Job ID = 4178514 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,539,123 reads read : 18,539,123 reads written : 18,539,123 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: 00:05:50 18539123 reads; of these: 18539123 (100.00%) were unpaired; of these: 1680323 (9.06%) aligned 0 times 11725057 (63.24%) aligned exactly 1 time 5133743 (27.69%) aligned >1 times 90.94% overall alignment rate Time searching: 00:05:50 Overall time: 00:05:50 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] 3371827 / 16858800 = 0.2000 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:51:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.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 12:51:36: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:51:36: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:51:41: 1000000 INFO @ Thu, 05 Dec 2019 12:51:46: 2000000 INFO @ Thu, 05 Dec 2019 12:51:51: 3000000 INFO @ Thu, 05 Dec 2019 12:51:56: 4000000 INFO @ Thu, 05 Dec 2019 12:52:00: 5000000 INFO @ Thu, 05 Dec 2019 12:52:05: 6000000 INFO @ Thu, 05 Dec 2019 12:52:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.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 12:52:06: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:52:06: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:52:10: 7000000 INFO @ Thu, 05 Dec 2019 12:52:11: 1000000 INFO @ Thu, 05 Dec 2019 12:52:15: 8000000 INFO @ Thu, 05 Dec 2019 12:52:16: 2000000 INFO @ Thu, 05 Dec 2019 12:52:20: 9000000 INFO @ Thu, 05 Dec 2019 12:52:21: 3000000 INFO @ Thu, 05 Dec 2019 12:52:24: 10000000 INFO @ Thu, 05 Dec 2019 12:52:25: 4000000 INFO @ Thu, 05 Dec 2019 12:52:29: 11000000 INFO @ Thu, 05 Dec 2019 12:52:30: 5000000 INFO @ Thu, 05 Dec 2019 12:52:34: 12000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:52:35: 6000000 INFO @ Thu, 05 Dec 2019 12:52:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.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 12:52:36: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:52:36: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:52:39: 13000000 INFO @ Thu, 05 Dec 2019 12:52:40: 7000000 INFO @ Thu, 05 Dec 2019 12:52:41: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:52:41: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:52:41: #1 total tags in treatment: 13486973 INFO @ Thu, 05 Dec 2019 12:52:41: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:52:41: #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 12:52:42: #1 tags after filtering in treatment: 13486973 INFO @ Thu, 05 Dec 2019 12:52:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:52:42: #1 finished! INFO @ Thu, 05 Dec 2019 12:52:42: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:52:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:52:42: 1000000 INFO @ Thu, 05 Dec 2019 12:52:43: #2 number of paired peaks: 161 WARNING @ Thu, 05 Dec 2019 12:52:43: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Thu, 05 Dec 2019 12:52:43: start model_add_line... INFO @ Thu, 05 Dec 2019 12:52:43: start X-correlation... INFO @ Thu, 05 Dec 2019 12:52:43: end of X-cor INFO @ Thu, 05 Dec 2019 12:52:43: #2 finished! INFO @ Thu, 05 Dec 2019 12:52:43: #2 predicted fragment length is 42 bps INFO @ Thu, 05 Dec 2019 12:52:43: #2 alternative fragment length(s) may be 42,60,191,509,534,551,592 bps INFO @ Thu, 05 Dec 2019 12:52:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.05_model.r WARNING @ Thu, 05 Dec 2019 12:52:43: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:52:43: #2 You may need to consider one of the other alternative d(s): 42,60,191,509,534,551,592 WARNING @ Thu, 05 Dec 2019 12:52:43: #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 12:52:43: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:52:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:52:44: 8000000 INFO @ Thu, 05 Dec 2019 12:52:47: 2000000 INFO @ Thu, 05 Dec 2019 12:52:49: 9000000 INFO @ Thu, 05 Dec 2019 12:52:52: 3000000 INFO @ Thu, 05 Dec 2019 12:52:54: 10000000 INFO @ Thu, 05 Dec 2019 12:52:57: 4000000 INFO @ Thu, 05 Dec 2019 12:52:58: 11000000 INFO @ Thu, 05 Dec 2019 12:53:02: 5000000 INFO @ Thu, 05 Dec 2019 12:53:03: 12000000 INFO @ Thu, 05 Dec 2019 12:53:06: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:53:07: 6000000 INFO @ Thu, 05 Dec 2019 12:53:08: 13000000 INFO @ Thu, 05 Dec 2019 12:53:10: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:53:10: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:53:10: #1 total tags in treatment: 13486973 INFO @ Thu, 05 Dec 2019 