Job ID = 1295081 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,559,305 reads read : 21,559,305 reads written : 21,559,305 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: 00:08:11 21559305 reads; of these: 21559305 (100.00%) were unpaired; of these: 1335784 (6.20%) aligned 0 times 15428661 (71.56%) aligned exactly 1 time 4794860 (22.24%) aligned >1 times 93.80% overall alignment rate Time searching: 00:08:11 Overall time: 00:08:11 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] 1890728 / 20223521 = 0.0935 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 11:57:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.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 11:57:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:57:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:57:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.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 11:57:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:57:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:57:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.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 11:57:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:57:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:58:06: 1000000 INFO @ Mon, 03 Jun 2019 11:58:07: 1000000 INFO @ Mon, 03 Jun 2019 11:58:09: 1000000 INFO @ Mon, 03 Jun 2019 11:58:14: 2000000 INFO @ Mon, 03 Jun 2019 11:58:15: 2000000 INFO @ Mon, 03 Jun 2019 11:58:19: 2000000 INFO @ Mon, 03 Jun 2019 11:58:21: 3000000 INFO @ Mon, 03 Jun 2019 11:58:24: 3000000 INFO @ Mon, 03 Jun 2019 11:58:28: 3000000 INFO @ Mon, 03 Jun 2019 11:58:29: 4000000 INFO @ Mon, 03 Jun 2019 11:58:32: 4000000 INFO @ Mon, 03 Jun 2019 11:58:36: 5000000 INFO @ Mon, 03 Jun 2019 11:58:39: 4000000 INFO @ Mon, 03 Jun 2019 11:58:40: 5000000 INFO @ Mon, 03 Jun 2019 11:58:44: 6000000 INFO @ Mon, 03 Jun 2019 11:58:48: 5000000 INFO @ Mon, 03 Jun 2019 11:58:49: 6000000 INFO @ Mon, 03 Jun 2019 11:58:51: 7000000 INFO @ Mon, 03 Jun 2019 11:58:57: 7000000 INFO @ Mon, 03 Jun 2019 11:58:58: 6000000 INFO @ Mon, 03 Jun 2019 11:58:59: 8000000 INFO @ Mon, 03 Jun 2019 11:59:05: 8000000 INFO @ Mon, 03 Jun 2019 11:59:06: 9000000 INFO @ Mon, 03 Jun 2019 11:59:08: 7000000 INFO @ Mon, 03 Jun 2019 11:59:13: 9000000 INFO @ Mon, 03 Jun 2019 11:59:14: 10000000 INFO @ Mon, 03 Jun 2019 11:59:18: 8000000 INFO @ Mon, 03 Jun 2019 11:59:21: 11000000 INFO @ Mon, 03 Jun 2019 11:59:21: 10000000 INFO @ Mon, 03 Jun 2019 11:59:28: 9000000 INFO @ Mon, 03 Jun 2019 11:59:29: 12000000 INFO @ Mon, 03 Jun 2019 11:59:29: 11000000 INFO @ Mon, 03 Jun 2019 11:59:36: 13000000 INFO @ Mon, 03 Jun 2019 11:59:37: 10000000 INFO @ Mon, 03 Jun 2019 11:59:38: 12000000 INFO @ Mon, 03 Jun 2019 11:59:44: 14000000 INFO @ Mon, 03 Jun 2019 11:59:46: 13000000 INFO @ Mon, 03 Jun 2019 11:59:47: 11000000 INFO @ Mon, 03 Jun 2019 11:59:51: 15000000 INFO @ Mon, 03 Jun 2019 11:59:54: 14000000 INFO @ Mon, 03 Jun 2019 11:59:57: 12000000 INFO @ Mon, 03 Jun 2019 11:59:59: 16000000 INFO @ Mon, 03 Jun 2019 12:00:02: 15000000 INFO @ Mon, 03 Jun 2019 12:00:06: 17000000 INFO @ Mon, 03 Jun 2019 12:00:07: 13000000 INFO @ Mon, 03 Jun 2019 12:00:11: 16000000 INFO @ Mon, 03 Jun 2019 12:00:14: 18000000 INFO @ Mon, 03 Jun 2019 12:00:16: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:00:16: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:00:16: #1 total tags in treatment: 18332793 INFO @ Mon, 03 Jun 2019 12:00:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:00:16: #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 12:00:16: 14000000 INFO @ Mon, 03 Jun 2019 12:00:17: #1 tags after filtering in treatment: 18332793 INFO @ Mon, 03 Jun 2019 12:00:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:00:17: #1 finished! INFO @ Mon, 03 Jun 2019 12:00:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:00:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:00:18: #2 number of paired peaks: 153 WARNING @ Mon, 03 Jun 2019 12:00:18: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Mon, 03 Jun 2019 12:00:18: start model_add_line... INFO @ Mon, 03 Jun 2019 12:00:18: start X-correlation... INFO @ Mon, 03 Jun 2019 12:00:18: end of X-cor INFO @ Mon, 03 Jun 2019 12:00:18: #2 finished! INFO @ Mon, 03 Jun 2019 12:00:18: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 12:00:18: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 12:00:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.05_model.r WARNING @ Mon, 03 Jun 2019 12:00:18: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:00:18: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 