Job ID = 1294302 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,478,435 reads read : 19,478,435 reads written : 19,478,435 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: 00:11:19 19478435 reads; of these: 19478435 (100.00%) were unpaired; of these: 698600 (3.59%) aligned 0 times 12844232 (65.94%) aligned exactly 1 time 5935603 (30.47%) aligned >1 times 96.41% overall alignment rate Time searching: 00:11:19 Overall time: 00:11:19 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] 2217739 / 18779835 = 0.1181 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 06:37:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.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 06:37:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:37:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:37:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.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 06:37:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:37:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:37:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.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 06:37:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:37:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:37:45: 1000000 INFO @ Mon, 03 Jun 2019 06:37:46: 1000000 INFO @ Mon, 03 Jun 2019 06:37:46: 1000000 INFO @ Mon, 03 Jun 2019 06:37:53: 2000000 INFO @ Mon, 03 Jun 2019 06:37:54: 2000000 INFO @ Mon, 03 Jun 2019 06:37:56: 2000000 INFO @ Mon, 03 Jun 2019 06:38:00: 3000000 INFO @ Mon, 03 Jun 2019 06:38:03: 3000000 INFO @ Mon, 03 Jun 2019 06:38:05: 3000000 INFO @ Mon, 03 Jun 2019 06:38:08: 4000000 INFO @ Mon, 03 Jun 2019 06:38:11: 4000000 INFO @ Mon, 03 Jun 2019 06:38:14: 4000000 INFO @ Mon, 03 Jun 2019 06:38:15: 5000000 INFO @ Mon, 03 Jun 2019 06:38:20: 5000000 INFO @ Mon, 03 Jun 2019 06:38:23: 6000000 INFO @ Mon, 03 Jun 2019 06:38:23: 5000000 INFO @ Mon, 03 Jun 2019 06:38:29: 6000000 INFO @ Mon, 03 Jun 2019 06:38:31: 7000000 INFO @ Mon, 03 Jun 2019 06:38:33: 6000000 INFO @ Mon, 03 Jun 2019 06:38:38: 7000000 INFO @ Mon, 03 Jun 2019 06:38:39: 8000000 INFO @ Mon, 03 Jun 2019 06:38:42: 7000000 INFO @ Mon, 03 Jun 2019 06:38:46: 9000000 INFO @ Mon, 03 Jun 2019 06:38:47: 8000000 INFO @ Mon, 03 Jun 2019 06:38:51: 8000000 INFO @ Mon, 03 Jun 2019 06:38:53: 10000000 INFO @ Mon, 03 Jun 2019 06:38:55: 9000000 INFO @ Mon, 03 Jun 2019 06:38:59: 9000000 INFO @ Mon, 03 Jun 2019 06:39:01: 11000000 INFO @ Mon, 03 Jun 2019 06:39:04: 10000000 INFO @ Mon, 03 Jun 2019 06:39:08: 10000000 INFO @ Mon, 03 Jun 2019 06:39:08: 12000000 INFO @ Mon, 03 Jun 2019 06:39:13: 11000000 INFO @ Mon, 03 Jun 2019 06:39:16: 13000000 INFO @ Mon, 03 Jun 2019 06:39:17: 11000000 INFO @ Mon, 03 Jun 2019 06:39:21: 12000000 INFO @ Mon, 03 Jun 2019 06:39:24: 14000000 INFO @ Mon, 03 Jun 2019 06:39:25: 12000000 INFO @ Mon, 03 Jun 2019 06:39:30: 13000000 INFO @ Mon, 03 Jun 2019 06:39:31: 15000000 INFO @ Mon, 03 Jun 2019 06:39:33: 13000000 INFO @ Mon, 03 Jun 2019 06:39:39: 16000000 INFO @ Mon, 03 Jun 2019 06:39:39: 14000000 INFO @ Mon, 03 Jun 2019 06:39:41: 14000000 INFO @ Mon, 03 Jun 2019 06:39:43: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:39:43: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:39:43: #1 total tags in treatment: 16562096 INFO @ Mon, 03 Jun 2019 06:39:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:39:43: #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 06:39:44: #1 tags after filtering in treatment: 16562096 INFO @ Mon, 03 Jun 2019 06:39:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:39:44: #1 finished! INFO @ Mon, 03 Jun 2019 06:39:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:39:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:39:45: #2 number of paired peaks: 857 WARNING @ Mon, 03 Jun 2019 06:39:45: Fewer paired peaks (857) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 857 pairs to build model! INFO @ Mon, 03 Jun 2019 06:39:45: start model_add_line... INFO @ Mon, 03 Jun 2019 06:39:45: start X-correlation... INFO @ Mon, 03 Jun 2019 06:39:46: end of X-cor INFO @ Mon, 03 Jun 2019 06:39:46: #2 finished! INFO @ Mon, 03 Jun 2019 06:39:46: #2 predicted fragment length is 66 bps INFO @ Mon, 03 Jun 2019 06:39:46: #2 alternative fragment length(s) may be 3,66 bps INFO @ Mon, 03 Jun 2019 06:39:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.10_model.r WARNING @ Mon, 03 Jun 2019 06:39:46: #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 06:39:46: #2 You may need to consider one of the other alternative d(s): 3,66 WARNING @ Mon, 03 Jun 2019 06:39:46: #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 