12:53:10: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:53:10: #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 12:53:10: #1 tags after filtering in treatment: 13486973 INFO @ Thu, 05 Dec 2019 12:53:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:53:10: #1 finished! INFO @ Thu, 05 Dec 2019 12:53:10: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:53:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:53:11: #2 number of paired peaks: 161 WARNING @ Thu, 05 Dec 2019 12:53:11: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Thu, 05 Dec 2019 12:53:11: start model_add_line... INFO @ Thu, 05 Dec 2019 12:53:11: start X-correlation... INFO @ Thu, 05 Dec 2019 12:53:11: end of X-cor INFO @ Thu, 05 Dec 2019 12:53:11: #2 finished! INFO @ Thu, 05 Dec 2019 12:53:11: #2 predicted fragment length is 42 bps INFO @ Thu, 05 Dec 2019 12:53:11: #2 alternative fragment length(s) may be 42,60,191,509,534,551,592 bps INFO @ Thu, 05 Dec 2019 12:53:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.10_model.r INFO @ Thu, 05 Dec 2019 12:53:12: 7000000 WARNING @ Thu, 05 Dec 2019 12:53:12: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:53:12: #2 You may need to consider one of the other alternative d(s): 42,60,191,509,534,551,592 WARNING @ Thu, 05 Dec 2019 12:53:12: #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 12:53:12: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:53:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:53:17: 8000000 INFO @ Thu, 05 Dec 2019 12:53:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:53:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:53:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.05_summits.bed INFO @ Thu, 05 Dec 2019 12:53:22: Done! INFO @ Thu, 05 Dec 2019 12:53:22: 9000000 pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2060 records, 4 fields): 840 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:53:27: 10000000 INFO @ Thu, 05 Dec 2019 12:53:32: 11000000 INFO @ Thu, 05 Dec 2019 12:53:35: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:53:36: 12000000 INFO @ Thu, 05 Dec 2019 12:53:41: 13000000 INFO @ Thu, 05 Dec 2019 12:53:44: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:53:44: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:53:44: #1 total tags in treatment: 13486973 INFO @ Thu, 05 Dec 2019 12:53:44: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:53:44: #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 12:53:44: #1 tags after filtering in treatment: 13486973 INFO @ Thu, 05 Dec 2019 12:53:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:53:44: #1 finished! INFO @ Thu, 05 Dec 2019 12:53:44: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:53:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:53:45: #2 number of paired peaks: 161 WARNING @ Thu, 05 Dec 2019 12:53:45: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Thu, 05 Dec 2019 12:53:45: start model_add_line... INFO @ Thu, 05 Dec 2019 12:53:45: start X-correlation... INFO @ Thu, 05 Dec 2019 12:53:45: end of X-cor INFO @ Thu, 05 Dec 2019 12:53:45: #2 finished! INFO @ Thu, 05 Dec 2019 12:53:45: #2 predicted fragment length is 42 bps INFO @ Thu, 05 Dec 2019 12:53:45: #2 alternative fragment length(s) may be 42,60,191,509,534,551,592 bps INFO @ Thu, 05 Dec 2019 12:53:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.20_model.r WARNING @ Thu, 05 Dec 2019 12:53:46: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:53:46: #2 You may need to consider one of the other alternative d(s): 42,60,191,509,534,551,592 WARNING @ Thu, 05 Dec 2019 12:53:46: #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 12:53:46: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:53:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:53:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:53:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:53:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.10_summits.bed INFO @ Thu, 05 Dec 2019 12:53:49: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (525 records, 4 fields): 1352 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:54:09: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:54:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:54:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:54:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717036/SRX5717036.20_summits.bed INFO @ Thu, 05 Dec 2019 12:54:24: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (128 records, 4 fields): 509 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。