12:00:18: #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 12:00:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:00:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:00:19: 17000000 INFO @ Mon, 03 Jun 2019 12:00:26: 15000000 INFO @ Mon, 03 Jun 2019 12:00:27: 18000000 INFO @ Mon, 03 Jun 2019 12:00:30: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:00:30: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:00:30: #1 total tags in treatment: 18332793 INFO @ Mon, 03 Jun 2019 12:00:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:00:30: #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 12:00:30: #1 tags after filtering in treatment: 18332793 INFO @ Mon, 03 Jun 2019 12:00:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:00:30: #1 finished! INFO @ Mon, 03 Jun 2019 12:00:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:00:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:00:32: #2 number of paired peaks: 153 WARNING @ Mon, 03 Jun 2019 12:00:32: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Mon, 03 Jun 2019 12:00:32: start model_add_line... INFO @ Mon, 03 Jun 2019 12:00:32: start X-correlation... INFO @ Mon, 03 Jun 2019 12:00:32: end of X-cor INFO @ Mon, 03 Jun 2019 12:00:32: #2 finished! INFO @ Mon, 03 Jun 2019 12:00:32: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 12:00:32: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 12:00:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.10_model.r WARNING @ Mon, 03 Jun 2019 12:00:32: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:00:32: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 12:00:32: #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 12:00:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:00:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:00:36: 16000000 INFO @ Mon, 03 Jun 2019 12:00:45: 17000000 INFO @ Mon, 03 Jun 2019 12:00:55: 18000000 INFO @ Mon, 03 Jun 2019 12:00:58: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:00:58: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:00:58: #1 total tags in treatment: 18332793 INFO @ Mon, 03 Jun 2019 12:00:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:00:58: #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 12:00:58: #1 tags after filtering in treatment: 18332793 INFO @ Mon, 03 Jun 2019 12:00:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:00:58: #1 finished! INFO @ Mon, 03 Jun 2019 12:00:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:00:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:01:00: #2 number of paired peaks: 153 WARNING @ Mon, 03 Jun 2019 12:01:00: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Mon, 03 Jun 2019 12:01:00: start model_add_line... INFO @ Mon, 03 Jun 2019 12:01:00: start X-correlation... INFO @ Mon, 03 Jun 2019 12:01:00: end of X-cor INFO @ Mon, 03 Jun 2019 12:01:00: #2 finished! INFO @ Mon, 03 Jun 2019 12:01:00: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 12:01:00: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 12:01:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.20_model.r WARNING @ Mon, 03 Jun 2019 12:01:00: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:01:00: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 12:01:00: #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 12:01:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:01:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:01:05: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:01:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:01:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:01:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:01:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.05_summits.bed INFO @ Mon, 03 Jun 2019 12:01:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1961 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:01:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:01:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:01:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.10_summits.bed INFO @ Mon, 03 Jun 2019 12:01:41: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1643 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:01:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:02:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:02:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:02:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318779/SRX318779.20_summits.bed INFO @ Mon, 03 Jun 2019 12:02:09: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1081 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。