Job ID = 1295244 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,621,255 reads read : 16,621,255 reads written : 16,621,255 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: 00:06:39 16621255 reads; of these: 16621255 (100.00%) were unpaired; of these: 991181 (5.96%) aligned 0 times 11910348 (71.66%) aligned exactly 1 time 3719726 (22.38%) aligned >1 times 94.04% overall alignment rate Time searching: 00:06:39 Overall time: 00:06:39 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] 1255964 / 15630074 = 0.0804 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 13:12:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.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 13:12:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:12:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:12:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.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 13:12:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:12:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:12:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.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 13:12:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:12:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:12:14: 1000000 INFO @ Mon, 03 Jun 2019 13:12:16: 1000000 INFO @ Mon, 03 Jun 2019 13:12:16: 1000000 INFO @ Mon, 03 Jun 2019 13:12:22: 2000000 INFO @ Mon, 03 Jun 2019 13:12:26: 2000000 INFO @ Mon, 03 Jun 2019 13:12:27: 2000000 INFO @ Mon, 03 Jun 2019 13:12:31: 3000000 INFO @ Mon, 03 Jun 2019 13:12:36: 3000000 INFO @ Mon, 03 Jun 2019 13:12:37: 3000000 INFO @ Mon, 03 Jun 2019 13:12:40: 4000000 INFO @ Mon, 03 Jun 2019 13:12:46: 4000000 INFO @ Mon, 03 Jun 2019 13:12:47: 4000000 INFO @ Mon, 03 Jun 2019 13:12:48: 5000000 INFO @ Mon, 03 Jun 2019 13:12:56: 5000000 INFO @ Mon, 03 Jun 2019 13:12:57: 6000000 INFO @ Mon, 03 Jun 2019 13:12:57: 5000000 INFO @ Mon, 03 Jun 2019 13:13:05: 7000000 INFO @ Mon, 03 Jun 2019 13:13:06: 6000000 INFO @ Mon, 03 Jun 2019 13:13:08: 6000000 INFO @ Mon, 03 Jun 2019 13:13:14: 8000000 INFO @ Mon, 03 Jun 2019 13:13:16: 7000000 INFO @ Mon, 03 Jun 2019 13:13:18: 7000000 INFO @ Mon, 03 Jun 2019 13:13:23: 9000000 INFO @ Mon, 03 Jun 2019 13:13:26: 8000000 INFO @ Mon, 03 Jun 2019 13:13:29: 8000000 INFO @ Mon, 03 Jun 2019 13:13:31: 10000000 INFO @ Mon, 03 Jun 2019 13:13:36: 9000000 INFO @ Mon, 03 Jun 2019 13:13:39: 9000000 INFO @ Mon, 03 Jun 2019 13:13:40: 11000000 INFO @ Mon, 03 Jun 2019 13:13:46: 10000000 INFO @ Mon, 03 Jun 2019 13:13:48: 12000000 INFO @ Mon, 03 Jun 2019 13:13:49: 10000000 INFO @ Mon, 03 Jun 2019 13:13:56: 11000000 INFO @ Mon, 03 Jun 2019 13:13:56: 13000000 INFO @ Mon, 03 Jun 2019 13:13:59: 11000000 INFO @ Mon, 03 Jun 2019 13:14:05: 14000000 INFO @ Mon, 03 Jun 2019 13:14:06: 12000000 INFO @ Mon, 03 Jun 2019 13:14:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:14:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:14:08: #1 total tags in treatment: 14374110 INFO @ Mon, 03 Jun 2019 13:14:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:14:08: #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 13:14:09: #1 tags after filtering in treatment: 14374110 INFO @ Mon, 03 Jun 2019 13:14:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:14:09: #1 finished! INFO @ Mon, 03 Jun 2019 13:14:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:14:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:14:09: 12000000 INFO @ Mon, 03 Jun 2019 13:14:10: #2 number of paired peaks: 156 WARNING @ Mon, 03 Jun 2019 13:14:10: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Mon, 03 Jun 2019 13:14:10: start model_add_line... INFO @ Mon, 03 Jun 2019 13:14:10: start X-correlation... INFO @ Mon, 03 Jun 2019 13:14:10: end of X-cor INFO @ Mon, 03 Jun 2019 13:14:10: #2 finished! INFO @ Mon, 03 Jun 2019 13:14:10: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 13:14:10: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 13:14:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.10_model.r WARNING @ Mon, 03 Jun 2019 13:14:10: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:14:10: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 13:14:10: #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 13:14:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:14:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:14:17: 13000000 INFO @ Mon, 03 Jun 2019 13:14:20: 13000000 INFO @ Mon, 03 Jun 2019 13:14:27: 14000000 INFO @ Mon, 03 Jun 2019 13:14:30: 14000000 INFO @ Mon, 03 Jun 2019 13:14:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:14:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:14:31: #1 total tags in treatment: 14374110 INFO @ Mon, 03 Jun 2019 13:14:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:14:31: #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 13:14:31: #1 tags after filtering in treatment: 14374110 INFO @ Mon, 03 Jun 2019 13:14:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:14:31: #1 finished! INFO @ Mon, 03 Jun 2019 13:14:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:14:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:14:33: #2 number of paired peaks: 156 WARNING @ Mon, 03 Jun 2019 13:14:33: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Mon, 03 Jun 2019 13:14:33: start model_add_line... INFO @ Mon, 03 Jun 2019 13:14:33: start X-correlation... INFO @ Mon, 03 Jun 2019 13:14:33: end of X-cor INFO @ Mon, 03 Jun 2019 13:14:33: #2 finished! INFO @ Mon, 03 Jun 2019 13:14:33: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 13:14:33: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 13:14:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.20_model.r WARNING @ Mon, 03 Jun 2019 13:14:33: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:14:33: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 13:14:33: #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 13:14:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:14:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:14:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:14:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:14:34: #1 total tags in treatment: 14374110 INFO @ Mon, 03 Jun 2019 13:14:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:14:34: #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 13:14:34: #1 tags after filtering in treatment: 14374110 INFO @ Mon, 03 Jun 2019 13:14:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:14:34: #1 finished! INFO @ Mon, 03 Jun 2019 13:14:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:14:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:14:35: #2 number of paired peaks: 156 WARNING @ Mon, 03 Jun 2019 13:14:35: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Mon, 03 Jun 2019 13:14:35: start model_add_line... INFO @ Mon, 03 Jun 2019 13:14:35: start X-correlation... INFO @ Mon, 03 Jun 2019 13:14:35: end of X-cor INFO @ Mon, 03 Jun 2019 13:14:35: #2 finished! INFO @ Mon, 03 Jun 2019 13:14:35: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 13:14:35: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 13:14:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.05_model.r WARNING @ Mon, 03 Jun 2019 13:14:35: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:14:35: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 13:14:35: #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 13:14:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:14:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:14:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:15:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.10_peaks.xls INFO @ Mon, 03 Jun 2019 13:15:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:15:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.10_summits.bed INFO @ Mon, 03 Jun 2019 13:15:09: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1570 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:15:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:15:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:15:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.20_peaks.xls INFO @ Mon, 03 Jun 2019 13:15:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:15:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.20_summits.bed INFO @ Mon, 03 Jun 2019 13:15:33: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1042 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:15:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.05_peaks.xls INFO @ Mon, 03 Jun 2019 13:15:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:15:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331406/SRX331406.05_summits.bed INFO @ Mon, 03 Jun 2019 13:15:35: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1913 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。