Job ID = 1294950 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,972,245 reads read : 12,972,245 reads written : 12,972,245 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: 00:07:51 12972245 reads; of these: 12972245 (100.00%) were unpaired; of these: 936051 (7.22%) aligned 0 times 5077003 (39.14%) aligned exactly 1 time 6959191 (53.65%) aligned >1 times 92.78% overall alignment rate Time searching: 00:07:51 Overall time: 00:07:52 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] 2050731 / 12036194 = 0.1704 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 11:10:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.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 11:10:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:10:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:10:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.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 11:10:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:10:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:10:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.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 11:10:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:10:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:11:04: 1000000 INFO @ Mon, 03 Jun 2019 11:11:04: 1000000 INFO @ Mon, 03 Jun 2019 11:11:04: 1000000 INFO @ Mon, 03 Jun 2019 11:11:13: 2000000 INFO @ Mon, 03 Jun 2019 11:11:13: 2000000 INFO @ Mon, 03 Jun 2019 11:11:13: 2000000 INFO @ Mon, 03 Jun 2019 11:11:22: 3000000 INFO @ Mon, 03 Jun 2019 11:11:22: 3000000 INFO @ Mon, 03 Jun 2019 11:11:23: 3000000 INFO @ Mon, 03 Jun 2019 11:11:32: 4000000 INFO @ Mon, 03 Jun 2019 11:11:32: 4000000 INFO @ Mon, 03 Jun 2019 11:11:32: 4000000 INFO @ Mon, 03 Jun 2019 11:11:40: 5000000 INFO @ Mon, 03 Jun 2019 11:11:41: 5000000 INFO @ Mon, 03 Jun 2019 11:11:41: 5000000 INFO @ Mon, 03 Jun 2019 11:11:49: 6000000 INFO @ Mon, 03 Jun 2019 11:11:50: 6000000 INFO @ Mon, 03 Jun 2019 11:11:51: 6000000 INFO @ Mon, 03 Jun 2019 11:11:59: 7000000 INFO @ Mon, 03 Jun 2019 11:11:59: 7000000 INFO @ Mon, 03 Jun 2019 11:12:01: 7000000 INFO @ Mon, 03 Jun 2019 11:12:08: 8000000 INFO @ Mon, 03 Jun 2019 11:12:09: 8000000 INFO @ Mon, 03 Jun 2019 11:12:11: 8000000 INFO @ Mon, 03 Jun 2019 11:12:17: 9000000 INFO @ Mon, 03 Jun 2019 11:12:17: 9000000 INFO @ Mon, 03 Jun 2019 11:12:20: 9000000 INFO @ Mon, 03 Jun 2019 11:12:25: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:12:25: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:12:25: #1 total tags in treatment: 9985463 INFO @ Mon, 03 Jun 2019 11:12:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:12:25: #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 11:12:25: #1 tags after filtering in treatment: 9985463 INFO @ Mon, 03 Jun 2019 11:12:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:12:25: #1 finished! INFO @ Mon, 03 Jun 2019 11:12:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:12:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:12:26: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:12:26: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:12:26: #1 total tags in treatment: 9985463 INFO @ Mon, 03 Jun 2019 11:12:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:12:26: #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 11:12:26: #1 tags after filtering in treatment: 9985463 INFO @ Mon, 03 Jun 2019 11:12:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:12:26: #1 finished! INFO @ Mon, 03 Jun 2019 11:12:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:12:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:12:26: #2 number of paired peaks: 893 WARNING @ Mon, 03 Jun 2019 11:12:26: Fewer paired peaks (893) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 893 pairs to build model! INFO @ Mon, 03 Jun 2019 11:12:26: start model_add_line... INFO @ Mon, 03 Jun 2019 11:12:26: start X-correlation... INFO @ Mon, 03 Jun 2019 11:12:26: end of X-cor INFO @ Mon, 03 Jun 2019 11:12:26: #2 finished! INFO @ Mon, 03 Jun 2019 11:12:26: #2 predicted fragment length is 72 bps INFO @ Mon, 03 Jun 2019 11:12:26: #2 alternative fragment length(s) may be 72 bps INFO @ Mon, 03 Jun 2019 11:12:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.20_model.r WARNING @ Mon, 03 Jun 2019 11:12:26: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:12:26: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Mon, 03 Jun 2019 11:12:26: #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 11:12:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:12:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:12:27: #2 number of paired peaks: 893 WARNING @ Mon, 03 Jun 2019 11:12:27: Fewer paired peaks (893) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 893 pairs to build model! INFO @ Mon, 03 Jun 2019 11:12:27: start model_add_line... INFO @ Mon, 03 Jun 2019 11:12:27: start X-correlation... INFO @ Mon, 03 Jun 2019 11:12:27: end of X-cor INFO @ Mon, 03 Jun 2019 11:12:27: #2 finished! INFO @ Mon, 03 Jun 2019 11:12:27: #2 predicted fragment length is 72 bps INFO @ Mon, 03 Jun 2019 11:12:27: #2 alternative fragment length(s) may be 72 bps INFO @ Mon, 03 Jun 2019 11:12:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.10_model.r WARNING @ Mon, 03 Jun 2019 11:12:27: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:12:27: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Mon, 03 Jun 2019 11:12:27: #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 11:12:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:12:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:12:29: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:12:29: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:12:29: #1 total tags in treatment: 9985463 INFO @ Mon, 03 Jun 2019 11:12:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:12:29: #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 11:12:29: #1 tags after filtering in treatment: 9985463 INFO @ Mon, 03 Jun 2019 11:12:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:12:29: #1 finished! INFO @ Mon, 03 Jun 2019 11:12:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:12:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:12:30: #2 number of paired peaks: 893 WARNING @ Mon, 03 Jun 2019 11:12:30: Fewer paired peaks (893) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 893 pairs to build model! INFO @ Mon, 03 Jun 2019 11:12:30: start model_add_line... INFO @ Mon, 03 Jun 2019 11:12:30: start X-correlation... INFO @ Mon, 03 Jun 2019 11:12:30: end of X-cor INFO @ Mon, 03 Jun 2019 11:12:30: #2 finished! INFO @ Mon, 03 Jun 2019 11:12:30: #2 predicted fragment length is 72 bps INFO @ Mon, 03 Jun 2019 11:12:30: #2 alternative fragment length(s) may be 72 bps INFO @ Mon, 03 Jun 2019 11:12:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.05_model.r WARNING @ Mon, 03 Jun 2019 11:12:30: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:12:30: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Mon, 03 Jun 2019 11:12:30: #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 11:12:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:12:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:12:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:12:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:12:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:13:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:13:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:13:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.20_summits.bed INFO @ Mon, 03 Jun 2019 11:13:09: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1174 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:13:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:13:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:13:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.10_summits.bed INFO @ Mon, 03 Jun 2019 11:13:09: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1992 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:13:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:13:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:13:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288013/SRX288013.05_summits.bed INFO @ Mon, 03 Jun 2019 11:13:14: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3691 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。