Job ID = 1293972 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,594,741 reads read : 19,594,741 reads written : 19,594,741 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: 00:05:44 19594741 reads; of these: 19594741 (100.00%) were unpaired; of these: 5681494 (28.99%) aligned 0 times 9306093 (47.49%) aligned exactly 1 time 4607154 (23.51%) aligned >1 times 71.01% overall alignment rate Time searching: 00:05:44 Overall time: 00:05:44 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_rmdupse_core] 1164899 / 13913247 = 0.0837 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 03:55:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.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 03:55:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:55:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:55:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.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 03:55:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:55:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:55:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.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 03:55:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:55:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:55:34: 1000000 INFO @ Mon, 03 Jun 2019 03:55:34: 1000000 INFO @ Mon, 03 Jun 2019 03:55:34: 1000000 INFO @ Mon, 03 Jun 2019 03:55:41: 2000000 INFO @ Mon, 03 Jun 2019 03:55:41: 2000000 INFO @ Mon, 03 Jun 2019 03:55:42: 2000000 INFO @ Mon, 03 Jun 2019 03:55:48: 3000000 INFO @ Mon, 03 Jun 2019 03:55:48: 3000000 INFO @ Mon, 03 Jun 2019 03:55:49: 3000000 INFO @ Mon, 03 Jun 2019 03:55:55: 4000000 INFO @ Mon, 03 Jun 2019 03:55:56: 4000000 INFO @ Mon, 03 Jun 2019 03:55:57: 4000000 INFO @ Mon, 03 Jun 2019 03:56:02: 5000000 INFO @ Mon, 03 Jun 2019 03:56:03: 5000000 INFO @ Mon, 03 Jun 2019 03:56:05: 5000000 INFO @ Mon, 03 Jun 2019 03:56:08: 6000000 INFO @ Mon, 03 Jun 2019 03:56:10: 6000000 INFO @ Mon, 03 Jun 2019 03:56:12: 6000000 INFO @ Mon, 03 Jun 2019 03:56:15: 7000000 INFO @ Mon, 03 Jun 2019 03:56:17: 7000000 INFO @ Mon, 03 Jun 2019 03:56:20: 7000000 INFO @ Mon, 03 Jun 2019 03:56:22: 8000000 INFO @ Mon, 03 Jun 2019 03:56:25: 8000000 INFO @ Mon, 03 Jun 2019 03:56:28: 8000000 INFO @ Mon, 03 Jun 2019 03:56:29: 9000000 INFO @ Mon, 03 Jun 2019 03:56:32: 9000000 INFO @ Mon, 03 Jun 2019 03:56:35: 9000000 INFO @ Mon, 03 Jun 2019 03:56:36: 10000000 INFO @ Mon, 03 Jun 2019 03:56:40: 10000000 INFO @ Mon, 03 Jun 2019 03:56:43: 10000000 INFO @ Mon, 03 Jun 2019 03:56:43: 11000000 INFO @ Mon, 03 Jun 2019 03:56:47: 11000000 INFO @ Mon, 03 Jun 2019 03:56:51: 12000000 INFO @ Mon, 03 Jun 2019 03:56:52: 11000000 INFO @ Mon, 03 Jun 2019 03:56:55: 12000000 INFO @ Mon, 03 Jun 2019 03:56:56: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 03:56:56: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 03:56:56: #1 total tags in treatment: 12748348 INFO @ Mon, 03 Jun 2019 03:56:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:56:56: #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 03:56:56: #1 tags after filtering in treatment: 12748348 INFO @ Mon, 03 Jun 2019 03:56:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:56:56: #1 finished! INFO @ Mon, 03 Jun 2019 03:56:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:56:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:56:57: #2 number of paired peaks: 750 WARNING @ Mon, 03 Jun 2019 03:56:57: Fewer paired peaks (750) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 750 pairs to build model! INFO @ Mon, 03 Jun 2019 03:56:57: start model_add_line... INFO @ Mon, 03 Jun 2019 03:56:58: start X-correlation... INFO @ Mon, 03 Jun 2019 03:56:58: end of X-cor INFO @ Mon, 03 Jun 2019 03:56:58: #2 finished! INFO @ Mon, 03 Jun 2019 03:56:58: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 03:56:58: #2 alternative fragment length(s) may be 4,42 bps INFO @ Mon, 03 Jun 2019 03:56:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.10_model.r WARNING @ Mon, 03 Jun 2019 03:56:58: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:56:58: #2 You may need to consider one of the other alternative d(s): 4,42 WARNING @ Mon, 03 Jun 2019 03:56:58: #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 03:56:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:56:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:57:00: 12000000 INFO @ Mon, 03 Jun 2019 