Job ID = 1294935 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,857,991 reads read : 17,857,991 reads written : 17,857,991 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: 00:08:52 17857991 reads; of these: 17857991 (100.00%) were unpaired; of these: 814028 (4.56%) aligned 0 times 11352353 (63.57%) aligned exactly 1 time 5691610 (31.87%) aligned >1 times 95.44% overall alignment rate Time searching: 00:08:52 Overall time: 00:08:52 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] 1803993 / 17043963 = 0.1058 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/SRX288000/SRX288000.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288000/SRX288000.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288000/SRX288000.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288000/SRX288000.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/SRX288000/SRX288000.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288000/SRX288000.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288000/SRX288000.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288000/SRX288000.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/SRX288000/SRX288000.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288000/SRX288000.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288000/SRX288000.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288000/SRX288000.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 11:09:16: 1000000 INFO @ Mon, 03 Jun 2019 11:09:16: 1000000 INFO @ Mon, 03 Jun 2019 11:09:24: 2000000 INFO @ Mon, 03 Jun 2019 11:09:24: 2000000 INFO @ Mon, 03 Jun 2019 11:09:25: 2000000 INFO @ Mon, 03 Jun 2019 11:09:32: 3000000 INFO @ Mon, 03 Jun 2019 11:09:32: 3000000 INFO @ Mon, 03 Jun 2019 11:09:34: 3000000 INFO @ Mon, 03 Jun 2019 11:09:40: 4000000 INFO @ Mon, 03 Jun 2019 11:09:40: 4000000 INFO @ Mon, 03 Jun 2019 11:09:43: 4000000 INFO @ Mon, 03 Jun 2019 11:09:48: 5000000 INFO @ Mon, 03 Jun 2019 11:09:49: 5000000 INFO @ Mon, 03 Jun 2019 11:09:52: 5000000 INFO @ Mon, 03 Jun 2019 11:09:57: 6000000 INFO @ Mon, 03 Jun 2019 11:09:57: 6000000 INFO @ Mon, 03 Jun 2019 11:10:01: 6000000 INFO @ Mon, 03 Jun 2019 11:10:04: 7000000 INFO @ Mon, 03 Jun 2019 11:10:05: 7000000 INFO @ Mon, 03 Jun 2019 11:10:10: 7000000 INFO @ Mon, 03 Jun 2019 11:10:12: 8000000 INFO @ Mon, 03 Jun 2019 11:10:13: 8000000 INFO @ Mon, 03 Jun 2019 11:10:19: 8000000 INFO @ Mon, 03 Jun 2019 11:10:20: 9000000 INFO @ Mon, 03 Jun 2019 11:10:21: 9000000 INFO @ Mon, 03 Jun 2019 11:10:28: 10000000 INFO @ Mon, 03 Jun 2019 11:10:28: 9000000 INFO @ Mon, 03 Jun 2019 11:10:29: 10000000 INFO @ Mon, 03 Jun 2019 11:10:36: 10000000 INFO @ Mon, 03 Jun 2019 11:10:36: 11000000 INFO @ Mon, 03 Jun 2019 11:10:37: 11000000 INFO @ Mon, 03 Jun 2019 11:10:45: 11000000 INFO @ Mon, 03 Jun 2019 11:10:45: 12000000 INFO @ Mon, 03 Jun 2019 11:10:45: 12000000 INFO @ Mon, 03 Jun 2019 11:10:53: 13000000 INFO @ Mon, 03 Jun 2019 11:10:54: 13000000 INFO @ Mon, 03 Jun 2019 11:10:54: 12000000 INFO @ Mon, 03 Jun 2019 11:11:02: 13000000 INFO @ Mon, 03 Jun 2019 11:11:02: 14000000 INFO @ Mon, 03 Jun 2019 11:11:02: 14000000 INFO @ Mon, 03 Jun 2019 11:11:10: 14000000 INFO @ Mon, 03 Jun 2019 11:11:11: 15000000 INFO @ Mon, 03 Jun 2019 11:11:11: 15000000 INFO @ Mon, 03 Jun 2019 11:11:13: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:11:13: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:11:13: #1 total tags in treatment: 15239970 INFO @ Mon, 03 Jun 2019 11:11:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:11:13: #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 11:11:13: #1 tags after filtering in treatment: 15239970 INFO @ Mon, 03 Jun 2019 11:11:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:11:13: #1 finished! INFO @ Mon, 03 Jun 2019 11:11:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:11:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:11:13: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:11:13: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:11:13: #1 total tags in treatment: 15239970 INFO @ Mon, 03 Jun 2019 11:11:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:11:13: #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 11:11:14: #1 tags after filtering in treatment: 15239970 INFO @ Mon, 03 Jun 2019 11:11:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:11:14: #1 finished! INFO @ Mon, 03 Jun 2019 11:11:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:11:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:11:15: #2 number of paired peaks: 248 WARNING @ Mon, 03 Jun 2019 11:11:15: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Mon, 03 Jun 2019 11:11:15: start model_add_line... INFO @ Mon, 03 Jun 2019 11:11:15: start X-correlation... INFO @ Mon, 03 Jun 