Job ID = 10175232 sra ファイルのダウンロード中... Completed: 156861K bytes transferred in 5 seconds (216178K 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 9354159 spots for /home/okishinya/chipatlas/results/dm3/SRX2458935/SRR5140284.sra Written 9354159 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:22 9354159 reads; of these: 9354159 (100.00%) were unpaired; of these: 229648 (2.46%) aligned 0 times 7058508 (75.46%) aligned exactly 1 time 2066003 (22.09%) aligned >1 times 97.54% overall alignment rate Time searching: 00:03:22 Overall time: 00:03:22 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_rmdupse_core] 1169039 / 9124511 = 0.1281 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, 06 Nov 2017 11:47:26: # Command line: callpeak -t SRX2458935.bam -f BAM -g dm -n SRX2458935.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2458935.20 # format = BAM # ChIP-seq file = ['SRX2458935.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, 06 Nov 2017 11:47:26: # Command line: callpeak -t SRX2458935.bam -f BAM -g dm -n SRX2458935.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2458935.10 # format = BAM # ChIP-seq file = ['SRX2458935.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, 06 Nov 2017 11:47:26: # Command line: callpeak -t SRX2458935.bam -f BAM -g dm -n SRX2458935.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2458935.05 # format = BAM # ChIP-seq file = ['SRX2458935.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, 06 Nov 2017 11:47:26: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:47:26: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:47:26: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:47:26: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:47:26: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:47:26: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:47:35: 1000000 INFO @ Mon, 06 Nov 2017 11:47:35: 1000000 INFO @ Mon, 06 Nov 2017 11:47:35: 1000000 INFO @ Mon, 06 Nov 2017 11:47:44: 2000000 INFO @ Mon, 06 Nov 2017 11:47:44: 2000000 INFO @ Mon, 06 Nov 2017 11:47:44: 2000000 INFO @ Mon, 06 Nov 2017 11:47:52: 3000000 INFO @ Mon, 06 Nov 2017 11:47:52: 3000000 INFO @ Mon, 06 Nov 2017 11:47:52: 3000000 INFO @ Mon, 06 Nov 2017 11:48:01: 4000000 INFO @ Mon, 06 Nov 2017 11:48:01: 4000000 INFO @ Mon, 06 Nov 2017 11:48:01: 4000000 INFO @ Mon, 06 Nov 2017 11:48:09: 5000000 INFO @ Mon, 06 Nov 2017 11:48:09: 5000000 INFO @ Mon, 06 Nov 2017 11:48:10: 5000000 INFO @ Mon, 06 Nov 2017 11:48:17: 6000000 INFO @ Mon, 06 Nov 2017 11:48:17: 6000000 INFO @ Mon, 06 Nov 2017 11:48:17: 6000000 INFO @ Mon, 06 Nov 2017 11:48:25: 7000000 INFO @ Mon, 06 Nov 2017 11:48:25: 7000000 INFO @ Mon, 06 Nov 2017 11:48:26: 7000000 INFO @ Mon, 06 Nov 2017 11:48:32: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:48:32: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:48:32: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:48:32: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:48:32: #1 total tags in treatment: 7955472 INFO @ Mon, 06 Nov 2017 11:48:32: #1 total tags in treatment: 7955472 INFO @ Mon, 06 Nov 2017 11:48:32: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:48:32: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:48:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 11:48:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 11:48:32: #1 tags after filtering in treatment: 7955472 INFO @ Mon, 06 Nov 2017 11:48:32: #1 tags after filtering in treatment: 7955472 INFO @ Mon, 06 Nov 2017 11:48:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:48:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:48:32: #1 finished! INFO @ Mon, 06 Nov 2017 11:48:32: #1 finished! INFO @ Mon, 06 Nov 2017 11:48:32: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:48:32: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:48:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:48:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:48:33: #2 number of paired peaks: 469 WARNING @ Mon, 06 Nov 2017 11:48:33: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Mon, 06 Nov 2017 11:48:33: start model_add_line... INFO @ Mon, 06 Nov 2017 11:48:33: #2 number of paired peaks: 469 WARNING @ Mon, 06 Nov 2017 11:48:33: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Mon, 06 Nov 2017 11:48:33: start model_add_line... INFO @ Mon, 06 Nov 2017 11:48:33: start X-correlation... INFO @ Mon, 