Job ID = 1294299 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,545,165 reads read : 19,545,165 reads written : 19,545,165 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: 00:10:08 19545165 reads; of these: 19545165 (100.00%) were unpaired; of these: 434530 (2.22%) aligned 0 times 13033251 (66.68%) aligned exactly 1 time 6077384 (31.09%) aligned >1 times 97.78% overall alignment rate Time searching: 00:10:08 Overall time: 00:10:08 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] 1957111 / 19110635 = 0.1024 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 06:35:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.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 06:35:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:35:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:35:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.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 06:35:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:35:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:35:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.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 06:35:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:35:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:35:29: 1000000 INFO @ Mon, 03 Jun 2019 06:35:29: 1000000 INFO @ Mon, 03 Jun 2019 06:35:30: 1000000 INFO @ Mon, 03 Jun 2019 06:35:36: 2000000 INFO @ Mon, 03 Jun 2019 06:35:36: 2000000 INFO @ Mon, 03 Jun 2019 06:35:38: 2000000 INFO @ Mon, 03 Jun 2019 06:35:44: 3000000 INFO @ Mon, 03 Jun 2019 06:35:44: 3000000 INFO @ Mon, 03 Jun 2019 06:35:47: 3000000 INFO @ Mon, 03 Jun 2019 06:35:52: 4000000 INFO @ Mon, 03 Jun 2019 06:35:52: 4000000 INFO @ Mon, 03 Jun 2019 06:35:55: 4000000 INFO @ Mon, 03 Jun 2019 06:35:59: 5000000 INFO @ Mon, 03 Jun 2019 06:35:59: 5000000 INFO @ Mon, 03 Jun 2019 06:36:04: 5000000 INFO @ Mon, 03 Jun 2019 06:36:07: 6000000 INFO @ Mon, 03 Jun 2019 06:36:07: 6000000 INFO @ Mon, 03 Jun 2019 06:36:13: 6000000 INFO @ Mon, 03 Jun 2019 06:36:16: 7000000 INFO @ Mon, 03 Jun 2019 06:36:16: 7000000 INFO @ Mon, 03 Jun 2019 06:36:21: 7000000 INFO @ Mon, 03 Jun 2019 06:36:24: 8000000 INFO @ Mon, 03 Jun 2019 06:36:24: 8000000 INFO @ Mon, 03 Jun 2019 06:36:30: 8000000 INFO @ Mon, 03 Jun 2019 06:36:31: 9000000 INFO @ Mon, 03 Jun 2019 06:36:32: 9000000 INFO @ Mon, 03 Jun 2019 06:36:38: 9000000 INFO @ Mon, 03 Jun 2019 06:36:39: 10000000 INFO @ Mon, 03 Jun 2019 06:36:39: 10000000 INFO @ Mon, 03 Jun 2019 06:36:46: 11000000 INFO @ Mon, 03 Jun 2019 06:36:47: 11000000 INFO @ Mon, 03 Jun 2019 06:36:48: 10000000 INFO @ Mon, 03 Jun 2019 06:36:54: 12000000 INFO @ Mon, 03 Jun 2019 06:36:55: 12000000 INFO @ Mon, 03 Jun 2019 06:36:57: 11000000 INFO @ Mon, 03 Jun 2019 06:37:02: 13000000 INFO @ Mon, 03 Jun 2019 06:37:02: 13000000 INFO @ Mon, 03 Jun 2019 06:37:05: 12000000 INFO @ Mon, 03 Jun 2019 06:37:09: 14000000 INFO @ Mon, 03 Jun 2019 06:37:10: 14000000 INFO @ Mon, 03 Jun 2019 06:37:14: 13000000 INFO @ Mon, 03 Jun 2019 06:37:17: 15000000 INFO @ Mon, 03 Jun 2019 06:37:18: 15000000 INFO @ Mon, 03 Jun 2019 06:37:23: 14000000 INFO @ Mon, 03 Jun 2019 06:37:24: 16000000 INFO @ Mon, 03 Jun 2019 06:37:25: 16000000 INFO @ Mon, 03 Jun 2019 06:37:31: 15000000 INFO @ Mon, 03 Jun 2019 06:37:32: 17000000 INFO @ Mon, 03 Jun 2019 06:37:33: 17000000 INFO @ Mon, 03 Jun 2019 06:37:33: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:37:33: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:37:33: #1 total tags in treatment: 17153524 INFO @ Mon, 03 Jun 2019 06:37:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:37:33: #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 06:37:34: #1 tags after filtering in treatment: 17153524 INFO @ Mon, 03 Jun 2019 06:37:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:37:34: #1 finished! INFO @ Mon, 03 Jun 2019 06:37:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:37:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:37:34: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:37:34: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:37:34: #1 total tags in treatment: 17153524 INFO @ Mon, 03 Jun 2019 06:37:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:37:34: #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 06:37:35: #1 tags after filtering in treatment: 17153524 INFO @ Mon, 03 Jun 2019 06:37:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:37:35: #1 finished! INFO @ Mon, 03 Jun 2019 06:37:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:37:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:37:35: #2 number of paired peaks: 873 WARNING @ Mon, 03 Jun 2019 06:37:35: Fewer paired peaks (873) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 873 pairs to build