Job ID = 4178580 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 49,997,396 reads read : 99,994,792 reads written : 49,997,396 reads 0-length : 49,997,396 rm: cannot remove ‘[DSE]RR*’: 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: 00:20:12 49997396 reads; of these: 49997396 (100.00%) were unpaired; of these: 5651240 (11.30%) aligned 0 times 32486316 (64.98%) aligned exactly 1 time 11859840 (23.72%) aligned >1 times 88.70% overall alignment rate Time searching: 00:20:12 Overall time: 00:20:12 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 20 files... [bam_rmdupse_core] 22743314 / 44346156 = 0.5129 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:57:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.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 @ Thu, 05 Dec 2019 13:57:29: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:57:29: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:57:43: 1000000 INFO @ Thu, 05 Dec 2019 13:57:55: 2000000 INFO @ Thu, 05 Dec 2019 13:57:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.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 @ Thu, 05 Dec 2019 13:57:58: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:57:58: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:58:08: 1000000 INFO @ Thu, 05 Dec 2019 13:58:09: 3000000 INFO @ Thu, 05 Dec 2019 13:58:21: 2000000 INFO @ Thu, 05 Dec 2019 13:58:24: 4000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:58:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.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 @ Thu, 05 Dec 2019 13:58:29: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:58:29: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:58:31: 3000000 INFO @ Thu, 05 Dec 2019 13:58:39: 5000000 INFO @ Thu, 05 Dec 2019 13:58:45: 4000000 INFO @ Thu, 05 Dec 2019 13:58:48: 1000000 INFO @ Thu, 05 Dec 2019 13:58:59: 5000000 INFO @ Thu, 05 Dec 2019 13:59:07: 6000000 INFO @ Thu, 05 Dec 2019 13:59:07: 2000000 INFO @ Thu, 05 Dec 2019 13:59:11: 6000000 INFO @ Thu, 05 Dec 2019 13:59:18: 3000000 INFO @ Thu, 05 Dec 2019 13:59:21: 7000000 INFO @ Thu, 05 Dec 2019 13:59:21: 7000000 INFO @ Thu, 05 Dec 2019 13:59:27: 4000000 INFO @ Thu, 05 Dec 2019 13:59:31: 8000000 INFO @ Thu, 05 Dec 2019 13:59:34: 8000000 INFO @ Thu, 05 Dec 2019 13:59:37: 5000000 INFO @ Thu, 05 Dec 2019 13:59:39: 9000000 INFO @ Thu, 05 Dec 2019 13:59:46: 6000000 INFO @ Thu, 05 Dec 2019 13:59:48: 9000000 INFO @ Thu, 05 Dec 2019 13:59:48: 10000000 INFO @ Thu, 05 Dec 2019 13:59:55: 7000000 INFO @ Thu, 05 Dec 2019 13:59:57: 11000000 INFO @ Thu, 05 Dec 2019 14:00:01: 10000000 INFO @ Thu, 05 Dec 2019 14:00:04: 8000000 INFO @ Thu, 05 Dec 2019 14:00:07: 12000000 INFO @ Thu, 05 Dec 2019 14:00:12: 9000000 INFO @ Thu, 05 Dec 2019 14:00:14: 11000000 INFO @ Thu, 05 Dec 2019 14:00:16: 13000000 INFO @ Thu, 05 Dec 2019 14:00:22: 10000000 INFO @ Thu, 05 Dec 2019 14:00:25: 12000000 INFO @ Thu, 05 Dec 2019 14:00:26: 14000000 INFO @ Thu, 05 Dec 2019 14:00:31: 11000000 INFO @ Thu, 05 Dec 2019 14:00:35: 15000000 INFO @ Thu, 05 Dec 2019 14:00:36: 13000000 INFO @ Thu, 05 Dec 2019 14:00:40: 12000000 INFO @ Thu, 05 Dec 2019 14:00:44: 16000000 INFO @ Thu, 05 Dec 2019 14:00:48: 14000000 INFO @ Thu, 05 Dec 2019 14:00:49: 13000000 INFO @ Thu, 05 Dec 2019 14:00:54: 17000000 INFO @ Thu, 05 Dec 2019 14:00:58: 14000000 INFO @ Thu, 05 Dec 2019 14:01:00: 15000000 INFO @ Thu, 05 Dec 2019 14:01:04: 18000000 INFO @ Thu, 05 Dec 2019 14:01:06: 15000000 INFO @ Thu, 05 Dec 2019 14:01:12: 16000000 INFO @ Thu, 05 Dec 2019 14:01:13: 19000000 INFO @ Thu, 05 Dec 2019 14:01:15: 16000000 INFO @ Thu, 05 Dec 2019 14:01:23: 20000000 INFO @ Thu, 05 Dec 2019 14:01:24: 17000000 INFO @ Thu, 05 Dec 2019 14:01:24: 17000000 INFO @ Thu, 05 Dec 2019 14:01:32: 21000000 INFO @ Thu, 05 Dec 2019 14:01:33: 18000000 INFO @ Thu, 05 Dec 2019 14:01:37: 18000000 INFO @ Thu, 05 Dec 2019 14:01:38: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 14:01:38: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 14:01:38: #1 total tags in treatment: 21602842 INFO @ Thu, 05 Dec 2019 14:01:38: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 14:01:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 14:01:38: #1 tags after filtering in treatment: 21602842 INFO @ Thu, 05 Dec 2019 14:01:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 14:01:38: #1 finished! INFO @ Thu, 05 Dec 2019 14:01:38: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 14:01:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 14:01:40: #2 number of paired peaks: 136 WARNING @ Thu, 05 Dec 2019 14:01:40: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Thu, 05 Dec 2019 14:01:40: start model_add_line... INFO @ Thu, 05 Dec 2019 14:01:40: start X-correlation... INFO @ Thu, 05 Dec 2019 14:01:40: end of X-cor INFO @ Thu, 05 Dec 2019 14:01:40: #2 finished! INFO @ Thu, 05 Dec 2019 14:01:40: #2 predicted fragment length is 47 bps INFO @ Thu, 05 Dec 2019 14:01:40: #2 alternative fragment length(s) may be 4,47 bps INFO @ Thu, 05 Dec 2019 14:01:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.10_model.r