Job ID = 1295594 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,794,592 reads read : 23,794,592 reads written : 23,794,592 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: 00:10:18 23794592 reads; of these: 23794592 (100.00%) were unpaired; of these: 1031632 (4.34%) aligned 0 times 15411072 (64.77%) aligned exactly 1 time 7351888 (30.90%) aligned >1 times 95.66% overall alignment rate Time searching: 00:10:18 Overall time: 00:10:18 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] 6008659 / 22762960 = 0.2640 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 14:44:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.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 14:44:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:44:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:44:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.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 14:44:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:44:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:44:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.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 14:44:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:44:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:44:51: 1000000 INFO @ Mon, 03 Jun 2019 14:44:52: 1000000 INFO @ Mon, 03 Jun 2019 14:44:52: 1000000 INFO @ Mon, 03 Jun 2019 14:44:59: 2000000 INFO @ Mon, 03 Jun 2019 14:45:00: 2000000 INFO @ Mon, 03 Jun 2019 14:45:01: 2000000 INFO @ Mon, 03 Jun 2019 14:45:06: 3000000 INFO @ Mon, 03 Jun 2019 14:45:08: 3000000 INFO @ Mon, 03 Jun 2019 14:45:10: 3000000 INFO @ Mon, 03 Jun 2019 14:45:13: 4000000 INFO @ Mon, 03 Jun 2019 14:45:15: 4000000 INFO @ Mon, 03 Jun 2019 14:45:18: 4000000 INFO @ Mon, 03 Jun 2019 14:45:19: 5000000 INFO @ Mon, 03 Jun 2019 14:45:23: 5000000 INFO @ Mon, 03 Jun 2019 14:45:26: 6000000 INFO @ Mon, 03 Jun 2019 14:45:27: 5000000 INFO @ Mon, 03 Jun 2019 14:45:31: 6000000 INFO @ Mon, 03 Jun 2019 14:45:34: 7000000 INFO @ Mon, 03 Jun 2019 14:45:35: 6000000 INFO @ Mon, 03 Jun 2019 14:45:39: 7000000 INFO @ Mon, 03 Jun 2019 14:45:41: 8000000 INFO @ Mon, 03 Jun 2019 14:45:44: 7000000 INFO @ Mon, 03 Jun 2019 14:45:48: 8000000 INFO @ Mon, 03 Jun 2019 14:45:48: 9000000 INFO @ Mon, 03 Jun 2019 14:45:53: 8000000 INFO @ Mon, 03 Jun 2019 14:45:56: 10000000 INFO @ Mon, 03 Jun 2019 14:45:56: 9000000 INFO @ Mon, 03 Jun 2019 14:46:02: 9000000 INFO @ Mon, 03 Jun 2019 14:46:03: 11000000 INFO @ Mon, 03 Jun 2019 14:46:05: 10000000 INFO @ Mon, 03 Jun 2019 14:46:10: 12000000 INFO @ Mon, 03 Jun 2019 14:46:11: 10000000 INFO @ Mon, 03 Jun 2019 14:46:13: 11000000 INFO @ Mon, 03 Jun 2019 14:46:17: 13000000 INFO @ Mon, 03 Jun 2019 14:46:20: 11000000 INFO @ Mon, 03 Jun 2019 14:46:22: 12000000 INFO @ Mon, 03 Jun 2019 14:46:25: 14000000 INFO @ Mon, 03 Jun 2019 14:46:29: 12000000 INFO @ Mon, 03 Jun 2019 14:46:31: 13000000 INFO @ Mon, 03 Jun 2019 14:46:32: 15000000 INFO @ Mon, 03 Jun 2019 14:46:39: 13000000 INFO @ Mon, 03 Jun 2019 14:46:39: 16000000 INFO @ Mon, 03 Jun 2019 14:46:40: 14000000 INFO @ Mon, 03 Jun 2019 14:46:45: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 14:46:45: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 14:46:45: #1 total tags in treatment: 16754301 INFO @ Mon, 03 Jun 2019 14:46:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:46:45: #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 14:46:45: #1 tags after filtering in treatment: 16754301 INFO @ Mon, 03 Jun 2019 14:46:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:46:45: #1 finished! INFO @ Mon, 03 Jun 2019 14:46:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:46:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:46:47: #2 number of paired peaks: 240 WARNING @ Mon, 03 Jun 2019 14:46:47: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Mon, 03 Jun 2019 14:46:47: start model_add_line... INFO @ Mon, 03 Jun 2019 14:46:47: start X-correlation... INFO @ Mon, 03 Jun 2019 14:46:47: end of X-cor INFO @ Mon, 03 Jun 2019 14:46:47: #2 finished! INFO @ Mon, 03 Jun 2019 14:46:47: #2 predicted fragment length is 82 bps INFO @ Mon, 03 Jun 2019 14:46:47: #2 alternative fragment length(s) may be 82 bps INFO @ Mon, 03 Jun 2019 14:46:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.20_model.r WARNING @ Mon, 03 Jun 2019 14:46:47: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:46:47: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Mon, 03 Jun 2019 14:46:47: #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 