2019 11:11:15: end of X-cor INFO @ Mon, 03 Jun 2019 11:11:15: #2 finished! INFO @ Mon, 03 Jun 2019 11:11:15: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 11:11:15: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 11:11:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288000/SRX288000.10_model.r WARNING @ Mon, 03 Jun 2019 11:11:15: #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 11:11:15: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 11:11:15: #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 11:11:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:11:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:11:15: #2 number of paired peaks: 248 WARNING @ Mon, 03 Jun 2019 11:11:15: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Mon, 03 Jun 2019 11:11:15: start model_add_line... INFO @ Mon, 03 Jun 2019 11:11:15: start X-correlation... INFO @ Mon, 03 Jun 2019 11:11:15: end of X-cor INFO @ Mon, 03 Jun 2019 11:11:15: #2 finished! INFO @ Mon, 03 Jun 2019 11:11:15: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 11:11:15: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 11:11:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288000/SRX288000.20_model.r WARNING @ Mon, 03 Jun 2019 11:11:15: #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 11:11:15: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 11:11:15: #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 11:11:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:11:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:11:18: 15000000 INFO @ Mon, 03 Jun 2019 11:11:20: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:11:20: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:11:20: #1 total tags in treatment: 15239970 INFO @ Mon, 03 Jun 2019 11:11:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:11:20: #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 11:11:20: #1 tags after filtering in treatment: 15239970 INFO @ Mon, 03 Jun 2019 11:11:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:11:20: #1 finished! INFO @ Mon, 03 Jun 2019 11:11:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:11:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:11:21: #2 number of paired peaks: 248 WARNING @ Mon, 03 Jun 2019 11:11:21: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Mon, 03 Jun 2019 11:11:21: start model_add_line... INFO @ Mon, 03 Jun 2019 11:11:21: start X-correlation... INFO @ Mon, 03 Jun 2019 11:11:21: end of X-cor INFO @ Mon, 03 Jun 2019 11:11:21: #2 finished! INFO @ Mon, 03 Jun 2019 11:11:21: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 11:11:21: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 11:11:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288000/SRX288000.05_model.r WARNING @ Mon, 03 Jun 2019 11:11:21: #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 11:11:21: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 11:11:21: #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 11:11:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:11:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:11:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:11:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:12:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:12:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288000/SRX288000.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:12:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288000/SRX288000.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:12:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288000/SRX288000.10_summits.bed INFO @ Mon, 03 Jun 2019 11:12:15: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (1740 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:12:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288000/SRX288000.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:12:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288000/SRX288000.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:12:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288000/SRX288000.20_summits.bed INFO @ Mon, 03 Jun 2019 11:12:16: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1332 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:12:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288000/SRX288000.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:12:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288000/SRX288000.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:12:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288000/SRX288000.05_summits.bed INFO @ Mon, 03 Jun 2019 11:12:22: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2117 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。