Job ID = 1293960 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,125,979 reads read : 16,125,979 reads written : 16,125,979 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: 00:04:47 16125979 reads; of these: 16125979 (100.00%) were unpaired; of these: 581669 (3.61%) aligned 0 times 13132711 (81.44%) aligned exactly 1 time 2411599 (14.95%) aligned >1 times 96.39% overall alignment rate Time searching: 00:04:47 Overall time: 00:04:47 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] 3452705 / 15544310 = 0.2221 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 03:50:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.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 03:50:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:50:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:50:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.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 03:50:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:50:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:50:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.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 03:50:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:50:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:50:17: 1000000 INFO @ Mon, 03 Jun 2019 03:50:17: 1000000 INFO @ Mon, 03 Jun 2019 03:50:19: 1000000 INFO @ Mon, 03 Jun 2019 03:50:25: 2000000 INFO @ Mon, 03 Jun 2019 03:50:26: 2000000 INFO @ Mon, 03 Jun 2019 03:50:29: 2000000 INFO @ Mon, 03 Jun 2019 03:50:34: 3000000 INFO @ Mon, 03 Jun 2019 03:50:35: 3000000 INFO @ Mon, 03 Jun 2019 03:50:39: 3000000 INFO @ Mon, 03 Jun 2019 03:50:43: 4000000 INFO @ Mon, 03 Jun 2019 03:50:43: 4000000 INFO @ Mon, 03 Jun 2019 03:50:48: 4000000 INFO @ Mon, 03 Jun 2019 03:50:51: 5000000 INFO @ Mon, 03 Jun 2019 03:50:52: 5000000 INFO @ Mon, 03 Jun 2019 03:50:58: 5000000 INFO @ Mon, 03 Jun 2019 03:51:00: 6000000 INFO @ Mon, 03 Jun 2019 03:51:01: 6000000 INFO @ Mon, 03 Jun 2019 03:51:07: 6000000 INFO @ Mon, 03 Jun 2019 03:51:08: 7000000 INFO @ Mon, 03 Jun 2019 03:51:09: 7000000 INFO @ Mon, 03 Jun 2019 03:51:16: 7000000 INFO @ Mon, 03 Jun 2019 03:51:16: 8000000 INFO @ Mon, 03 Jun 2019 03:51:18: 8000000 INFO @ Mon, 03 Jun 2019 03:51:25: 9000000 INFO @ Mon, 03 Jun 2019 03:51:25: 8000000 INFO @ Mon, 03 Jun 2019 03:51:26: 9000000 INFO @ Mon, 03 Jun 2019 03:51:33: 10000000 INFO @ Mon, 03 Jun 2019 03:51:35: 9000000 INFO @ Mon, 03 Jun 2019 03:51:35: 10000000 INFO @ Mon, 03 Jun 2019 03:51:42: 11000000 INFO @ Mon, 03 Jun 2019 03:51:44: 11000000 INFO @ Mon, 03 Jun 2019 03:51:44: 10000000 INFO @ Mon, 03 Jun 2019 03:51:50: 12000000 INFO @ Mon, 03 Jun 2019 03:51:51: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:51:51: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:51:51: #1 total tags in treatment: 12091605 INFO @ Mon, 03 Jun 2019 03:51:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:51:51: #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 03:51:51: #1 tags after filtering in treatment: 12091605 INFO @ Mon, 03 Jun 2019 03:51:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:51:51: #1 finished! INFO @ Mon, 03 Jun 2019 03:51:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:51:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:51:52: 12000000 INFO @ Mon, 03 Jun 2019 03:51:53: #2 number of paired peaks: 122 WARNING @ Mon, 03 Jun 2019 03:51:53: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Mon, 03 Jun 2019 03:51:53: start model_add_line... INFO @ Mon, 03 Jun 2019 03:51:53: start X-correlation... INFO @ Mon, 03 Jun 2019 03:51:53: end of X-cor INFO @ Mon, 03 Jun 2019 03:51:53: #2 finished! INFO @ Mon, 03 Jun 2019 03:51:53: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 03:51:53: #2 alternative fragment length(s) may be 4,11,44 bps INFO @ Mon, 03 Jun 2019 03:51:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.20_model.r WARNING @ Mon, 03 Jun 2019 03:51:53: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:51:53: #2 You may need to consider one of the other alternative d(s): 4,11,44 WARNING @ Mon, 03 Jun 2019 03:51:53: #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 03:51:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:51:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:51:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:51:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:51:53: #1 total tags in treatment: 12091605 INFO @ Mon, 03 Jun 2019 03:51:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:51:53: #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 03:51:53: #1 tags after filtering in treatment: 12091605 INFO @ Mon, 03 Jun 2019 03:51:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:51:53: #1 finished! INFO @ Mon, 03 Jun 2019 03:51:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:51:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:51:54: 11000000 INFO @ Mon, 03 Jun 2019 03:51:54: #2 number of paired peaks: 122 WARNING @ Mon, 03 Jun 2019 03:51:54: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Mon, 03 Jun 2019 03:51:54: start model_add_line... INFO @ Mon, 03 Jun 2019 03:51:55: start X-correlation... INFO @ Mon, 03 Jun 2019 03:51:55: end of X-cor INFO @ Mon, 03 Jun 2019 03:51:55: #2 finished! INFO @ Mon, 03 Jun 2019 03:51:55: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 03:51:55: #2 alternative fragment length(s) may be 4,11,44 bps INFO @ Mon, 03 Jun 2019 03:51:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.05_model.r WARNING @ Mon, 03 Jun 2019 03:51:55: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:51:55: #2 You may need to consider one of the other alternative d(s): 4,11,44 WARNING @ Mon, 03 Jun 2019 03:51:55: #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 03:51:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:51:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:52:03: 12000000 INFO @ Mon, 03 Jun 2019 03:52:03: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:52:03: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:52:03: #1 total tags in treatment: 12091605 INFO @ Mon, 03 Jun 2019 03:52:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:52:03: #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 03:52:04: #1 tags after filtering in treatment: 12091605 INFO @ Mon, 03 Jun 2019 03:52:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:52:04: #1 finished! INFO @ Mon, 03 Jun 2019 03:52:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:52:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:52:05: #2 number of paired peaks: 122 WARNING @ Mon, 03 Jun 2019 03:52:05: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Mon, 03 Jun 2019 03:52:05: start model_add_line... INFO @ Mon, 03 Jun 2019 03:52:05: start X-correlation... INFO @ Mon, 03 Jun 2019 03:52:05: end of X-cor INFO @ Mon, 03 Jun 2019 03:52:05: #2 finished! INFO @ Mon, 03 Jun 2019 03:52:05: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 03:52:05: #2 alternative fragment length(s) may be 4,11,44 bps INFO @ Mon, 03 Jun 2019 03:52:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.10_model.r WARNING @ Mon, 03 Jun 2019 03:52:05: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:52:05: #2 You may need to consider one of the other alternative d(s): 4,11,44 WARNING @ Mon, 03 Jun 2019 03:52:05: #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 03:52:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:52:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:52:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:52:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:52:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:52:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:52:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:52:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.20_summits.bed INFO @ Mon, 03 Jun 2019 03:52:42: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (36 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:52:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:52:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:52:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.05_summits.bed INFO @ Mon, 03 Jun 2019 03:52:44: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2242 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:52:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:52:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:52:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX152094/SRX152094.10_summits.bed INFO @ Mon, 03 Jun 2019 03:52:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (384 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。