Job ID = 1295558 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,727,205 reads read : 29,727,205 reads written : 29,727,205 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: 00:00:01 Multiseed full-index search: 00:09:29 29727205 reads; of these: 29727205 (100.00%) were unpaired; of these: 4113177 (13.84%) aligned 0 times 21062295 (70.85%) aligned exactly 1 time 4551733 (15.31%) aligned >1 times 86.16% overall alignment rate Time searching: 00:09:30 Overall time: 00:09:30 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 12 files... [bam_rmdupse_core] 2685286 / 25614028 = 0.1048 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 14:40:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.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 14:40:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:40:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:40:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.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 14:40:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:40:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:40:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.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 14:40:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:40:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:40:47: 1000000 INFO @ Mon, 03 Jun 2019 14:40:47: 1000000 INFO @ Mon, 03 Jun 2019 14:40:48: 1000000 INFO @ Mon, 03 Jun 2019 14:40:57: 2000000 INFO @ Mon, 03 Jun 2019 14:40:58: 2000000 INFO @ Mon, 03 Jun 2019 14:40:59: 2000000 INFO @ Mon, 03 Jun 2019 14:41:06: 3000000 INFO @ Mon, 03 Jun 2019 14:41:07: 3000000 INFO @ Mon, 03 Jun 2019 14:41:08: 3000000 INFO @ Mon, 03 Jun 2019 14:41:15: 4000000 INFO @ Mon, 03 Jun 2019 14:41:16: 4000000 INFO @ Mon, 03 Jun 2019 14:41:17: 4000000 INFO @ Mon, 03 Jun 2019 14:41:24: 5000000 INFO @ Mon, 03 Jun 2019 14:41:25: 5000000 INFO @ Mon, 03 Jun 2019 14:41:26: 5000000 INFO @ Mon, 03 Jun 2019 14:41:33: 6000000 INFO @ Mon, 03 Jun 2019 14:41:34: 6000000 INFO @ Mon, 03 Jun 2019 14:41:36: 6000000 INFO @ Mon, 03 Jun 2019 14:41:42: 7000000 INFO @ Mon, 03 Jun 2019 14:41:43: 7000000 INFO @ Mon, 03 Jun 2019 14:41:45: 7000000 INFO @ Mon, 03 Jun 2019 14:41:52: 8000000 INFO @ Mon, 03 Jun 2019 14:41:52: 8000000 INFO @ Mon, 03 Jun 2019 14:41:54: 8000000 INFO @ Mon, 03 Jun 2019 14:42:01: 9000000 INFO @ Mon, 03 Jun 2019 14:42:01: 9000000 INFO @ Mon, 03 Jun 2019 14:42:05: 9000000 INFO @ Mon, 03 Jun 2019 14:42:11: 10000000 INFO @ Mon, 03 Jun 2019 14:42:11: 10000000 INFO @ Mon, 03 Jun 2019 14:42:16: 10000000 INFO @ Mon, 03 Jun 2019 14:42:20: 11000000 INFO @ Mon, 03 Jun 2019 14:42:21: 11000000 INFO @ Mon, 03 Jun 2019 14:42:25: 11000000 INFO @ Mon, 03 Jun 2019 14:42:29: 12000000 INFO @ Mon, 03 Jun 2019 14:42:29: 12000000 INFO @ Mon, 03 Jun 2019 14:42:34: 12000000 INFO @ Mon, 03 Jun 2019 14:42:38: 13000000 INFO @ Mon, 03 Jun 2019 14:42:38: 13000000 INFO @ Mon, 03 Jun 2019 14:42:43: 13000000 INFO @ Mon, 03 Jun 2019 14:42:47: 14000000 INFO @ Mon, 03 Jun 2019 14:42:47: 14000000 INFO @ Mon, 03 Jun 2019 14:42:52: 14000000 INFO @ Mon, 03 Jun 2019 14:42:56: 15000000 INFO @ Mon, 03 Jun 2019 14:42:56: 15000000 INFO @ Mon, 03 Jun 2019 14:43:02: 15000000 INFO @ Mon, 03 Jun 2019 14:43:06: 16000000 INFO @ Mon, 03 Jun 2019 14:43:06: 16000000 INFO @ Mon, 03 Jun 2019 14:43:11: 16000000 INFO @ Mon, 03 Jun 2019 14:43:15: 17000000 INFO @ Mon, 03 Jun 2019 14:43:15: 17000000 INFO @ Mon, 03 Jun 2019 14:43:21: 17000000 INFO @ Mon, 03 Jun 2019 14:43:24: 18000000 INFO @ Mon, 03 Jun 2019 14:43:25: 18000000 INFO @ Mon, 03 Jun 2019 14:43:32: 18000000 INFO @ Mon, 03 Jun 2019 14:43:34: 19000000 INFO @ Mon, 03 Jun 2019 14:43:35: 19000000 INFO @ Mon, 03 Jun 2019 14:43:41: 19000000 INFO @ Mon, 03 Jun 2019 14:43:43: 20000000 INFO @ Mon, 03 Jun 2019 14:43:44: 20000000 INFO @ Mon, 03 Jun 2019 14:43:51: 20000000 INFO @ Mon, 03 Jun 2019 14:43:52: 21000000 INFO @ Mon, 03 Jun 2019 14:43:53: 21000000 INFO @ Mon, 03 Jun 2019 14:44:00: 21000000 INFO @ Mon, 03 Jun 2019 14:44:01: 22000000 INFO @ Mon, 03 Jun 2019 14:44:03: 22000000 INFO @ Mon, 03 Jun 2019 14:44:10: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 14:44:10: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 14:44:10: #1 total tags in treatment: 22928742 INFO @ Mon, 03 Jun 2019 14:44:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:44:10: #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 14:44:10: 22000000 INFO @ Mon, 03 Jun 2019 14:44:10: #1 tags after filtering in treatment: 22928742 INFO @ Mon, 03 Jun 2019 14:44:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:44:10: #1 finished! INFO @ Mon, 03 Jun 2019 14:44:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:44:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:44:12: #2 number of paired peaks: 114 WARNING @ Mon, 03 Jun 2019 14:44:12: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Mon, 03 Jun 2019 14:44:12: start model_add_line... INFO @ Mon, 03 Jun 2019 14:44:12: start X-correlation... INFO @ Mon, 03 Jun 2019 14:44:12: end of X-cor INFO @ Mon, 03 Jun 2019 14:44:12: #2 finished! INFO @ Mon, 03 Jun 2019 14:44:12: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 14:44:12: #2 alternative fragment length(s) may be 1,50,106,168,197,235,250,275,295,353,417,477,534,550,553,576,596 bps INFO @ Mon, 03 Jun 2019 14:44:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.20_model.r WARNING @ Mon, 03 Jun 2019 14:44:12: #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 14:44:12: #2 You may need to consider one of the other alternative d(s): 1,50,106,168,197,235,250,275,295,353,417,477,534,550,553,576,596 WARNING @ Mon, 03 Jun 2019 14:44:12: #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 14:44:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:44:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:44:13: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 14:44:13: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 14:44:13: #1 total tags in treatment: 22928742 INFO @ Mon, 03 Jun 2019 14:44:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:44:13: #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 14:44:14: #1 tags after filtering in treatment: 22928742 INFO @ Mon, 03 Jun 2019 14:44:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:44:14: #1 finished! INFO @ Mon, 03 Jun 2019 14:44:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:44:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:44:16: #2 number of paired peaks: 114 WARNING @ Mon, 03 Jun 2019 14:44:16: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Mon, 03 Jun 2019 14:44:16: start model_add_line... INFO @ Mon, 03 Jun 2019 14:44:16: start X-correlation... INFO @ Mon, 03 Jun 2019 14:44:16: end of X-cor INFO @ Mon, 03 Jun 2019 14:44:16: #2 finished! INFO @ Mon, 03 Jun 2019 14:44:16: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 14:44:16: #2 alternative fragment length(s) may be 1,50,106,168,197,235,250,275,295,353,417,477,534,550,553,576,596 bps INFO @ Mon, 03 Jun 2019 14:44:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.05_model.r WARNING @ Mon, 03 Jun 2019 14:44:16: #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 14:44:16: #2 You may need to consider one of the other alternative d(s): 1,50,106,168,197,235,250,275,295,353,417,477,534,550,553,576,596 WARNING @ Mon, 03 Jun 2019 14:44:16: #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 14:44:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:44:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:44:19: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 14:44:19: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 14:44:19: #1 total tags in treatment: 22928742 INFO @ Mon, 03 Jun 2019 14:44:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:44:19: #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 14:44:19: #1 tags after filtering in treatment: 22928742 INFO @ Mon, 03 Jun 2019 14:44:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:44:19: #1 finished! INFO @ Mon, 03 Jun 2019 14:44:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:44:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:44:21: #2 number of paired peaks: 114 WARNING @ Mon, 03 Jun 2019 14:44:21: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Mon, 03 Jun 2019 14:44:21: start model_add_line... INFO @ Mon, 03 Jun 2019 14:44:21: start X-correlation... INFO @ Mon, 03 Jun 2019 14:44:21: end of X-cor INFO @ Mon, 03 Jun 2019 14:44:21: #2 finished! INFO @ Mon, 03 Jun 2019 14:44:21: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 14:44:21: #2 alternative fragment length(s) may be 1,50,106,168,197,235,250,275,295,353,417,477,534,550,553,576,596 bps INFO @ Mon, 03 Jun 2019 14:44:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.10_model.r WARNING @ Mon, 03 Jun 2019 14:44:21: #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 14:44:21: #2 You may need to consider one of the other alternative d(s): 1,50,106,168,197,235,250,275,295,353,417,477,534,550,553,576,596 WARNING @ Mon, 03 Jun 2019 14:44:21: #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 14:44:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:44:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:45:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:45:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:45:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:45:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:45:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:45:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.20_summits.bed INFO @ Mon, 03 Jun 2019 14:45:33: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (167 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:45:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:45:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:45:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.05_summits.bed INFO @ Mon, 03 Jun 2019 14:45:38: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (982 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:45:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:45:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:45:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3663168/SRX3663168.10_summits.bed INFO @ Mon, 03 Jun 2019 14:45:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (691 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。