WARNING @ Thu, 05 Dec 2019 14:01:40: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 14:01:40: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Thu, 05 Dec 2019 14:01:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 14:01:40: #3 Call peaks... INFO @ Thu, 05 Dec 2019 14:01:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 14:01:42: 19000000 INFO @ Thu, 05 Dec 2019 14:01:49: 19000000 INFO @ Thu, 05 Dec 2019 14:01:51: 20000000 INFO @ Thu, 05 Dec 2019 14:02:00: 21000000 INFO @ Thu, 05 Dec 2019 14:02:02: 20000000 INFO @ Thu, 05 Dec 2019 14:02:05: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 14:02:05: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 14:02:05: #1 total tags in treatment: 21602842 INFO @ Thu, 05 Dec 2019 14:02:05: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 14:02:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 14:02:05: #1 tags after filtering in treatment: 21602842 INFO @ Thu, 05 Dec 2019 14:02:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 14:02:05: #1 finished! INFO @ Thu, 05 Dec 2019 14:02:05: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 14:02:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 14:02:07: #2 number of paired peaks: 136 WARNING @ Thu, 05 Dec 2019 14:02:07: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Thu, 05 Dec 2019 14:02:07: start model_add_line... INFO @ Thu, 05 Dec 2019 14:02:07: start X-correlation... INFO @ Thu, 05 Dec 2019 14:02:07: end of X-cor INFO @ Thu, 05 Dec 2019 14:02:07: #2 finished! INFO @ Thu, 05 Dec 2019 14:02:07: #2 predicted fragment length is 47 bps INFO @ Thu, 05 Dec 2019 14:02:07: #2 alternative fragment length(s) may be 4,47 bps INFO @ Thu, 05 Dec 2019 14:02:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.20_model.r WARNING @ Thu, 05 Dec 2019 14:02:07: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 14:02:07: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Thu, 05 Dec 2019 14:02:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 14:02:07: #3 Call peaks... INFO @ Thu, 05 Dec 2019 14:02:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 14:02:13: 21000000 INFO @ Thu, 05 Dec 2019 14:02:19: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 14:02:19: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 14:02:19: #1 total tags in treatment: 21602842 INFO @ Thu, 05 Dec 2019 14:02:19: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 14:02:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 14:02:20: #1 tags after filtering in treatment: 21602842 INFO @ Thu, 05 Dec 2019 14:02:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 14:02:20: #1 finished! INFO @ Thu, 05 Dec 2019 14:02:20: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 14:02:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 14:02:21: #2 number of paired peaks: 136 WARNING @ Thu, 05 Dec 2019 14:02:21: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Thu, 05 Dec 2019 14:02:21: start model_add_line... INFO @ Thu, 05 Dec 2019 14:02:22: start X-correlation... INFO @ Thu, 05 Dec 2019 14:02:22: end of X-cor INFO @ Thu, 05 Dec 2019 14:02:22: #2 finished! INFO @ Thu, 05 Dec 2019 14:02:22: #2 predicted fragment length is 47 bps INFO @ Thu, 05 Dec 2019 14:02:22: #2 alternative fragment length(s) may be 4,47 bps INFO @ Thu, 05 Dec 2019 14:02:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.05_model.r WARNING @ Thu, 05 Dec 2019 14:02:22: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 14:02:22: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Thu, 05 Dec 2019 14:02:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 14:02:22: #3 Call peaks... INFO @ Thu, 05 Dec 2019 14:02:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 14:02:36: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 14:03:02: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 14:03:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.10_peaks.xls INFO @ Thu, 05 Dec 2019 14:03:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 14:03:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.10_summits.bed INFO @ Thu, 05 Dec 2019 14:03:04: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1485 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 14:03:18: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 14:03:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.20_peaks.xls INFO @ Thu, 05 Dec 2019 14:03:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 14:03:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.20_summits.bed INFO @ Thu, 05 Dec 2019 14:03:30: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (1050 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 14:03:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.05_peaks.xls INFO @ Thu, 05 Dec 2019 14:03:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 14:03:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827844/SRX5827844.05_summits.bed INFO @ Thu, 05 Dec 2019 14:03:50: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2042 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。