Job ID = 1294393 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,916,545 reads read : 14,916,545 reads written : 14,916,545 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: 00:07:09 14916545 reads; of these: 14916545 (100.00%) were unpaired; of these: 945435 (6.34%) aligned 0 times 8769278 (58.79%) aligned exactly 1 time 5201832 (34.87%) aligned >1 times 93.66% overall alignment rate Time searching: 00:07:09 Overall time: 00:07:09 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] 3978942 / 13971110 = 0.2848 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 07:25:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.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 07:25:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:25:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:25:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.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 07:25:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:25:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:25:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.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 07:25:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:25:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:25:33: 1000000 INFO @ Mon, 03 Jun 2019 07:25:36: 1000000 INFO @ Mon, 03 Jun 2019 07:25:36: 1000000 INFO @ Mon, 03 Jun 2019 07:25:40: 2000000 INFO @ Mon, 03 Jun 2019 07:25:47: 2000000 INFO @ Mon, 03 Jun 2019 07:25:47: 2000000 INFO @ Mon, 03 Jun 2019 07:25:48: 3000000 INFO @ Mon, 03 Jun 2019 07:25:55: 4000000 INFO @ Mon, 03 Jun 2019 07:25:57: 3000000 INFO @ Mon, 03 Jun 2019 07:25:57: 3000000 INFO @ Mon, 03 Jun 2019 07:26:03: 5000000 INFO @ Mon, 03 Jun 2019 07:26:07: 4000000 INFO @ Mon, 03 Jun 2019 07:26:07: 4000000 INFO @ Mon, 03 Jun 2019 07:26:10: 6000000 INFO @ Mon, 03 Jun 2019 07:26:17: 7000000 INFO @ Mon, 03 Jun 2019 07:26:18: 5000000 INFO @ Mon, 03 Jun 2019 07:26:18: 5000000 INFO @ Mon, 03 Jun 2019 07:26:25: 8000000 INFO @ Mon, 03 Jun 2019 07:26:28: 6000000 INFO @ Mon, 03 Jun 2019 07:26:28: 6000000 INFO @ Mon, 03 Jun 2019 07:26:32: 9000000 INFO @ Mon, 03 Jun 2019 07:26:38: 7000000 INFO @ Mon, 03 Jun 2019 07:26:39: 7000000 INFO @ Mon, 03 Jun 2019 07:26:40: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:26:40: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:26:40: #1 total tags in treatment: 9992168 INFO @ Mon, 03 Jun 2019 07:26:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:26:40: #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 07:26:40: #1 tags after filtering in treatment: 9992168 INFO @ Mon, 03 Jun 2019 07:26:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:26:40: #1 finished! INFO @ Mon, 03 Jun 2019 07:26:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:26:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:26:41: #2 number of paired peaks: 616 WARNING @ Mon, 03 Jun 2019 07:26:41: Fewer paired peaks (616) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 616 pairs to build model! INFO @ Mon, 03 Jun 2019 07:26:41: start model_add_line... INFO @ Mon, 03 Jun 2019 07:26:41: start X-correlation... INFO @ Mon, 03 Jun 2019 07:26:41: end of X-cor INFO @ Mon, 03 Jun 2019 07:26:41: #2 finished! INFO @ Mon, 03 Jun 2019 07:26:41: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 07:26:41: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 07:26:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.10_model.r WARNING @ Mon, 03 Jun 2019 07:26:41: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:26:41: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 07:26:41: #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 07:26:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:26:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:26:49: 8000000 INFO @ Mon, 03 Jun 2019 07:26:49: 8000000 INFO @ Mon, 03 Jun 2019 07:26:59: 9000000 INFO @ Mon, 03 Jun 2019 07:27:00: 9000000 INFO @ Mon, 03 Jun 2019 07:27:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:27:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:27:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:27:09: #1 total tags in treatment: 9992168 INFO @ Mon, 03 Jun 2019 07:27:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:27:09: #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 07:27:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:27:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:27:09: #1 total tags in treatment: 9992168 INFO @ Mon, 03 Jun 2019 07:27:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:27:09: #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 07:27:10: #1 tags after filtering in treatment: 9992168 INFO @ Mon, 03 Jun 2019 07:27:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:27:10: #1 finished! INFO @ Mon, 03 Jun 2019 07:27:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:27:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:27:10: #1 tags after filtering in treatment: 9992168 INFO @ Mon, 03 Jun 2019 07:27:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:27:10: #1 finished! INFO @ Mon, 03 Jun 2019 07:27:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:27:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:27:11: #2 number of paired peaks: 616 WARNING @ Mon, 03 Jun 2019 07:27:11: Fewer paired peaks (616) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 616 pairs to build model! INFO @ Mon, 03 Jun 2019 07:27:11: start model_add_line... INFO @ Mon, 03 Jun 2019 07:27:11: start X-correlation... INFO @ Mon, 03 Jun 2019 07:27:11: end of X-cor INFO @ Mon, 03 Jun 2019 07:27:11: #2 finished! INFO @ Mon, 03 Jun 2019 07:27:11: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 07:27:11: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 07:27:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.05_model.r WARNING @ Mon, 03 Jun 2019 07:27:11: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:27:11: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 07:27:11: #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 07:27:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:27:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:27:11: #2 number of paired peaks: 616 WARNING @ Mon, 03 Jun 2019 07:27:11: Fewer paired peaks (616) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 616 pairs to build model! INFO @ Mon, 03 Jun 2019 07:27:11: start model_add_line... INFO @ Mon, 03 Jun 2019 07:27:11: start X-correlation... INFO @ Mon, 03 Jun 2019 07:27:11: end of X-cor INFO @ Mon, 03 Jun 2019 07:27:11: #2 finished! INFO @ Mon, 03 Jun 2019 07:27:11: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 07:27:11: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 07:27:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.20_model.r WARNING @ Mon, 03 Jun 2019 07:27:11: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:27:11: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 07:27:11: #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 07:27:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:27:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:27:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:27:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:27:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.10_summits.bed INFO @ Mon, 03 Jun 2019 07:27:23: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1877 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:27:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:27:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:27:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.05_peaks.xls INFO @ Mon, 03 Jun 2019 07:27:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:27:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.05_summits.bed INFO @ Mon, 03 Jun 2019 07:27:52: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2226 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:27:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:27:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:27:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287570/SRX287570.20_summits.bed INFO @ Mon, 03 Jun 2019 07:27:53: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1420 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。