Job ID = 1292537 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,509,609 reads read : 21,509,609 reads written : 21,509,609 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: 00:04:49 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 256442 (1.19%) aligned 0 times 17820719 (82.85%) aligned exactly 1 time 3432448 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:04:49 Overall time: 00:04:49 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3667544 / 21253167 = 0.1726 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 @ Sun, 02 Jun 2019 19:34:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 19:34:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:34:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:34:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 19:34:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:34:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:34:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 19:34:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:34:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:34:36: 1000000 INFO @ Sun, 02 Jun 2019 19:34:37: 1000000 INFO @ Sun, 02 Jun 2019 19:34:37: 1000000 INFO @ Sun, 02 Jun 2019 19:34:44: 2000000 INFO @ Sun, 02 Jun 2019 19:34:45: 2000000 INFO @ Sun, 02 Jun 2019 19:34:45: 2000000 INFO @ Sun, 02 Jun 2019 19:34:51: 3000000 INFO @ Sun, 02 Jun 2019 19:34:53: 3000000 INFO @ Sun, 02 Jun 2019 19:34:53: 3000000 INFO @ Sun, 02 Jun 2019 19:34:59: 4000000 INFO @ Sun, 02 Jun 2019 19:35:01: 4000000 INFO @ Sun, 02 Jun 2019 19:35:01: 4000000 INFO @ Sun, 02 Jun 2019 19:35:06: 5000000 INFO @ Sun, 02 Jun 2019 19:35:10: 5000000 INFO @ Sun, 02 Jun 2019 19:35:10: 5000000 INFO @ Sun, 02 Jun 2019 19:35:13: 6000000 INFO @ Sun, 02 Jun 2019 19:35:18: 6000000 INFO @ Sun, 02 Jun 2019 19:35:18: 6000000 INFO @ Sun, 02 Jun 2019 19:35:21: 7000000 INFO @ Sun, 02 Jun 2019 19:35:26: 7000000 INFO @ Sun, 02 Jun 2019 19:35:26: 7000000 INFO @ Sun, 02 Jun 2019 19:35:28: 8000000 INFO @ Sun, 02 Jun 2019 19:35:34: 8000000 INFO @ Sun, 02 Jun 2019 19:35:34: 8000000 INFO @ Sun, 02 Jun 2019 19:35:36: 9000000 INFO @ Sun, 02 Jun 2019 19:35:42: 9000000 INFO @ Sun, 02 Jun 2019 19:35:43: 9000000 INFO @ Sun, 02 Jun 2019 19:35:43: 10000000 INFO @ Sun, 02 Jun 2019 19:35:50: 10000000 INFO @ Sun, 02 Jun 2019 19:35:50: 10000000 INFO @ Sun, 02 Jun 2019 19:35:51: 11000000 INFO @ Sun, 02 Jun 2019 19:35:59: 11000000 INFO @ Sun, 02 Jun 2019 19:35:59: 11000000 INFO @ Sun, 02 Jun 2019 19:35:59: 12000000 INFO @ Sun, 02 Jun 2019 19:36:07: 12000000 INFO @ Sun, 02 Jun 2019 19:36:07: 12000000 INFO @ Sun, 02 Jun 2019 19:36:08: 13000000 INFO @ Sun, 02 Jun 2019 19:36:16: 14000000 INFO @ Sun, 02 Jun 2019 19:36:16: 13000000 INFO @ Sun, 02 Jun 2019 19:36:16: 13000000 INFO @ Sun, 02 Jun 2019 19:36:24: 15000000 INFO @ Sun, 02 Jun 2019 19:36:24: 14000000 INFO @ Sun, 02 Jun 2019 19:36:24: 14000000 INFO @ Sun, 02 Jun 2019 19:36:32: 16000000 INFO @ Sun, 02 Jun 2019 19:36:32: 15000000 INFO @ Sun, 02 Jun 2019 19:36:32: 15000000 INFO @ Sun, 02 Jun 2019 19:36:39: 17000000 INFO @ Sun, 02 Jun 2019 19:36:40: 16000000 INFO @ Sun, 02 Jun 2019 19:36:40: 16000000 INFO @ Sun, 02 Jun 2019 19:36:44: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:36:44: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:36:44: #1 total tags in treatment: 17585623 INFO @ Sun, 02 Jun 2019 19:36:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:36:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:36:44: #1 tags after filtering in treatment: 17585623 INFO @ Sun, 02 Jun 2019 19:36:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:36:44: #1 finished! INFO @ Sun, 02 Jun 2019 19:36:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:36:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:36:45: #2 number of paired peaks: 212 WARNING @ Sun, 02 Jun 2019 19:36:45: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sun, 02 Jun 2019 19:36:45: start model_add_line... INFO @ Sun, 02 Jun 2019 19:36:46: start X-correlation... INFO @ Sun, 02 Jun 2019 19:36:46: end of X-cor INFO @ Sun, 02 Jun 2019 19:36:46: #2 finished! INFO @ Sun, 02 Jun 2019 19:36:46: #2 predicted fragment length is 40 bps INFO @ Sun, 02 Jun 2019 19:36:46: #2 alternative fragment length(s) may be 2,40,128,587 bps INFO @ Sun, 02 Jun 2019 19:36:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.20_model.r WARNING @ Sun, 02 Jun 2019 19:36:46: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:36:46: #2 You may need to consider one of the other alternative d(s): 2,40,128,587 WARNING @ Sun, 02 Jun 2019 