Job ID = 2590311 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,575,683 reads read : 21,575,683 reads written : 21,575,683 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:36 21575683 reads; of these: 21575683 (100.00%) were unpaired; of these: 2893562 (13.41%) aligned 0 times 11812706 (54.75%) aligned exactly 1 time 6869415 (31.84%) aligned >1 times 86.59% overall alignment rate Time searching: 00:08:37 Overall time: 00:08:37 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] 2372082 / 18682121 = 0.1270 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, 12 Aug 2019 21:01:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.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, 12 Aug 2019 21:01:54: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:01:54: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:01:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.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, 12 Aug 2019 21:01:55: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:01:55: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:01:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.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, 12 Aug 2019 21:01:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:01:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:02:01: 1000000 INFO @ Mon, 12 Aug 2019 21:02:02: 1000000 INFO @ Mon, 12 Aug 2019 21:02:04: 1000000 INFO @ Mon, 12 Aug 2019 21:02:09: 2000000 INFO @ Mon, 12 Aug 2019 21:02:10: 2000000 INFO @ Mon, 12 Aug 2019 21:02:11: 2000000 INFO @ Mon, 12 Aug 2019 21:02:16: 3000000 INFO @ Mon, 12 Aug 2019 21:02:17: 3000000 INFO @ Mon, 12 Aug 2019 21:02:18: 3000000 INFO @ Mon, 12 Aug 2019 21:02:23: 4000000 INFO @ Mon, 12 Aug 2019 21:02:24: 4000000 INFO @ Mon, 12 Aug 2019 21:02:26: 4000000 INFO @ Mon, 12 Aug 2019 21:02:30: 5000000 INFO @ Mon, 12 Aug 2019 21:02:31: 5000000 INFO @ Mon, 12 Aug 2019 21:02:33: 5000000 INFO @ Mon, 12 Aug 2019 21:02:38: 6000000 INFO @ Mon, 12 Aug 2019 21:02:38: 6000000 INFO @ Mon, 12 Aug 2019 21:02:40: 6000000 INFO @ Mon, 12 Aug 2019 21:02:45: 7000000 INFO @ Mon, 12 Aug 2019 21:02:46: 7000000 INFO @ Mon, 12 Aug 2019 21:02:47: 7000000 INFO @ Mon, 12 Aug 2019 21:02:52: 8000000 INFO @ Mon, 12 Aug 2019 21:02:53: 8000000 INFO @ Mon, 12 Aug 2019 21:02:54: 8000000 INFO @ Mon, 12 Aug 2019 21:02:59: 9000000 INFO @ Mon, 12 Aug 2019 21:03:00: 9000000 INFO @ Mon, 12 Aug 2019 21:03:02: 9000000 INFO @ Mon, 12 Aug 2019 21:03:06: 10000000 INFO @ Mon, 12 Aug 2019 21:03:07: 10000000 INFO @ Mon, 12 Aug 2019 21:03:09: 10000000 INFO @ Mon, 12 Aug 2019 21:03:13: 11000000 INFO @ Mon, 12 Aug 2019 21:03:14: 11000000 INFO @ Mon, 12 Aug 2019 21:03:16: 11000000 INFO @ Mon, 12 Aug 2019 21:03:21: 12000000 INFO @ Mon, 12 Aug 2019 21:03:21: 12000000 INFO @ Mon, 12 Aug 2019 21:03:23: 12000000 INFO @ Mon, 12 Aug 2019 21:03:28: 13000000 INFO @ Mon, 12 Aug 2019 21:03:29: 13000000 INFO @ Mon, 12 Aug 2019 21:03:30: 13000000 INFO @ Mon, 12 Aug 2019 21:03:35: 14000000 INFO @ Mon, 12 Aug 2019 21:03:36: 14000000 INFO @ Mon, 12 Aug 2019 21:03:38: 14000000 INFO @ Mon, 12 Aug 2019 21:03:42: 15000000 INFO @ Mon, 12 Aug 2019 21:03:43: 15000000 INFO @ Mon, 12 Aug 2019 21:03:45: 15000000 INFO @ Mon, 12 Aug 2019 21:03:49: 16000000 INFO @ Mon, 12 Aug 2019 21:03:50: 16000000 INFO @ Mon, 12 Aug 2019 21:03:52: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:03:52: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:03:52: #1 total tags in treatment: 16310039 INFO @ Mon, 12 Aug 2019 21:03:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:03:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:03:52: #1 tags after filtering in treatment: 16310039 INFO @ Mon, 12 Aug 2019 21:03:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:03:52: #1 finished! INFO @ Mon, 12 Aug 2019 21:03:52: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:03:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:03:52: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:03:52: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:03:52: #1 total tags in treatment: 16310039 INFO @ Mon, 12 Aug 2019 21:03:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:03:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:03:53: 16000000 INFO @ Mon, 12 Aug 2019 21:03:53: #1 tags after filtering in treatment: 16310039 INFO @ Mon, 12 Aug 2019 21:03:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:03:53: #1 finished! INFO @ Mon, 12 Aug 2019 21:03:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:03:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:03:54: #2 number of paired peaks: 422 WARNING @ Mon, 12 Aug 