03 Jun 2019 10:27:40: 1000000 INFO @ Mon, 03 Jun 2019 10:27:40: 1000000 INFO @ Mon, 03 Jun 2019 10:27:46: 2000000 INFO @ Mon, 03 Jun 2019 10:27:48: 2000000 INFO @ Mon, 03 Jun 2019 10:27:48: 2000000 INFO @ Mon, 03 Jun 2019 10:27:53: 3000000 INFO @ Mon, 03 Jun 2019 10:27:55: 3000000 INFO @ Mon, 03 Jun 2019 10:27:55: 3000000 INFO @ Mon, 03 Jun 2019 10:28:00: 4000000 INFO @ Mon, 03 Jun 2019 10:28:03: 4000000 INFO @ Mon, 03 Jun 2019 10:28:03: 4000000 INFO @ Mon, 03 Jun 2019 10:28:07: 5000000 INFO @ Mon, 03 Jun 2019 10:28:11: 5000000 INFO @ Mon, 03 Jun 2019 10:28:11: 5000000 INFO @ Mon, 03 Jun 2019 10:28:14: 6000000 INFO @ Mon, 03 Jun 2019 10:28:18: 6000000 INFO @ Mon, 03 Jun 2019 10:28:18: 6000000 INFO @ Mon, 03 Jun 2019 10:28:21: 7000000 INFO @ Mon, 03 Jun 2019 10:28:25: 7000000 INFO @ Mon, 03 Jun 2019 10:28:25: 7000000 INFO @ Mon, 03 Jun 2019 10:28:27: 8000000 INFO @ Mon, 03 Jun 2019 10:28:33: 8000000 INFO @ Mon, 03 Jun 2019 10:28:33: 8000000 INFO @ Mon, 03 Jun 2019 10:28:34: 9000000 INFO @ Mon, 03 Jun 2019 10:28:40: 9000000 INFO @ Mon, 03 Jun 2019 10:28:41: 9000000 INFO @ Mon, 03 Jun 2019 10:28:42: 10000000 INFO @ Mon, 03 Jun 2019 10:28:49: 10000000 INFO @ Mon, 03 Jun 2019 10:28:49: 11000000 INFO @ Mon, 03 Jun 2019 10:28:49: 10000000 INFO @ Mon, 03 Jun 2019 10:28:56: 12000000 INFO @ Mon, 03 Jun 2019 10:28:56: 11000000 INFO @ Mon, 03 Jun 2019 10:28:57: 11000000 INFO @ Mon, 03 Jun 2019 10:29:03: 13000000 INFO @ Mon, 03 Jun 2019 10:29:04: 12000000 INFO @ Mon, 03 Jun 2019 10:29:05: 12000000 INFO @ Mon, 03 Jun 2019 10:29:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:29:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:29:08: #1 total tags in treatment: 13797365 INFO @ Mon, 03 Jun 2019 10:29:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:29:08: #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 10:29:09: #1 tags after filtering in treatment: 13797365 INFO @ Mon, 03 Jun 2019 10:29:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:29:09: #1 finished! INFO @ Mon, 03 Jun 2019 10:29:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:29:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:29:10: #2 number of paired peaks: 278 WARNING @ Mon, 03 Jun 2019 10:29:10: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Mon, 03 Jun 2019 10:29:10: start model_add_line... INFO @ Mon, 03 Jun 2019 10:29:10: start X-correlation... INFO @ Mon, 03 Jun 2019 10:29:10: end of X-cor INFO @ Mon, 03 Jun 2019 10:29:10: #2 finished! INFO @ Mon, 03 Jun 2019 10:29:10: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 10:29:10: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 10:29:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.05_model.r WARNING @ Mon, 03 Jun 2019 10:29:10: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:29:10: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 10:29:10: #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 10:29:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:29:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:29:12: 13000000 INFO @ Mon, 03 Jun 2019 10:29:13: 13000000 INFO @ Mon, 03 Jun 2019 10:29:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:29:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:29:19: #1 total tags in treatment: 13797365 INFO @ Mon, 03 Jun 2019 10:29:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:29:19: #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 10:29:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:29:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:29:19: #1 total tags in treatment: 13797365 INFO @ Mon, 03 Jun 2019 10:29:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:29:19: #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 10:29:19: #1 tags after filtering in treatment: 13797365 INFO @ Mon, 03 Jun 2019 10:29:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:29:19: #1 finished! INFO @ Mon, 03 Jun 2019 10:29:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:29:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:29:19: #1 tags after filtering in treatment: 13797365 INFO @ Mon, 03 Jun 2019 10:29:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:29:19: #1 finished! INFO @ Mon, 03 Jun 2019 10:29:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:29:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:29:20: #2 number of paired peaks: 278 WARNING @ Mon, 03 Jun 2019 10:29:20: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Mon, 03 Jun 2019 10:29:20: start model_add_line... INFO @ Mon, 03 Jun 2019 10:29:20: start X-correlation... INFO @ Mon, 03 Jun 2019 10:29:20: end of X-cor INFO @ Mon, 03 Jun 2019 10:29:20: #2 finished! INFO @ Mon, 03 Jun 2019 10:29:20: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 10:29:20: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 10:29:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.10_model.r WARNING @ Mon, 03 Jun 2019 10:29:20: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:29:20: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 10:29:20: #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 10:29:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:29:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:29:20: #2 number of paired peaks: 278 WARNING @ Mon, 03 Jun 2019 10:29:20: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Mon, 03 Jun 2019 10:29:20: start model_add_line... INFO @ Mon, 03 Jun 2019 10:29:20: start X-correlation... INFO @ Mon, 03 Jun 2019 10:29:20: end of X-cor INFO @ Mon, 03 Jun 2019 10:29:20: #2 finished! INFO @ Mon, 03 Jun 2019 10:29:20: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 10:29:20: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 10:29:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.20_model.r WARNING @ Mon, 03 Jun 2019 10:29:20: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:29:20: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 10:29:20: #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 10:29:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:29:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:29:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:29:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:29:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:30:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:30:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:30:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.05_summits.bed INFO @ Mon, 03 Jun 2019 10:30:05: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2169 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:30:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:30:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:30:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.10_summits.bed INFO @ Mon, 03 Jun 2019 10:30:15: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1751 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:30:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:30:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:30:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287885/SRX287885.20_summits.bed INFO @ Mon, 03 Jun 2019 10:30:16: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1299 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。