Job ID = 1309260 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,187,151 reads read : 14,374,302 reads written : 7,187,151 reads 0-length : 7,187,151 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: 00:02:38 7187151 reads; of these: 7187151 (100.00%) were unpaired; of these: 348987 (4.86%) aligned 0 times 5610196 (78.06%) aligned exactly 1 time 1227968 (17.09%) aligned >1 times 95.14% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 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] 274268 / 6838164 = 0.0401 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 23:17:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.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 23:17:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:17:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:17:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.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 23:17:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:17:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:17:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.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 23:17:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:17:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:17:58: 1000000 INFO @ Mon, 03 Jun 2019 23:17:58: 1000000 INFO @ Mon, 03 Jun 2019 23:17:58: 1000000 INFO @ Mon, 03 Jun 2019 23:18:08: 2000000 INFO @ Mon, 03 Jun 2019 23:18:08: 2000000 INFO @ Mon, 03 Jun 2019 23:18:09: 2000000 INFO @ Mon, 03 Jun 2019 23:18:19: 3000000 INFO @ Mon, 03 Jun 2019 23:18:19: 3000000 INFO @ Mon, 03 Jun 2019 23:18:20: 3000000 INFO @ Mon, 03 Jun 2019 23:18:30: 4000000 INFO @ Mon, 03 Jun 2019 23:18:30: 4000000 INFO @ Mon, 03 Jun 2019 23:18:30: 4000000 INFO @ Mon, 03 Jun 2019 23:18:40: 5000000 INFO @ Mon, 03 Jun 2019 23:18:41: 5000000 INFO @ Mon, 03 Jun 2019 23:18:41: 5000000 INFO @ Mon, 03 Jun 2019 23:18:51: 6000000 INFO @ Mon, 03 Jun 2019 23:18:51: 6000000 INFO @ Mon, 03 Jun 2019 23:18:52: 6000000 INFO @ Mon, 03 Jun 2019 23:18:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 23:18:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 23:18:57: #1 total tags in treatment: 6563896 INFO @ Mon, 03 Jun 2019 23:18:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:18:57: #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 23:18:57: #1 tags after filtering in treatment: 6563896 INFO @ Mon, 03 Jun 2019 23:18:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:18:57: #1 finished! INFO @ Mon, 03 Jun 2019 23:18:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:18:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:18:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 23:18:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 23:18:57: #1 total tags in treatment: 6563896 INFO @ Mon, 03 Jun 2019 23:18:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:18:57: #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 23:18:57: #1 tags after filtering in treatment: 6563896 INFO @ Mon, 03 Jun 2019 23:18:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:18:57: #1 finished! INFO @ Mon, 03 Jun 2019 23:18:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:18:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:18:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 23:18:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 23:18:57: #1 total tags in treatment: 6563896 INFO @ Mon, 03 Jun 2019 23:18:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:18:57: #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 23:18:58: #1 tags after filtering in treatment: 6563896 INFO @ Mon, 03 Jun 2019 23:18:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:18:58: #1 finished! INFO @ Mon, 03 Jun 2019 23:18:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:18:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:18:58: #2 number of paired peaks: 125 WARNING @ Mon, 03 Jun 2019 23:18:58: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Mon, 03 Jun 2019 23:18:58: start model_add_line... INFO @ Mon, 03 Jun 2019 23:18:58: start X-correlation... INFO @ Mon, 03 Jun 2019 23:18:58: end of X-cor INFO @ Mon, 03 Jun 2019 23:18:58: #2 finished! INFO @ Mon, 03 Jun 2019 23:18:58: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 23:18:58: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 03 Jun 2019 23:18:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.10_model.r WARNING @ Mon, 03 Jun 2019 23:18:58: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:18:58: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 03 Jun 2019 23:18:58: #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 23:18:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:18:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:18:58: #2 number of paired peaks: 125 WARNING @ Mon, 03 Jun 2019 23:18:58: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Mon, 03 Jun 2019 23:18:58: start model_add_line... INFO @ Mon, 03 Jun 2019 23:18:58: start X-correlation... INFO @ Mon, 03 Jun 2019 23:18:58: end of X-cor INFO @ Mon, 03 Jun 2019 23:18:58: #2 finished! INFO @ Mon, 03 Jun 2019 23:18:58: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 23:18:58: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 03 Jun 2019 23:18:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.05_model.r WARNING @ Mon, 03 Jun 2019 23:18:58: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:18:58: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 03 Jun 2019 23:18:58: #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 23:18:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:18:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:18:58: #2 number of paired peaks: 125 WARNING @ Mon, 03 Jun 2019 23:18:58: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Mon, 03 Jun 2019 23:18:58: start model_add_line... INFO @ Mon, 03 Jun 2019 23:18:58: start X-correlation... INFO @ Mon, 03 Jun 2019 23:18:58: end of X-cor INFO @ Mon, 03 Jun 2019 23:18:58: #2 finished! INFO @ Mon, 03 Jun 2019 23:18:58: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 23:18:58: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 03 Jun 2019 23:18:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.20_model.r WARNING @ Mon, 03 Jun 2019 23:18:58: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:18:58: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 03 Jun 2019 23:18:58: #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 23:18:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:18:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:19:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:19:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:19:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:19:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:19:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:19:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.10_summits.bed INFO @ Mon, 03 Jun 2019 23:19:26: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (739 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:19:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:19:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:19:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.05_summits.bed INFO @ Mon, 03 Jun 2019 23:19:28: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1121 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:19:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:19:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:19:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX864528/SRX864528.20_summits.bed INFO @ Mon, 03 Jun 2019 23:19:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (349 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。