Job ID = 1293872 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,077,910 reads read : 12,077,910 reads written : 12,077,910 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: 00:05:15 12077910 reads; of these: 12077910 (100.00%) were unpaired; of these: 571948 (4.74%) aligned 0 times 8477449 (70.19%) aligned exactly 1 time 3028513 (25.07%) aligned >1 times 95.26% overall alignment rate Time searching: 00:05:15 Overall time: 00:05:15 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] 4653511 / 11505962 = 0.4044 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 03:02:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.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 03:02:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:02:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:02:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.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 03:02:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:02:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:02:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.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 03:02:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:02:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:02:13: 1000000 INFO @ Mon, 03 Jun 2019 03:02:14: 1000000 INFO @ Mon, 03 Jun 2019 03:02:15: 1000000 INFO @ Mon, 03 Jun 2019 03:02:20: 2000000 INFO @ Mon, 03 Jun 2019 03:02:23: 2000000 INFO @ Mon, 03 Jun 2019 03:02:24: 2000000 INFO @ Mon, 03 Jun 2019 03:02:27: 3000000 INFO @ Mon, 03 Jun 2019 03:02:31: 3000000 INFO @ Mon, 03 Jun 2019 03:02:33: 3000000 INFO @ Mon, 03 Jun 2019 03:02:34: 4000000 INFO @ Mon, 03 Jun 2019 03:02:39: 4000000 INFO @ Mon, 03 Jun 2019 03:02:40: 5000000 INFO @ Mon, 03 Jun 2019 03:02:42: 4000000 INFO @ Mon, 03 Jun 2019 03:02:47: 5000000 INFO @ Mon, 03 Jun 2019 03:02:47: 6000000 INFO @ Mon, 03 Jun 2019 03:02:51: 5000000 INFO @ Mon, 03 Jun 2019 03:02:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:02:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:02:53: #1 total tags in treatment: 6852451 INFO @ Mon, 03 Jun 2019 03:02:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:02:53: #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 03:02:54: #1 tags after filtering in treatment: 6852451 INFO @ Mon, 03 Jun 2019 03:02:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:02:54: #1 finished! INFO @ Mon, 03 Jun 2019 03:02:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:02:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:02:54: #2 number of paired peaks: 209 WARNING @ Mon, 03 Jun 2019 03:02:54: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Mon, 03 Jun 2019 03:02:54: start model_add_line... INFO @ Mon, 03 Jun 2019 03:02:54: start X-correlation... INFO @ Mon, 03 Jun 2019 03:02:54: end of X-cor INFO @ Mon, 03 Jun 2019 03:02:54: #2 finished! INFO @ Mon, 03 Jun 2019 03:02:54: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 03:02:54: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 03:02:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.05_model.r WARNING @ Mon, 03 Jun 2019 03:02:54: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:02:54: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 03:02:54: #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 03:02:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:02:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:02:54: 6000000 INFO @ Mon, 03 Jun 2019 03:03:00: 6000000 INFO @ Mon, 03 Jun 2019 03:03:01: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:03:01: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:03:01: #1 total tags in treatment: 6852451 INFO @ Mon, 03 Jun 2019 03:03:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:03:01: #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 03:03:01: #1 tags after filtering in treatment: 6852451 INFO @ Mon, 03 Jun 2019 03:03:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:03:01: #1 finished! INFO @ Mon, 03 Jun 2019 03:03:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:03:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:03:02: #2 number of paired peaks: 209 WARNING @ Mon, 03 Jun 2019 03:03:02: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Mon, 03 Jun 2019 03:03:02: start model_add_line... INFO @ Mon, 03 Jun 2019 03:03:02: start X-correlation... INFO @ Mon, 03 Jun 2019 03:03:02: end of X-cor INFO @ Mon, 03 Jun 2019 03:03:02: #2 finished! INFO @ Mon, 03 Jun 2019 03:03:02: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 03:03:02: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 03:03:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.10_model.r WARNING @ Mon, 03 Jun 2019 03:03:02: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:03:02: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 03:03:02: #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 03:03:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:03:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:03:07: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:03:07: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:03:07: #1 total tags in treatment: 6852451 INFO @ Mon, 03 Jun 2019 03:03:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:03:07: #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 03:03:07: #1 tags after filtering in treatment: 6852451 INFO @ Mon, 03 Jun 2019 03:03:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:03:07: #1 finished! INFO @ Mon, 03 Jun 2019 03:03:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:03:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:03:08: #2 number of paired peaks: 209 WARNING @ Mon, 03 Jun 2019 03:03:08: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Mon, 03 Jun 2019 03:03:08: start model_add_line... INFO @ Mon, 03 Jun 2019 03:03:08: start X-correlation... INFO @ Mon, 03 Jun 2019 03:03:08: end of X-cor INFO @ Mon, 03 Jun 2019 03:03:08: #2 finished! INFO @ Mon, 03 Jun 2019 03:03:08: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 03:03:08: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 03:03:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.20_model.r WARNING @ Mon, 03 Jun 2019 03:03:08: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:03:08: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 03:03:08: #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 03:03:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:03:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:03:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:03:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:03:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:03:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:03:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.05_summits.bed INFO @ Mon, 03 Jun 2019 03:03:24: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2036 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:03:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:03:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:03:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:03:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.10_summits.bed INFO @ Mon, 03 Jun 2019 03:03:31: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1276 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:03:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:03:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:03:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX131083/SRX131083.20_summits.bed INFO @ Mon, 03 Jun 2019 03:03:37: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (786 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。