Job ID = 10194822 sra ファイルのダウンロード中... Completed: 535830K bytes transferred in 13 seconds (336082K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 28590420 spots for /home/okishinya/chipatlas/results/rn6/SRX1977112/SRR3952244.sra Written 28590420 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:24:47 28590420 reads; of these: 28590420 (100.00%) were unpaired; of these: 22808790 (79.78%) aligned 0 times 3407109 (11.92%) aligned exactly 1 time 2374521 (8.31%) aligned >1 times 20.22% overall alignment rate Time searching: 00:24:52 Overall time: 00:24:52 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 764357 / 5781630 = 0.1322 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 @ Sat, 11 Nov 2017 01:28:07: # Command line: callpeak -t SRX1977112.bam -f BAM -g 2.15e9 -n SRX1977112.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977112.20 # format = BAM # ChIP-seq file = ['SRX1977112.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 11 Nov 2017 01:28:07: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:28:07: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:28:07: # Command line: callpeak -t SRX1977112.bam -f BAM -g 2.15e9 -n SRX1977112.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977112.05 # format = BAM # ChIP-seq file = ['SRX1977112.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 11 Nov 2017 01:28:07: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:28:07: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:28:07: # Command line: callpeak -t SRX1977112.bam -f BAM -g 2.15e9 -n SRX1977112.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977112.10 # format = BAM # ChIP-seq file = ['SRX1977112.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 11 Nov 2017 01:28:07: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:28:07: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:28:20: 1000000 INFO @ Sat, 11 Nov 2017 01:28:20: 1000000 INFO @ Sat, 11 Nov 2017 01:28:21: 1000000 INFO @ Sat, 11 Nov 2017 01:28:34: 2000000 INFO @ Sat, 11 Nov 2017 01:28:34: 2000000 INFO @ Sat, 11 Nov 2017 01:28:34: 2000000 INFO @ Sat, 11 Nov 2017 01:28:47: 3000000 INFO @ Sat, 11 Nov 2017 01:28:47: 3000000 INFO @ Sat, 11 Nov 2017 01:28:48: 3000000 INFO @ Sat, 11 Nov 2017 01:29:00: 4000000 INFO @ Sat, 11 Nov 2017 01:29:00: 4000000 INFO @ Sat, 11 Nov 2017 01:29:01: 4000000 INFO @ Sat, 11 Nov 2017 01:29:13: 5000000 INFO @ Sat, 11 Nov 2017 01:29:13: 5000000 INFO @ Sat, 11 Nov 2017 01:29:14: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 01:29:14: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 01:29:14: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 01:29:14: #1 total tags in treatment: 5017273 INFO @ Sat, 11 Nov 2017 01:29:14: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 01:29:14: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:29:14: #1 total tags in treatment: 5017273 INFO @ Sat, 11 Nov 2017 01:29:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 01:29:14: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:29:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 01:29:14: #1 tags after filtering in treatment: 5017009 INFO @ Sat, 11 Nov 2017 01:29:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:29:14: #1 finished! INFO @ Sat, 11 Nov 2017 01:29:14: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:29:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:29:14: #1 tags after filtering in treatment: 5017009 INFO @ Sat, 11 Nov 2017 01:29:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:29:14: #1 finished! INFO @ Sat, 11 Nov 2017 01:29:14: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:29:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:29:14: 5000000 INFO @ Sat, 11 Nov 2017 01:29:15: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 01:29:15: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 01:29:15: #1 total tags in treatment: 5017273 INFO @ Sat, 11 Nov 2017 01:29:15: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:29:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 01:29:15: #1 tags after filtering in treatment: 5017009 INFO @ Sat, 11 Nov 2017 01:29:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:29:15: #1 finished! INFO @ Sat, 11 Nov 2017 01:29:15: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:29:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:29:16: #2 number of paired peaks: 49113 INFO @ Sat, 11 Nov 2017 01:29:16: start model_add_line... INFO @ Sat, 11 Nov 2017 01:29:17: start X-correlation... INFO @ Sat, 11 Nov 2017 01:29:17: end of X-cor INFO @ Sat, 11 Nov 2017 01:29:17: #2 finished! INFO @ Sat, 11 Nov 2017 01:29:17: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Nov 2017 01:29:17: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Nov 2017 01:29:17: #2.2 Generate R script for model : SRX1977112.20_model.r WARNING @ Sat, 11 Nov 2017 01:29:17: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:29:17: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Nov 2017 01:29:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 01:29:17: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:29:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:29:17: #2 number of paired peaks: 49113 INFO @ Sat, 11 Nov 2017 01:29:17: start model_add_line... INFO @ Sat, 11 Nov 2017 01:29:17: start X-correlation... INFO @ Sat, 11 Nov 2017 01:29:17: end of X-cor INFO @ Sat, 11 Nov 2017 01:29:17: #2 finished! INFO @ Sat, 11 Nov 2017 01:29:17: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Nov 2017 01:29:17: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Nov 2017 01:29:17: #2.2 Generate R script for model : SRX1977112.10_model.r WARNING @ Sat, 11 Nov 2017 01:29:17: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:29:17: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Nov 2017 01:29:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 01:29:17: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:29:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:29:18: #2 number of paired peaks: 49113 INFO @ Sat, 11 Nov 2017 01:29:18: start model_add_line... INFO @ Sat, 11 Nov 2017 01:29:18: start X-correlation... INFO @ Sat, 11 Nov 2017 01:29:18: end of X-cor INFO @ Sat, 11 Nov 2017 01:29:18: #2 finished! INFO @ Sat, 11 Nov 2017 01:29:18: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Nov 2017 01:29:18: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Nov 2017 01:29:18: #2.2 Generate R script for model : SRX1977112.05_model.r WARNING @ Sat, 11 Nov 2017 01:29:18: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:29:18: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Nov 2017 01:29:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 01:29:18: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:29:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:29:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:29:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:29:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:29:36: #4 Write output xls file... SRX1977112.20_peaks.xls INFO @ Sat, 11 Nov 2017 01:29:36: #4 Write peak in narrowPeak format file... SRX1977112.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:29:36: #4 Write summits bed file... SRX1977112.20_summits.bed INFO @ Sat, 11 Nov 2017 01:29:36: Done! pass1 - making usageList (52 chroms): 1 millis pass2 - checking and writing primary data (543 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:29:38: #4 Write output xls file... SRX1977112.10_peaks.xls INFO @ Sat, 11 Nov 2017 01:29:38: #4 Write peak in narrowPeak format file... SRX1977112.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:29:38: #4 Write summits bed file... SRX1977112.10_summits.bed INFO @ Sat, 11 Nov 2017 01:29:38: Done! INFO @ Sat, 11 Nov 2017 01:29:38: #4 Write output xls file... SRX1977112.05_peaks.xls INFO @ Sat, 11 Nov 2017 01:29:38: #4 Write peak in narrowPeak format file... SRX1977112.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:29:38: #4 Write summits bed file... SRX1977112.05_summits.bed pass1 - making usageList (69 chroms): 2 millis pass2 - checking and writing primary data (1901 records, 4 fields): 7 millis INFO @ Sat, 11 Nov 2017 01:29:38: Done! CompletedMACS2peakCalling pass1 - making usageList (97 chroms): 2 millis pass2 - checking and writing primary data (5638 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。