Job ID = 1294834 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,764,096 reads read : 13,764,096 reads written : 13,764,096 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: 00:06:36 13764096 reads; of these: 13764096 (100.00%) were unpaired; of these: 516328 (3.75%) aligned 0 times 8673601 (63.02%) aligned exactly 1 time 4574167 (33.23%) aligned >1 times 96.25% overall alignment rate Time searching: 00:06:36 Overall time: 00:06:36 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] 1452455 / 13247768 = 0.1096 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 10:36:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.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 10:36:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:36:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:36:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.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 10:36:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:36:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:36:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.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 10:36:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:36:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:36:18: 1000000 INFO @ Mon, 03 Jun 2019 10:36:19: 1000000 INFO @ Mon, 03 Jun 2019 10:36:19: 1000000 INFO @ Mon, 03 Jun 2019 10:36:25: 2000000 INFO @ Mon, 03 Jun 2019 10:36:27: 2000000 INFO @ Mon, 03 Jun 2019 10:36:28: 2000000 INFO @ Mon, 03 Jun 2019 10:36:32: 3000000 INFO @ Mon, 03 Jun 2019 10:36:34: 3000000 INFO @ Mon, 03 Jun 2019 10:36:37: 3000000 INFO @ Mon, 03 Jun 2019 10:36:39: 4000000 INFO @ Mon, 03 Jun 2019 10:36:42: 4000000 INFO @ Mon, 03 Jun 2019 10:36:45: 4000000 INFO @ Mon, 03 Jun 2019 10:36:46: 5000000 INFO @ Mon, 03 Jun 2019 10:36:50: 5000000 INFO @ Mon, 03 Jun 2019 10:36:54: 6000000 INFO @ Mon, 03 Jun 2019 10:36:54: 5000000 INFO @ Mon, 03 Jun 2019 10:36:58: 6000000 INFO @ Mon, 03 Jun 2019 10:37:01: 7000000 INFO @ Mon, 03 Jun 2019 10:37:02: 6000000 INFO @ Mon, 03 Jun 2019 10:37:06: 7000000 INFO @ Mon, 03 Jun 2019 10:37:08: 8000000 INFO @ Mon, 03 Jun 2019 10:37:11: 7000000 INFO @ Mon, 03 Jun 2019 10:37:14: 8000000 INFO @ Mon, 03 Jun 2019 10:37:15: 9000000 INFO @ Mon, 03 Jun 2019 10:37:19: 8000000 INFO @ Mon, 03 Jun 2019 10:37:22: 9000000 INFO @ Mon, 03 Jun 2019 10:37:22: 10000000 INFO @ Mon, 03 Jun 2019 10:37:28: 9000000 INFO @ Mon, 03 Jun 2019 10:37:29: 11000000 INFO @ Mon, 03 Jun 2019 10:37:30: 10000000 INFO @ Mon, 03 Jun 2019 10:37:35: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:37:35: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:37:35: #1 total tags in treatment: 11795313 INFO @ Mon, 03 Jun 2019 10:37:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:37:35: #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 10:37:36: #1 tags after filtering in treatment: 11795313 INFO @ Mon, 03 Jun 2019 10:37:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:37:36: #1 finished! INFO @ Mon, 03 Jun 2019 10:37:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:37:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:37:36: 10000000 INFO @ Mon, 03 Jun 2019 10:37:37: #2 number of paired peaks: 277 WARNING @ Mon, 03 Jun 2019 10:37:37: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Mon, 03 Jun 2019 10:37:37: start model_add_line... INFO @ Mon, 03 Jun 2019 10:37:37: start X-correlation... INFO @ Mon, 03 Jun 2019 10:37:37: end of X-cor INFO @ Mon, 03 Jun 2019 10:37:37: #2 finished! INFO @ Mon, 03 Jun 2019 10:37:37: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 10:37:37: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 10:37:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.20_model.r WARNING @ Mon, 03 Jun 2019 10:37:37: #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 10:37:37: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 10:37:37: #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 10:37:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:37:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:37:38: 11000000 INFO @ Mon, 03 Jun 2019 10:37:44: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:37:44: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:37:44: #1 total tags in treatment: 11795313 INFO @ Mon, 03 Jun 2019 10:37:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:37:44: #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 10:37:44: 11000000 INFO @ Mon, 03 Jun 2019 10:37:44: #1 tags after filtering in treatment: 11795313 INFO @ Mon, 03 Jun 2019 10:37:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:37:44: #1 finished! INFO @ Mon, 03 Jun 2019 10:37:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:37:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:37:46: #2 number of paired peaks: 277 WARNING @ Mon, 03 Jun 2019 10:37:46: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Mon, 03 Jun 2019 10:37:46: start model_add_line... INFO @ Mon, 03 Jun 2019 10:37:46: start X-correlation... INFO @ Mon, 03 Jun 2019 10:37:46: end of X-cor INFO @ Mon, 03 Jun 2019 10:37:46: #2 finished! INFO @ Mon, 03 Jun 2019 10:37:46: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 10:37:46: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 10:37:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.10_model.r WARNING @ Mon, 03 Jun 2019 10:37:46: #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 10:37:46: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 10:37:46: #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 10:37:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:37:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:37:51: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:37:51: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:37:51: #1 total tags in treatment: 11795313 INFO @ Mon, 03 Jun 2019 10:37:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:37:51: #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 10:37:51: #1 tags after filtering in treatment: 11795313 INFO @ Mon, 03 Jun 2019 10:37:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:37:51: #1 finished! INFO @ Mon, 03 Jun 2019 10:37:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:37:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:37:52: #2 number of paired peaks: 277 WARNING @ Mon, 03 Jun 2019 10:37:52: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Mon, 03 Jun 2019 10:37:52: start model_add_line... INFO @ Mon, 03 Jun 2019 10:37:52: start X-correlation... INFO @ Mon, 03 Jun 2019 10:37:52: end of X-cor INFO @ Mon, 03 Jun 2019 10:37:52: #2 finished! INFO @ Mon, 03 Jun 2019 10:37:52: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 10:37:52: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 10:37:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.05_model.r WARNING @ Mon, 03 Jun 2019 10:37:52: #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 10:37:52: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 10:37:52: #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 10:37:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:37:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:38:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:38:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:38:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:38:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:38:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.20_summits.bed INFO @ Mon, 03 Jun 2019 10:38:25: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1069 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:38:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:38:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:38:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:38:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.10_summits.bed INFO @ Mon, 03 Jun 2019 10:38:34: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1517 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:38:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:38:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:38:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287933/SRX287933.05_summits.bed INFO @ Mon, 03 Jun 2019 10:38:41: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1893 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。