2019 21:03:54: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Mon, 12 Aug 2019 21:03:54: start model_add_line... INFO @ Mon, 12 Aug 2019 21:03:54: start X-correlation... INFO @ Mon, 12 Aug 2019 21:03:54: end of X-cor INFO @ Mon, 12 Aug 2019 21:03:54: #2 finished! INFO @ Mon, 12 Aug 2019 21:03:54: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 21:03:54: #2 alternative fragment length(s) may be 2,50,559 bps INFO @ Mon, 12 Aug 2019 21:03:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.05_model.r WARNING @ Mon, 12 Aug 2019 21:03:54: #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, 12 Aug 2019 21:03:54: #2 You may need to consider one of the other alternative d(s): 2,50,559 WARNING @ Mon, 12 Aug 2019 21:03:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 21:03:54: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:03:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:03:54: #2 number of paired peaks: 422 WARNING @ Mon, 12 Aug 2019 21:03:54: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Mon, 12 Aug 2019 21:03:54: start model_add_line... INFO @ Mon, 12 Aug 2019 21:03:54: start X-correlation... INFO @ Mon, 12 Aug 2019 21:03:54: end of X-cor INFO @ Mon, 12 Aug 2019 21:03:54: #2 finished! INFO @ Mon, 12 Aug 2019 21:03:54: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 21:03:54: #2 alternative fragment length(s) may be 2,50,559 bps INFO @ Mon, 12 Aug 2019 21:03:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.10_model.r WARNING @ Mon, 12 Aug 2019 21:03:54: #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, 12 Aug 2019 21:03:54: #2 You may need to consider one of the other alternative d(s): 2,50,559 WARNING @ Mon, 12 Aug 2019 21:03:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 21:03:54: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:03:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:03:55: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:03:55: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:03:55: #1 total tags in treatment: 16310039 INFO @ Mon, 12 Aug 2019 21:03:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:03:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:03:55: #1 tags after filtering in treatment: 16310039 INFO @ Mon, 12 Aug 2019 21:03:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:03:55: #1 finished! INFO @ Mon, 12 Aug 2019 21:03:55: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:03:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:03:57: #2 number of paired peaks: 422 WARNING @ Mon, 12 Aug 2019 21:03:57: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Mon, 12 Aug 2019 21:03:57: start model_add_line... INFO @ Mon, 12 Aug 2019 21:03:57: start X-correlation... INFO @ Mon, 12 Aug 2019 21:03:57: end of X-cor INFO @ Mon, 12 Aug 2019 21:03:57: #2 finished! INFO @ Mon, 12 Aug 2019 21:03:57: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 21:03:57: #2 alternative fragment length(s) may be 2,50,559 bps INFO @ Mon, 12 Aug 2019 21:03:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.20_model.r WARNING @ Mon, 12 Aug 2019 21:03:57: #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, 12 Aug 2019 21:03:57: #2 You may need to consider one of the other alternative d(s): 2,50,559 WARNING @ Mon, 12 Aug 2019 21:03:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 21:03:57: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:03:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:04:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:04:37: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:04:40: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:04:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:04:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:04:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.05_summits.bed INFO @ Mon, 12 Aug 2019 21:04:58: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2655 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:04:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:04:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:04:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.10_summits.bed INFO @ Mon, 12 Aug 2019 21:04:59: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1347 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:05:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:05:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:05:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331417/SRX331417.20_summits.bed INFO @ Mon, 12 Aug 2019 21:05:02: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (456 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。