06:39:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:39:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:39:48: 15000000 INFO @ Mon, 03 Jun 2019 06:39:49: 15000000 INFO @ Mon, 03 Jun 2019 06:39:57: 16000000 INFO @ Mon, 03 Jun 2019 06:39:57: 16000000 INFO @ Mon, 03 Jun 2019 06:40:01: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:40:01: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:40:01: #1 total tags in treatment: 16562096 INFO @ Mon, 03 Jun 2019 06:40:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:40:01: #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 06:40:02: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:40:02: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:40:02: #1 total tags in treatment: 16562096 INFO @ Mon, 03 Jun 2019 06:40:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:40:02: #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 06:40:02: #1 tags after filtering in treatment: 16562096 INFO @ Mon, 03 Jun 2019 06:40:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:40:02: #1 finished! INFO @ Mon, 03 Jun 2019 06:40:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:40:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:40:02: #1 tags after filtering in treatment: 16562096 INFO @ Mon, 03 Jun 2019 06:40:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:40:02: #1 finished! INFO @ Mon, 03 Jun 2019 06:40:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:40:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:40:03: #2 number of paired peaks: 857 WARNING @ Mon, 03 Jun 2019 06:40:03: Fewer paired peaks (857) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 857 pairs to build model! INFO @ Mon, 03 Jun 2019 06:40:03: start model_add_line... INFO @ Mon, 03 Jun 2019 06:40:04: #2 number of paired peaks: 857 WARNING @ Mon, 03 Jun 2019 06:40:04: Fewer paired peaks (857) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 857 pairs to build model! INFO @ Mon, 03 Jun 2019 06:40:04: start model_add_line... INFO @ Mon, 03 Jun 2019 06:40:04: start X-correlation... INFO @ Mon, 03 Jun 2019 06:40:04: end of X-cor INFO @ Mon, 03 Jun 2019 06:40:04: #2 finished! INFO @ Mon, 03 Jun 2019 06:40:04: #2 predicted fragment length is 66 bps INFO @ Mon, 03 Jun 2019 06:40:04: #2 alternative fragment length(s) may be 3,66 bps INFO @ Mon, 03 Jun 2019 06:40:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.20_model.r WARNING @ Mon, 03 Jun 2019 06:40:04: #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 06:40:04: #2 You may need to consider one of the other alternative d(s): 3,66 WARNING @ Mon, 03 Jun 2019 06:40:04: #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 06:40:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:40:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:40:04: start X-correlation... INFO @ Mon, 03 Jun 2019 06:40:04: end of X-cor INFO @ Mon, 03 Jun 2019 06:40:04: #2 finished! INFO @ Mon, 03 Jun 2019 06:40:04: #2 predicted fragment length is 66 bps INFO @ Mon, 03 Jun 2019 06:40:04: #2 alternative fragment length(s) may be 3,66 bps INFO @ Mon, 03 Jun 2019 06:40:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.05_model.r WARNING @ Mon, 03 Jun 2019 06:40:04: #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 06:40:04: #2 You may need to consider one of the other alternative d(s): 3,66 WARNING @ Mon, 03 Jun 2019 06:40:04: #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 06:40:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:40:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:40:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:40:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:40:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:40:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:40:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:40:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.10_summits.bed INFO @ Mon, 03 Jun 2019 06:40:55: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2170 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:41:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:41:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:41:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.05_summits.bed INFO @ Mon, 03 Jun 2019 06:41:13: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3750 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:41:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:41:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:41:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422632/SRX2422632.20_summits.bed INFO @ Mon, 03 Jun 2019 06:41:15: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (991 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。