Job ID = 1294233 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 160,193,948 reads read : 160,193,948 reads written : 160,193,948 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: 00:39:40 160193948 reads; of these: 160193948 (100.00%) were unpaired; of these: 89681733 (55.98%) aligned 0 times 50794007 (31.71%) aligned exactly 1 time 19718208 (12.31%) aligned >1 times 44.02% overall alignment rate Time searching: 00:39:40 Overall time: 00:39:40 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 32 files... [bam_rmdupse_core] 60314392 / 70512215 = 0.8554 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 06:44:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.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 06:44:19: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:44:19: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:44:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.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 06:44:19: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:44:19: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:44:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.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 06:44:19: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:44:19: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:44:29: 1000000 INFO @ Mon, 03 Jun 2019 06:44:31: 1000000 INFO @ Mon, 03 Jun 2019 06:44:31: 1000000 INFO @ Mon, 03 Jun 2019 06:44:37: 2000000 INFO @ Mon, 03 Jun 2019 06:44:41: 2000000 INFO @ Mon, 03 Jun 2019 06:44:41: 2000000 INFO @ Mon, 03 Jun 2019 06:44:46: 3000000 INFO @ Mon, 03 Jun 2019 06:44:52: 3000000 INFO @ Mon, 03 Jun 2019 06:44:52: 3000000 INFO @ Mon, 03 Jun 2019 06:44:55: 4000000 INFO @ Mon, 03 Jun 2019 06:45:02: 4000000 INFO @ Mon, 03 Jun 2019 06:45:03: 4000000 INFO @ Mon, 03 Jun 2019 06:45:04: 5000000 INFO @ Mon, 03 Jun 2019 06:45:13: 6000000 INFO @ Mon, 03 Jun 2019 06:45:13: 5000000 INFO @ Mon, 03 Jun 2019 06:45:13: 5000000 INFO @ Mon, 03 Jun 2019 06:45:21: 7000000 INFO @ Mon, 03 Jun 2019 06:45:23: 6000000 INFO @ Mon, 03 Jun 2019 06:45:24: 6000000 INFO @ Mon, 03 Jun 2019 06:45:30: 8000000 INFO @ Mon, 03 Jun 2019 06:45:34: 7000000 INFO @ Mon, 03 Jun 2019 06:45:34: 7000000 INFO @ Mon, 03 Jun 2019 06:45:39: 9000000 INFO @ Mon, 03 Jun 2019 06:45:44: 8000000 INFO @ Mon, 03 Jun 2019 06:45:44: 8000000 INFO @ Mon, 03 Jun 2019 06:45:47: 10000000 INFO @ Mon, 03 Jun 2019 06:45:49: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 06:45:49: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 06:45:49: #1 total tags in treatment: 10197823 INFO @ Mon, 03 Jun 2019 06:45:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:45:49: #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 06:45:49: #1 tags after filtering in treatment: 10197823 INFO @ Mon, 03 Jun 2019 06:45:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:45:49: #1 finished! INFO @ Mon, 03 Jun 2019 06:45:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:45:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:45:50: #2 number of paired peaks: 1210 INFO @ Mon, 03 Jun 2019 06:45:50: start model_add_line... INFO @ Mon, 03 Jun 2019 06:45:51: start X-correlation... INFO @ Mon, 03 Jun 2019 06:45:51: end of X-cor INFO @ Mon, 03 Jun 2019 06:45:51: #2 finished! INFO @ Mon, 03 Jun 2019 06:45:51: #2 predicted fragment length is 70 bps INFO @ Mon, 03 Jun 2019 06:45:51: #2 alternative fragment length(s) may be 70 bps INFO @ Mon, 03 Jun 2019 06:45:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.10_model.r WARNING @ Mon, 03 Jun 2019 06:45:51: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:45:51: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Mon, 03 Jun 2019 06:45:51: #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 06:45:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:45:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:45:55: 9000000 INFO @ Mon, 03 Jun 2019 06:45:55: 9000000 INFO @ Mon, 03 Jun 2019 06:46:05: 10000000 INFO @ Mon, 03 Jun 2019 06:46:05: 10000000 INFO @ Mon, 03 Jun 2019 06:46:07: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 06:46:07: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 06:46:07: #1 total tags in treatment: 10197823 INFO @ Mon, 03 Jun 2019 06:46:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:46:07: #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 06:46:07: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 06:46:07: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 06:46:07: #1 total tags in treatment: 10197823 INFO @ Mon, 03 Jun 2019 06:46:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:46:07: #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 06:46:07: #1 tags after filtering in treatment: 10197823 INFO @ Mon, 03 Jun 2019 06:46:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:46:07: #1 finished! INFO @ Mon, 03 Jun 2019 06:46:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:46:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:46:07: #1 tags after filtering in treatment: 10197823 INFO @ Mon, 03 Jun 2019 06:46:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:46:07: #1 finished! INFO @ Mon, 03 Jun 2019 06:46:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:46:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:46:08: #2 number of paired peaks: 1210 INFO @ Mon, 03 Jun 2019 06:46:08: start model_add_line... INFO @ Mon, 03 Jun 2019 06:46:08: #2 number of paired peaks: 1210 INFO @ Mon, 03 Jun 2019 06:46:08: start model_add_line... INFO @ Mon, 03 Jun 2019 06:46:09: start X-correlation... INFO @ Mon, 03 Jun 2019 06:46:09: end of X-cor INFO @ Mon, 03 Jun 2019 06:46:09: #2 finished! INFO @ Mon, 03 Jun 2019 06:46:09: #2 predicted fragment length is 70 bps INFO @ Mon, 03 Jun 2019 06:46:09: #2 alternative fragment length(s) may be 70 bps INFO @ Mon, 03 Jun 2019 06:46:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.05_model.r WARNING @ Mon, 03 Jun 2019 06:46:09: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:46:09: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Mon, 03 Jun 2019 06:46:09: #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 06:46:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:46:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:46:09: start X-correlation... INFO @ Mon, 03 Jun 2019 06:46:09: end of X-cor INFO @ Mon, 03 Jun 2019 06:46:09: #2 finished! INFO @ Mon, 03 Jun 2019 06:46:09: #2 predicted fragment length is 70 bps INFO @ Mon, 03 Jun 2019 06:46:09: #2 alternative fragment length(s) may be 70 bps INFO @ Mon, 03 Jun 2019 06:46:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.20_model.r WARNING @ Mon, 03 Jun 2019 06:46:09: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:46:09: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Mon, 03 Jun 2019 06:46:09: #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 06:46:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:46:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:46:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:46:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:46:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:46:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.10_summits.bed INFO @ Mon, 03 Jun 2019 06:46:35: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4082 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:46:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:46:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:46:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:46:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:46:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.20_summits.bed INFO @ Mon, 03 Jun 2019 06:46:53: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1242 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:46:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:46:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:46:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX202122/SRX202122.05_summits.bed INFO @ Mon, 03 Jun 2019 06:46:54: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11485 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。