14:46:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:46:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:46:48: 14000000 INFO @ Mon, 03 Jun 2019 14:46:48: 15000000 INFO @ Mon, 03 Jun 2019 14:46:57: 16000000 INFO @ Mon, 03 Jun 2019 14:46:57: 15000000 INFO @ Mon, 03 Jun 2019 14:47:03: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 14:47:03: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 14:47:03: #1 total tags in treatment: 16754301 INFO @ Mon, 03 Jun 2019 14:47:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:47:03: #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 14:47:03: #1 tags after filtering in treatment: 16754301 INFO @ Mon, 03 Jun 2019 14:47:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:47:03: #1 finished! INFO @ Mon, 03 Jun 2019 14:47:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:47:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:47:04: #2 number of paired peaks: 240 WARNING @ Mon, 03 Jun 2019 14:47:04: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Mon, 03 Jun 2019 14:47:04: start model_add_line... INFO @ Mon, 03 Jun 2019 14:47:05: start X-correlation... INFO @ Mon, 03 Jun 2019 14:47:05: end of X-cor INFO @ Mon, 03 Jun 2019 14:47:05: #2 finished! INFO @ Mon, 03 Jun 2019 14:47:05: #2 predicted fragment length is 82 bps INFO @ Mon, 03 Jun 2019 14:47:05: #2 alternative fragment length(s) may be 82 bps INFO @ Mon, 03 Jun 2019 14:47:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.05_model.r WARNING @ Mon, 03 Jun 2019 14:47:05: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:47:05: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Mon, 03 Jun 2019 14:47:05: #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 14:47:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:47:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:47:06: 16000000 INFO @ Mon, 03 Jun 2019 14:47:13: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 14:47:13: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 14:47:13: #1 total tags in treatment: 16754301 INFO @ Mon, 03 Jun 2019 14:47:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:47:13: #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 14:47:13: #1 tags after filtering in treatment: 16754301 INFO @ Mon, 03 Jun 2019 14:47:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:47:13: #1 finished! INFO @ Mon, 03 Jun 2019 14:47:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:47:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:47:15: #2 number of paired peaks: 240 WARNING @ Mon, 03 Jun 2019 14:47:15: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Mon, 03 Jun 2019 14:47:15: start model_add_line... INFO @ Mon, 03 Jun 2019 14:47:15: start X-correlation... INFO @ Mon, 03 Jun 2019 14:47:15: end of X-cor INFO @ Mon, 03 Jun 2019 14:47:15: #2 finished! INFO @ Mon, 03 Jun 2019 14:47:15: #2 predicted fragment length is 82 bps INFO @ Mon, 03 Jun 2019 14:47:15: #2 alternative fragment length(s) may be 82 bps INFO @ Mon, 03 Jun 2019 14:47:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.10_model.r WARNING @ Mon, 03 Jun 2019 14:47:15: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:47:15: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Mon, 03 Jun 2019 14:47:15: #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 14:47:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:47:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:47:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:47:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:47:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:47:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:47:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.20_summits.bed INFO @ Mon, 03 Jun 2019 14:47:52: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1095 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:47:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:48:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:48:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:48:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.05_summits.bed INFO @ Mon, 03 Jun 2019 14:48:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3350 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:48:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:48:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:48:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX372808/SRX372808.10_summits.bed INFO @ Mon, 03 Jun 2019 14:48:20: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1792 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。