03:57:00: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 03:57:00: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 03:57:00: #1 total tags in treatment: 12748348 INFO @ Mon, 03 Jun 2019 03:57:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:57:00: #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 03:57:01: #1 tags after filtering in treatment: 12748348 INFO @ Mon, 03 Jun 2019 03:57:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:57:01: #1 finished! INFO @ Mon, 03 Jun 2019 03:57:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:57:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:57:02: #2 number of paired peaks: 750 WARNING @ Mon, 03 Jun 2019 03:57:02: Fewer paired peaks (750) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 750 pairs to build model! INFO @ Mon, 03 Jun 2019 03:57:02: start model_add_line... INFO @ Mon, 03 Jun 2019 03:57:02: start X-correlation... INFO @ Mon, 03 Jun 2019 03:57:02: end of X-cor INFO @ Mon, 03 Jun 2019 03:57:02: #2 finished! INFO @ Mon, 03 Jun 2019 03:57:02: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 03:57:02: #2 alternative fragment length(s) may be 4,42 bps INFO @ Mon, 03 Jun 2019 03:57:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.05_model.r WARNING @ Mon, 03 Jun 2019 03:57:02: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:57:02: #2 You may need to consider one of the other alternative d(s): 4,42 WARNING @ Mon, 03 Jun 2019 03:57:02: #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 03:57:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:57:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:57:06: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 03:57:06: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 03:57:06: #1 total tags in treatment: 12748348 INFO @ Mon, 03 Jun 2019 03:57:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:57:06: #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 03:57:06: #1 tags after filtering in treatment: 12748348 INFO @ Mon, 03 Jun 2019 03:57:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:57:06: #1 finished! INFO @ Mon, 03 Jun 2019 03:57:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:57:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:57:07: #2 number of paired peaks: 750 WARNING @ Mon, 03 Jun 2019 03:57:07: Fewer paired peaks (750) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 750 pairs to build model! INFO @ Mon, 03 Jun 2019 03:57:07: start model_add_line... INFO @ Mon, 03 Jun 2019 03:57:07: start X-correlation... INFO @ Mon, 03 Jun 2019 03:57:07: end of X-cor INFO @ Mon, 03 Jun 2019 03:57:07: #2 finished! INFO @ Mon, 03 Jun 2019 03:57:07: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 03:57:07: #2 alternative fragment length(s) may be 4,42 bps INFO @ Mon, 03 Jun 2019 03:57:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.20_model.r WARNING @ Mon, 03 Jun 2019 03:57:07: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:57:07: #2 You may need to consider one of the other alternative d(s): 4,42 WARNING @ Mon, 03 Jun 2019 03:57:07: #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 03:57:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:57:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:57:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:57:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:57:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:57:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:57:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:57:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.10_summits.bed INFO @ Mon, 03 Jun 2019 03:57:50: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2074 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:57:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:57:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:57:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.05_summits.bed INFO @ Mon, 03 Jun 2019 03:57:55: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3645 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:57:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:57:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:57:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX152112/SRX152112.20_summits.bed INFO @ Mon, 03 Jun 2019 03:57:59: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (923 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。