Job ID = 1295043 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,607,828 reads read : 9,215,656 reads written : 4,607,828 reads 0-length : 4,607,828 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: 00:03:57 4607828 reads; of these: 4607828 (100.00%) were unpaired; of these: 393065 (8.53%) aligned 0 times 3302699 (71.68%) aligned exactly 1 time 912064 (19.79%) aligned >1 times 91.47% overall alignment rate Time searching: 00:03:57 Overall time: 00:03:57 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_rmdupse_core] 1200075 / 4214763 = 0.2847 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 11:31:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.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 11:31:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:31:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:31:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.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 11:31:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:31:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:31:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.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 11:31:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:31:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:32:03: 1000000 INFO @ Mon, 03 Jun 2019 11:32:07: 1000000 INFO @ Mon, 03 Jun 2019 11:32:08: 1000000 INFO @ Mon, 03 Jun 2019 11:32:20: 2000000 INFO @ Mon, 03 Jun 2019 11:32:29: 2000000 INFO @ Mon, 03 Jun 2019 11:32:29: 2000000 INFO @ Mon, 03 Jun 2019 11:32:38: 3000000 INFO @ Mon, 03 Jun 2019 11:32:38: #1 tag size is determined as 151 bps INFO @ Mon, 03 Jun 2019 11:32:38: #1 tag size = 151 INFO @ Mon, 03 Jun 2019 11:32:38: #1 total tags in treatment: 3014688 INFO @ Mon, 03 Jun 2019 11:32:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:32:38: #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 11:32:38: #1 tags after filtering in treatment: 3014688 INFO @ Mon, 03 Jun 2019 11:32:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:32:38: #1 finished! INFO @ Mon, 03 Jun 2019 11:32:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:32:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:32:39: #2 number of paired peaks: 4836 INFO @ Mon, 03 Jun 2019 11:32:39: start model_add_line... INFO @ Mon, 03 Jun 2019 11:32:39: start X-correlation... INFO @ Mon, 03 Jun 2019 11:32:39: end of X-cor INFO @ Mon, 03 Jun 2019 11:32:39: #2 finished! INFO @ Mon, 03 Jun 2019 11:32:39: #2 predicted fragment length is 207 bps INFO @ Mon, 03 Jun 2019 11:32:39: #2 alternative fragment length(s) may be 207 bps INFO @ Mon, 03 Jun 2019 11:32:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.20_model.r WARNING @ Mon, 03 Jun 2019 11:32:39: #2 Since the d (207) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:32:39: #2 You may need to consider one of the other alternative d(s): 207 WARNING @ Mon, 03 Jun 2019 11:32:39: #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 11:32:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:32:39: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 11:32:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:32:51: 3000000 INFO @ Mon, 03 Jun 2019 11:32:51: #1 tag size is determined as 151 bps INFO @ Mon, 03 Jun 2019 11:32:51: #1 tag size = 151 INFO @ Mon, 03 Jun 2019 11:32:51: #1 total tags in treatment: 3014688 INFO @ Mon, 03 Jun 2019 11:32:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:32:51: #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 11:32:51: #1 tags after filtering in treatment: 3014688 INFO @ Mon, 03 Jun 2019 11:32:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:32:51: #1 finished! INFO @ Mon, 03 Jun 2019 11:32:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:32:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:32:52: #2 number of paired peaks: 4836 INFO @ Mon, 03 Jun 2019 11:32:52: start model_add_line... INFO @ Mon, 03 Jun 2019 11:32:52: start X-correlation... INFO @ Mon, 03 Jun 2019 11:32:52: end of X-cor INFO @ Mon, 03 Jun 2019 11:32:52: #2 finished! INFO @ Mon, 03 Jun 2019 11:32:52: #2 predicted fragment length is 207 bps INFO @ Mon, 03 Jun 2019 11:32:52: #2 alternative fragment length(s) may be 207 bps INFO @ Mon, 03 Jun 2019 11:32:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.05_model.r INFO @ Mon, 03 Jun 2019 11:32:52: 3000000 WARNING @ Mon, 03 Jun 2019 11:32:52: #2 Since the d (207) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:32:52: #2 You may need to consider one of the other alternative d(s): 207 WARNING @ Mon, 03 Jun 2019 11:32:52: #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 11:32:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:32:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:32:52: #1 tag size is determined as 151 bps INFO @ Mon, 03 Jun 2019 11:32:52: #1 tag size = 151 INFO @ Mon, 03 Jun 2019 11:32:52: #1 total tags in treatment: 3014688 INFO @ Mon, 03 Jun 2019 11:32:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:32:52: #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 11:32:52: #1 tags after filtering in treatment: 3014688 INFO @ Mon, 03 Jun 2019 11:32:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:32:52: #1 finished! INFO @ Mon, 03 Jun 2019 11:32:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:32:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:32:53: #2 number of paired peaks: 4836 INFO @ Mon, 03 Jun 2019 11:32:53: start model_add_line... INFO @ Mon, 03 Jun 2019 11:32:53: start X-correlation... INFO @ Mon, 03 Jun 2019 11:32:53: end of X-cor INFO @ Mon, 03 Jun 2019 11:32:53: #2 finished! INFO @ Mon, 03 Jun 2019 11:32:53: #2 predicted fragment length is 207 bps INFO @ Mon, 03 Jun 2019 11:32:53: #2 alternative fragment length(s) may be 207 bps INFO @ Mon, 03 Jun 2019 11:32:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.10_model.r WARNING @ Mon, 03 Jun 2019 11:32:53: #2 Since the d (207) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:32:53: #2 You may need to consider one of the other alternative d(s): 207 WARNING @ Mon, 03 Jun 2019 11:32:53: #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 11:32:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:32:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 11:32:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:32:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:32:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.20_summits.bed INFO @ Mon, 03 Jun 2019 11:32:56: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3031 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:33:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:33:05: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:33:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:33:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:33:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.05_summits.bed INFO @ Mon, 03 Jun 2019 11:33:09: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5592 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:33:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:33:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:33:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX315135/SRX315135.10_summits.bed INFO @ Mon, 03 Jun 2019 11:33:10: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (4347 records, 4 fields): 7 millis CompletedMACS2peakCalling