19:36:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:36:46: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:36:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:36:48: 17000000 INFO @ Sun, 02 Jun 2019 19:36:48: 17000000 INFO @ Sun, 02 Jun 2019 19:36:53: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:36:53: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:36:53: #1 total tags in treatment: 17585623 INFO @ Sun, 02 Jun 2019 19:36:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:36:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:36:53: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:36:53: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:36:53: #1 total tags in treatment: 17585623 INFO @ Sun, 02 Jun 2019 19:36:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:36:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:36:53: #1 tags after filtering in treatment: 17585623 INFO @ Sun, 02 Jun 2019 19:36:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:36:53: #1 finished! INFO @ Sun, 02 Jun 2019 19:36:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:36:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:36:53: #1 tags after filtering in treatment: 17585623 INFO @ Sun, 02 Jun 2019 19:36:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:36:53: #1 finished! INFO @ Sun, 02 Jun 2019 19:36:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:36:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:36:54: #2 number of paired peaks: 212 WARNING @ Sun, 02 Jun 2019 19:36:54: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sun, 02 Jun 2019 19:36:54: start model_add_line... INFO @ Sun, 02 Jun 2019 19:36:55: start X-correlation... INFO @ Sun, 02 Jun 2019 19:36:55: #2 number of paired peaks: 212 WARNING @ Sun, 02 Jun 2019 19:36:55: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sun, 02 Jun 2019 19:36:55: start model_add_line... INFO @ Sun, 02 Jun 2019 19:36:55: end of X-cor INFO @ Sun, 02 Jun 2019 19:36:55: #2 finished! INFO @ Sun, 02 Jun 2019 19:36:55: #2 predicted fragment length is 40 bps INFO @ Sun, 02 Jun 2019 19:36:55: #2 alternative fragment length(s) may be 2,40,128,587 bps INFO @ Sun, 02 Jun 2019 19:36:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.10_model.r WARNING @ Sun, 02 Jun 2019 19:36:55: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:36:55: #2 You may need to consider one of the other alternative d(s): 2,40,128,587 WARNING @ Sun, 02 Jun 2019 19:36:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:36:55: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:36:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:36:55: start X-correlation... INFO @ Sun, 02 Jun 2019 19:36:55: end of X-cor INFO @ Sun, 02 Jun 2019 19:36:55: #2 finished! INFO @ Sun, 02 Jun 2019 19:36:55: #2 predicted fragment length is 40 bps INFO @ Sun, 02 Jun 2019 19:36:55: #2 alternative fragment length(s) may be 2,40,128,587 bps INFO @ Sun, 02 Jun 2019 19:36:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.05_model.r WARNING @ Sun, 02 Jun 2019 19:36:55: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:36:55: #2 You may need to consider one of the other alternative d(s): 2,40,128,587 WARNING @ Sun, 02 Jun 2019 19:36:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:36:55: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:36:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:37:27: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:37:36: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:37:37: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:37:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:37:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:37:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.20_summits.bed INFO @ Sun, 02 Jun 2019 19:37:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (109 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:37:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:37:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:37:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.10_summits.bed INFO @ Sun, 02 Jun 2019 19:37:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (347 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:37:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:37:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:37:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466552/SRX466552.05_summits.bed INFO @ Sun, 02 Jun 2019 19:37:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (713 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。