Job ID = 1292474 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,196,513 reads read : 18,196,513 reads written : 18,196,513 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: 00:05:01 18196513 reads; of these: 18196513 (100.00%) were unpaired; of these: 550677 (3.03%) aligned 0 times 12352160 (67.88%) aligned exactly 1 time 5293676 (29.09%) aligned >1 times 96.97% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 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] 4808827 / 17645836 = 0.2725 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 19:14:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.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 19:14:20: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:14:20: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:14:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.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 19:14:20: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:14:20: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:14:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.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 19:14:20: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:14:20: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:14:30: 1000000 INFO @ Sun, 02 Jun 2019 19:14:30: 1000000 INFO @ Sun, 02 Jun 2019 19:14:30: 1000000 INFO @ Sun, 02 Jun 2019 19:14:37: 2000000 INFO @ Sun, 02 Jun 2019 19:14:39: 2000000 INFO @ Sun, 02 Jun 2019 19:14:40: 2000000 INFO @ Sun, 02 Jun 2019 19:14:44: 3000000 INFO @ Sun, 02 Jun 2019 19:14:48: 3000000 INFO @ Sun, 02 Jun 2019 19:14:49: 3000000 INFO @ Sun, 02 Jun 2019 19:14:52: 4000000 INFO @ Sun, 02 Jun 2019 19:14:58: 4000000 INFO @ Sun, 02 Jun 2019 19:14:59: 4000000 INFO @ Sun, 02 Jun 2019 19:14:59: 5000000 INFO @ Sun, 02 Jun 2019 19:15:06: 6000000 INFO @ Sun, 02 Jun 2019 19:15:07: 5000000 INFO @ Sun, 02 Jun 2019 19:15:08: 5000000 INFO @ Sun, 02 Jun 2019 19:15:14: 7000000 INFO @ Sun, 02 Jun 2019 19:15:17: 6000000 INFO @ Sun, 02 Jun 2019 19:15:18: 6000000 INFO @ Sun, 02 Jun 2019 19:15:21: 8000000 INFO @ Sun, 02 Jun 2019 19:15:26: 7000000 INFO @ Sun, 02 Jun 2019 19:15:27: 7000000 INFO @ Sun, 02 Jun 2019 19:15:29: 9000000 INFO @ Sun, 02 Jun 2019 19:15:36: 8000000 INFO @ Sun, 02 Jun 2019 19:15:37: 8000000 INFO @ Sun, 02 Jun 2019 19:15:37: 10000000 INFO @ Sun, 02 Jun 2019 19:15:45: 9000000 INFO @ Sun, 02 Jun 2019 19:15:46: 9000000 INFO @ Sun, 02 Jun 2019 19:15:46: 11000000 INFO @ Sun, 02 Jun 2019 19:15:55: 12000000 INFO @ Sun, 02 Jun 2019 19:15:56: 10000000 INFO @ Sun, 02 Jun 2019 19:15:56: 10000000 INFO @ Sun, 02 Jun 2019 19:16:02: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:16:02: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:16:02: #1 total tags in treatment: 12837009 INFO @ Sun, 02 Jun 2019 19:16:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:16:02: #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 19:16:02: #1 tags after filtering in treatment: 12837009 INFO @ Sun, 02 Jun 2019 19:16:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:16:02: #1 finished! INFO @ Sun, 02 Jun 2019 19:16:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:16:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:16:03: #2 number of paired peaks: 1580 INFO @ Sun, 02 Jun 2019 19:16:03: start model_add_line... INFO @ Sun, 02 Jun 2019 19:16:04: start X-correlation... INFO @ Sun, 02 Jun 2019 19:16:04: end of X-cor INFO @ Sun, 02 Jun 2019 19:16:04: #2 finished! INFO @ Sun, 02 Jun 2019 19:16:04: #2 predicted fragment length is 91 bps INFO @ Sun, 02 Jun 2019 19:16:04: #2 alternative fragment length(s) may be 2,66,91 bps INFO @ Sun, 02 Jun 2019 19:16:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.05_model.r WARNING @ Sun, 02 Jun 2019 19:16:04: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:16:04: #2 You may need to consider one of the other alternative d(s): 2,66,91 WARNING @ Sun, 02 Jun 2019 19:16:04: #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 19:16:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:16:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:16:06: 11000000 INFO @ Sun, 02 Jun 2019 19:16:06: 11000000 INFO @ Sun, 02 Jun 2019 19:16:15: 12000000 INFO @ Sun, 02 Jun 2019 19:16:16: 12000000 INFO @ Sun, 02 Jun 2019 19:16:23: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:16:23: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:16:23: #1 total tags in treatment: 12837009 INFO @ Sun, 02 Jun 2019 19:16:23: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:16:23: #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 19:16:23: #1 tags after filtering in treatment: 12837009 INFO @ Sun, 02 Jun 2019 19:16:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:16:23: #1 finished! INFO @ Sun, 02 Jun 2019 19:16:23: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:16:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:16:24: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:16:24: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:16:24: #1 total tags in treatment: 12837009 INFO @ Sun, 02 Jun 2019 19:16:24: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:16:24: #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 19:16:24: #1 tags after filtering in treatment: 12837009 INFO @ Sun, 02 Jun 2019 19:16:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:16:24: #1 finished! INFO @ Sun, 02 Jun 2019 19:16:24: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:16:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:16:25: #2 number of paired peaks: 1580 INFO @ Sun, 02 Jun 2019 19:16:25: start model_add_line... INFO @ Sun, 02 Jun 2019 19:16:25: start X-correlation... INFO @ Sun, 02 Jun 2019 19:16:25: end of X-cor INFO @ Sun, 02 Jun 2019 19:16:25: #2 finished! INFO @ Sun, 02 Jun 2019 19:16:25: #2 predicted fragment length is 91 bps INFO @ Sun, 02 Jun 2019 19:16:25: #2 alternative fragment length(s) may be 2,66,91 bps INFO @ Sun, 02 Jun 2019 19:16:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.20_model.r WARNING @ Sun, 02 Jun 2019 19:16:25: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:16:25: #2 You may need to consider one of the other alternative d(s): 2,66,91 WARNING @ Sun, 02 Jun 2019 19:16:25: #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 19:16:25: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:16:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:16:25: #2 number of paired peaks: 1580 INFO @ Sun, 02 Jun 2019 19:16:25: start model_add_line... INFO @ Sun, 02 Jun 2019 19:16:25: start X-correlation... INFO @ Sun, 02 Jun 2019 19:16:25: end of X-cor INFO @ Sun, 02 Jun 2019 19:16:25: #2 finished! INFO @ Sun, 02 Jun 2019 19:16:25: #2 predicted fragment length is 91 bps INFO @ Sun, 02 Jun 2019 19:16:25: #2 alternative fragment length(s) may be 2,66,91 bps INFO @ Sun, 02 Jun 2019 19:16:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.10_model.r WARNING @ Sun, 02 Jun 2019 19:16:25: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:16:25: #2 You may need to consider one of the other alternative d(s): 2,66,91 WARNING @ Sun, 02 Jun 2019 19:16:25: #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 19:16:25: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:16:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:16:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:16:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:16:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:16:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.05_summits.bed INFO @ Sun, 02 Jun 2019 19:16:58: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1786 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:17:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:17:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:17:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:17:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:17:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.20_summits.bed INFO @ Sun, 02 Jun 2019 19:17:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (286 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:17:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:17:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:17:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466462/SRX466462.10_summits.bed INFO @ Sun, 02 Jun 2019 19:17:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (704 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。