model! INFO @ Mon, 03 Jun 2019 06:37:35: start model_add_line... INFO @ Mon, 03 Jun 2019 06:37:35: start X-correlation... INFO @ Mon, 03 Jun 2019 06:37:35: end of X-cor INFO @ Mon, 03 Jun 2019 06:37:35: #2 finished! INFO @ Mon, 03 Jun 2019 06:37:35: #2 predicted fragment length is 66 bps INFO @ Mon, 03 Jun 2019 06:37:35: #2 alternative fragment length(s) may be 3,66 bps INFO @ Mon, 03 Jun 2019 06:37:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.05_model.r WARNING @ Mon, 03 Jun 2019 06:37:35: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:37:35: #2 You may need to consider one of the other alternative d(s): 3,66 WARNING @ Mon, 03 Jun 2019 06:37:35: #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 06:37:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:37:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:37:36: #2 number of paired peaks: 873 WARNING @ Mon, 03 Jun 2019 06:37:36: Fewer paired peaks (873) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 873 pairs to build model! INFO @ Mon, 03 Jun 2019 06:37:36: start model_add_line... INFO @ Mon, 03 Jun 2019 06:37:36: start X-correlation... INFO @ Mon, 03 Jun 2019 06:37:36: end of X-cor INFO @ Mon, 03 Jun 2019 06:37:36: #2 finished! INFO @ Mon, 03 Jun 2019 06:37:36: #2 predicted fragment length is 66 bps INFO @ Mon, 03 Jun 2019 06:37:36: #2 alternative fragment length(s) may be 3,66 bps INFO @ Mon, 03 Jun 2019 06:37:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.20_model.r WARNING @ Mon, 03 Jun 2019 06:37:36: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:37:36: #2 You may need to consider one of the other alternative d(s): 3,66 WARNING @ Mon, 03 Jun 2019 06:37:36: #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 06:37:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:37:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:37:40: 16000000 INFO @ Mon, 03 Jun 2019 06:37:48: 17000000 INFO @ Mon, 03 Jun 2019 06:37:50: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:37:50: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:37:50: #1 total tags in treatment: 17153524 INFO @ Mon, 03 Jun 2019 06:37:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:37:50: #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 06:37:50: #1 tags after filtering in treatment: 17153524 INFO @ Mon, 03 Jun 2019 06:37:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:37:50: #1 finished! INFO @ Mon, 03 Jun 2019 06:37:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:37:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:37:52: #2 number of paired peaks: 873 WARNING @ Mon, 03 Jun 2019 06:37:52: Fewer paired peaks (873) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 873 pairs to build model! INFO @ Mon, 03 Jun 2019 06:37:52: start model_add_line... INFO @ Mon, 03 Jun 2019 06:37:52: start X-correlation... INFO @ Mon, 03 Jun 2019 06:37:52: end of X-cor INFO @ Mon, 03 Jun 2019 06:37:52: #2 finished! INFO @ Mon, 03 Jun 2019 06:37:52: #2 predicted fragment length is 66 bps INFO @ Mon, 03 Jun 2019 06:37:52: #2 alternative fragment length(s) may be 3,66 bps INFO @ Mon, 03 Jun 2019 06:37:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.10_model.r WARNING @ Mon, 03 Jun 2019 06:37:52: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:37:52: #2 You may need to consider one of the other alternative d(s): 3,66 WARNING @ Mon, 03 Jun 2019 06:37:52: #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 06:37:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:37:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:38:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:38:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:38:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:38:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:38:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:38:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.05_summits.bed INFO @ Mon, 03 Jun 2019 06:38:44: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3373 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:38:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:38:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:38:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.20_summits.bed INFO @ Mon, 03 Jun 2019 06:38:45: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (895 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:39:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:39:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:39:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422629/SRX2422629.10_summits.bed INFO @ Mon, 03 Jun 2019 06:39:00: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1863 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。