06 Nov 2017 11:48:33: start X-correlation... INFO @ Mon, 06 Nov 2017 11:48:33: end of X-cor INFO @ Mon, 06 Nov 2017 11:48:33: #2 finished! INFO @ Mon, 06 Nov 2017 11:48:33: #2 predicted fragment length is 63 bps INFO @ Mon, 06 Nov 2017 11:48:33: end of X-cor INFO @ Mon, 06 Nov 2017 11:48:33: #2 alternative fragment length(s) may be 63 bps INFO @ Mon, 06 Nov 2017 11:48:33: #2 finished! INFO @ Mon, 06 Nov 2017 11:48:33: #2.2 Generate R script for model : SRX2458935.20_model.r INFO @ Mon, 06 Nov 2017 11:48:33: #2 predicted fragment length is 63 bps INFO @ Mon, 06 Nov 2017 11:48:33: #2 alternative fragment length(s) may be 63 bps INFO @ Mon, 06 Nov 2017 11:48:33: #2.2 Generate R script for model : SRX2458935.10_model.r WARNING @ Mon, 06 Nov 2017 11:48:33: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 11:48:33: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Mon, 06 Nov 2017 11:48:33: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 11:48:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Mon, 06 Nov 2017 11:48:33: #2 You may need to consider one of the other alternative d(s): 63 INFO @ Mon, 06 Nov 2017 11:48:33: #3 Call peaks... WARNING @ Mon, 06 Nov 2017 11:48:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 11:48:33: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:48:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:48:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:48:33: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:48:33: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:48:33: #1 total tags in treatment: 7955472 INFO @ Mon, 06 Nov 2017 11:48:33: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:48:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 11:48:33: #1 tags after filtering in treatment: 7955472 INFO @ Mon, 06 Nov 2017 11:48:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:48:33: #1 finished! INFO @ Mon, 06 Nov 2017 11:48:33: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:48:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:48:34: #2 number of paired peaks: 469 WARNING @ Mon, 06 Nov 2017 11:48:34: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Mon, 06 Nov 2017 11:48:34: start model_add_line... INFO @ Mon, 06 Nov 2017 11:48:34: start X-correlation... INFO @ Mon, 06 Nov 2017 11:48:34: end of X-cor INFO @ Mon, 06 Nov 2017 11:48:34: #2 finished! INFO @ Mon, 06 Nov 2017 11:48:34: #2 predicted fragment length is 63 bps INFO @ Mon, 06 Nov 2017 11:48:34: #2 alternative fragment length(s) may be 63 bps INFO @ Mon, 06 Nov 2017 11:48:34: #2.2 Generate R script for model : SRX2458935.05_model.r WARNING @ Mon, 06 Nov 2017 11:48:34: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 11:48:34: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Mon, 06 Nov 2017 11:48:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 11:48:34: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:48:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:48:52: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:48:52: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:48:52: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:49:02: #4 Write output xls file... SRX2458935.20_peaks.xls INFO @ Mon, 06 Nov 2017 11:49:02: #4 Write peak in narrowPeak format file... SRX2458935.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:49:02: #4 Write summits bed file... SRX2458935.20_summits.bed INFO @ Mon, 06 Nov 2017 11:49:02: Done! pass1 - making usageList (10 chroms): 13 millis pass2 - checking and writing primary data (301 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 11:49:03: #4 Write output xls file... SRX2458935.05_peaks.xls INFO @ Mon, 06 Nov 2017 11:49:03: #4 Write peak in narrowPeak format file... SRX2458935.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:49:03: #4 Write summits bed file... SRX2458935.05_summits.bed INFO @ Mon, 06 Nov 2017 11:49:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1252 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 11:49:03: #4 Write output xls file... SRX2458935.10_peaks.xls INFO @ Mon, 06 Nov 2017 11:49:03: #4 Write peak in narrowPeak format file... SRX2458935.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:49:03: #4 Write summits bed file... SRX2458935.10_summits.bed INFO @ Mon, 06 Nov 2017 11:49:03: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (675 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。