Job ID = 1293076 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,440,500 reads read : 16,440,500 reads written : 16,440,500 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: 00:04:43 16440500 reads; of these: 16440500 (100.00%) were unpaired; of these: 138367 (0.84%) aligned 0 times 13512753 (82.19%) aligned exactly 1 time 2789380 (16.97%) aligned >1 times 99.16% overall alignment rate Time searching: 00:04:43 Overall time: 00:04:43 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] 1797581 / 16302133 = 0.1103 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 21:52:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.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 21:52:13: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:52:13: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:52:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.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 21:52:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.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 21:52:13: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:52:13: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:52:13: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:52:13: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:52:21: 1000000 INFO @ Sun, 02 Jun 2019 21:52:21: 1000000 INFO @ Sun, 02 Jun 2019 21:52:22: 1000000 INFO @ Sun, 02 Jun 2019 21:52:28: 2000000 INFO @ Sun, 02 Jun 2019 21:52:28: 2000000 INFO @ Sun, 02 Jun 2019 21:52:30: 2000000 INFO @ Sun, 02 Jun 2019 21:52:35: 3000000 INFO @ Sun, 02 Jun 2019 21:52:35: 3000000 INFO @ Sun, 02 Jun 2019 21:52:38: 3000000 INFO @ Sun, 02 Jun 2019 21:52:42: 4000000 INFO @ Sun, 02 Jun 2019 21:52:43: 4000000 INFO @ Sun, 02 Jun 2019 21:52:45: 4000000 INFO @ Sun, 02 Jun 2019 21:52:49: 5000000 INFO @ Sun, 02 Jun 2019 21:52:50: 5000000 INFO @ Sun, 02 Jun 2019 21:52:53: 5000000 INFO @ Sun, 02 Jun 2019 21:52:56: 6000000 INFO @ Sun, 02 Jun 2019 21:52:57: 6000000 INFO @ Sun, 02 Jun 2019 21:53:01: 6000000 INFO @ Sun, 02 Jun 2019 21:53:04: 7000000 INFO @ Sun, 02 Jun 2019 21:53:04: 7000000 INFO @ Sun, 02 Jun 2019 21:53:09: 7000000 INFO @ Sun, 02 Jun 2019 21:53:11: 8000000 INFO @ Sun, 02 Jun 2019 21:53:12: 8000000 INFO @ Sun, 02 Jun 2019 21:53:17: 8000000 INFO @ Sun, 02 Jun 2019 21:53:18: 9000000 INFO @ Sun, 02 Jun 2019 21:53:19: 9000000 INFO @ Sun, 02 Jun 2019 21:53:25: 10000000 INFO @ Sun, 02 Jun 2019 21:53:25: 9000000 INFO @ Sun, 02 Jun 2019 21:53:26: 10000000 INFO @ Sun, 02 Jun 2019 21:53:32: 11000000 INFO @ Sun, 02 Jun 2019 21:53:33: 10000000 INFO @ Sun, 02 Jun 2019 21:53:33: 11000000 INFO @ Sun, 02 Jun 2019 21:53:39: 12000000 INFO @ Sun, 02 Jun 2019 21:53:41: 12000000 INFO @ Sun, 02 Jun 2019 21:53:41: 11000000 INFO @ Sun, 02 Jun 2019 21:53:47: 13000000 INFO @ Sun, 02 Jun 2019 21:53:48: 13000000 INFO @ Sun, 02 Jun 2019 21:53:49: 12000000 INFO @ Sun, 02 Jun 2019 21:53:54: 14000000 INFO @ Sun, 02 Jun 2019 21:53:56: 14000000 INFO @ Sun, 02 Jun 2019 21:53:57: 13000000 INFO @ Sun, 02 Jun 2019 21:53:58: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:53:58: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:53:58: #1 total tags in treatment: 14504552 INFO @ Sun, 02 Jun 2019 21:53:58: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:53:58: #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 21:53:59: #1 tags after filtering in treatment: 14504552 INFO @ Sun, 02 Jun 2019 21:53:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:53:59: #1 finished! INFO @ Sun, 02 Jun 2019 21:53:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:53:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:54:00: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:54:00: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:54:00: #1 total tags in treatment: 14504552 INFO @ Sun, 02 Jun 2019 21:54:00: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:54:00: #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 21:54:00: #2 number of paired peaks: 331 WARNING @ Sun, 02 Jun 2019 21:54:00: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Sun, 02 Jun 2019 21:54:00: start model_add_line... INFO @ Sun, 02 Jun 2019 21:54:00: #1 tags after filtering in treatment: 14504552 INFO @ Sun, 02 Jun 2019 21:54:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:54:00: #1 finished! INFO @ Sun, 02 Jun 2019 21:54:00: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:54:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:54:00: start X-correlation... INFO @ Sun, 02 Jun 2019 21:54:00: end of X-cor INFO @ Sun, 02 Jun 2019 21:54:00: #2 finished! INFO @ Sun, 02 Jun 2019 21:54:00: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 21:54:00: #2 alternative fragment length(s) may be 2,48 bps INFO @ Sun, 02 Jun 2019 21:54:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.05_model.r WARNING @ Sun, 02 Jun 2019 21:54:00: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:54:00: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Sun, 02 Jun 2019 21:54:00: #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 21:54:00: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:54:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:54:01: #2 number of paired peaks: 331 WARNING @ Sun, 02 Jun 2019 21:54:01: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Sun, 02 Jun 2019 21:54:01: start model_add_line... INFO @ Sun, 02 Jun 2019 21:54:01: start X-correlation... INFO @ Sun, 02 Jun 2019 21:54:01: end of X-cor INFO @ Sun, 02 Jun 2019 21:54:01: #2 finished! INFO @ Sun, 02 Jun 2019 21:54:01: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 21:54:01: #2 alternative fragment length(s) may be 2,48 bps INFO @ Sun, 02 Jun 2019 21:54:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.10_model.r WARNING @ Sun, 02 Jun 2019 21:54:01: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:54:01: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Sun, 02 Jun 2019 21:54:01: #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 21:54:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:54:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:54:05: 14000000 INFO @ Sun, 02 Jun 2019 21:54:09: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:54:09: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:54:09: #1 total tags in treatment: 14504552 INFO @ Sun, 02 Jun 2019 21:54:09: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:54:09: #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 21:54:10: #1 tags after filtering in treatment: 14504552 INFO @ Sun, 02 Jun 2019 21:54:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:54:10: #1 finished! INFO @ Sun, 02 Jun 2019 21:54:10: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:54:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:54:11: #2 number of paired peaks: 331 WARNING @ Sun, 02 Jun 2019 21:54:11: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Sun, 02 Jun 2019 21:54:11: start model_add_line... INFO @ Sun, 02 Jun 2019 21:54:11: start X-correlation... INFO @ Sun, 02 Jun 2019 21:54:11: end of X-cor INFO @ Sun, 02 Jun 2019 21:54:11: #2 finished! INFO @ Sun, 02 Jun 2019 21:54:11: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 21:54:11: #2 alternative fragment length(s) may be 2,48 bps INFO @ Sun, 02 Jun 2019 21:54:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.20_model.r WARNING @ Sun, 02 Jun 2019 21:54:11: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:54:11: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Sun, 02 Jun 2019 21:54:11: #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 21:54:11: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:54:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:54:36: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:54:37: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:54:47: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:54:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:54:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:54:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.05_summits.bed INFO @ Sun, 02 Jun 2019 21:54:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (714 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:54:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:54:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:54:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.10_summits.bed INFO @ Sun, 02 Jun 2019 21:54:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (498 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:55:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:55:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:55:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020838/SRX5020838.20_summits.bed INFO @ Sun, 02 Jun 2019 21:55:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (192 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。