Job ID = 11171332 sra ファイルのダウンロード中... Completed: 156019K bytes transferred in 8 seconds (154762K 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... Read 3935133 spots for /home/okishinya/chipatlas/results/dm3/SRX3511959/SRR6418944.sra Written 3935133 spots for /home/okishinya/chipatlas/results/dm3/SRX3511959/SRR6418944.sra 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:23 3935133 reads; of these: 3935133 (100.00%) were unpaired; of these: 371003 (9.43%) aligned 0 times 2642645 (67.16%) aligned exactly 1 time 921485 (23.42%) aligned >1 times 90.57% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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] 268686 / 3564130 = 0.0754 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, 08 Sep 2018 13:48:49: # Command line: callpeak -t SRX3511959.bam -f BAM -g dm -n SRX3511959.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3511959.10 # format = BAM # ChIP-seq file = ['SRX3511959.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 @ Sat, 08 Sep 2018 13:48:49: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:48:49: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:48:49: # Command line: callpeak -t SRX3511959.bam -f BAM -g dm -n SRX3511959.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3511959.05 # format = BAM # ChIP-seq file = ['SRX3511959.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 @ Sat, 08 Sep 2018 13:48:49: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:48:49: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:48:49: # Command line: callpeak -t SRX3511959.bam -f BAM -g dm -n SRX3511959.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3511959.20 # format = BAM # ChIP-seq file = ['SRX3511959.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 @ Sat, 08 Sep 2018 13:48:49: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:48:49: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:48:57: 1000000 INFO @ Sat, 08 Sep 2018 13:48:58: 1000000 INFO @ Sat, 08 Sep 2018 13:48:58: 1000000 INFO @ Sat, 08 Sep 2018 13:49:06: 2000000 INFO @ Sat, 08 Sep 2018 13:49:07: 2000000 INFO @ Sat, 08 Sep 2018 13:49:07: 2000000 INFO @ Sat, 08 Sep 2018 13:49:15: 3000000 INFO @ Sat, 08 Sep 2018 13:49:17: 3000000 INFO @ Sat, 08 Sep 2018 13:49:17: 3000000 INFO @ Sat, 08 Sep 2018 13:49:17: #1 tag size is determined as 99 bps INFO @ Sat, 08 Sep 2018 13:49:17: #1 tag size = 99 INFO @ Sat, 08 Sep 2018 13:49:17: #1 total tags in treatment: 3295444 INFO @ Sat, 08 Sep 2018 13:49:17: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:49:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:49:17: #1 tags after filtering in treatment: 3295444 INFO @ Sat, 08 Sep 2018 13:49:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:49:17: #1 finished! INFO @ Sat, 08 Sep 2018 13:49:17: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:49:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:49:18: #2 number of paired peaks: 802 WARNING @ Sat, 08 Sep 2018 13:49:18: Fewer paired peaks (802) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 802 pairs to build model! INFO @ Sat, 08 Sep 2018 13:49:18: start model_add_line... INFO @ Sat, 08 Sep 2018 13:49:18: start X-correlation... INFO @ Sat, 08 Sep 2018 13:49:18: end of X-cor INFO @ Sat, 08 Sep 2018 13:49:18: #2 finished! INFO @ Sat, 08 Sep 2018 13:49:18: #2 predicted fragment length is 133 bps INFO @ Sat, 08 Sep 2018 13:49:18: #2 alternative fragment length(s) may be 2,133,204 bps INFO @ Sat, 08 Sep 2018 13:49:18: #2.2 Generate R script for model : SRX3511959.10_model.r WARNING @ Sat, 08 Sep 2018 13:49:18: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:49:18: #2 You may need to consider one of the other alternative d(s): 2,133,204 WARNING @ Sat, 08 Sep 2018 13:49:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:49:18: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:49:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:49:20: #1 tag size is determined as 99 bps INFO @ Sat, 08 Sep 2018 13:49:20: #1 tag size = 99 INFO @ Sat, 08 Sep 2018 13:49:20: #1 total tags in treatment: 3295444 INFO @ Sat, 08 Sep 2018 13:49:20: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:49:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:49:20: #1 tags after filtering in treatment: 3295444 INFO @ Sat, 08 Sep 2018 13:49:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:49:20: #1 finished! INFO @ Sat, 08 Sep 2018 13:49:20: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:49:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:49:20: #1 tag size is determined as 99 bps INFO @ Sat, 08 Sep 2018 13:49:20: #1 tag size = 99 INFO @ Sat, 08 Sep 2018 13:49:20: #1 total tags in treatment: 3295444 INFO @ Sat, 08 Sep 2018 13:49:20: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:49:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:49:20: #1 tags after filtering in treatment: 3295444 INFO @ Sat, 08 Sep 2018 13:49:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:49:20: #1 finished! INFO @ Sat, 08 Sep 2018 13:49:20: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:49:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:49:20: #2 number of paired peaks: 802 WARNING @ Sat, 08 Sep 2018 13:49:20: Fewer paired peaks (802) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 802 pairs to build model! INFO @ Sat, 08 Sep 2018 13:49:20: start model_add_line... INFO @ Sat, 08 Sep 2018 13:49:20: start X-correlation... INFO @ Sat, 08 Sep 2018 13:49:20: end of X-cor INFO @ Sat, 08 Sep 2018 13:49:20: #2 finished! INFO @ Sat, 08 Sep 2018 13:49:20: #2 predicted fragment length is 133 bps INFO @ Sat, 08 Sep 2018 13:49:20: #2 alternative fragment length(s) may be 2,133,204 bps INFO @ Sat, 08 Sep 2018 13:49:20: #2.2 Generate R script for model : SRX3511959.05_model.r WARNING @ Sat, 08 Sep 2018 13:49:20: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:49:20: #2 You may need to consider one of the other alternative d(s): 2,133,204 WARNING @ Sat, 08 Sep 2018 13:49:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:49:20: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:49:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:49:20: #2 number of paired peaks: 802 WARNING @ Sat, 08 Sep 2018 13:49:20: Fewer paired peaks (802) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 802 pairs to build model! INFO @ Sat, 08 Sep 2018 13:49:20: start model_add_line... INFO @ Sat, 08 Sep 2018 13:49:20: start X-correlation... INFO @ Sat, 08 Sep 2018 13:49:20: end of X-cor INFO @ Sat, 08 Sep 2018 13:49:20: #2 finished! INFO @ Sat, 08 Sep 2018 13:49:20: #2 predicted fragment length is 133 bps INFO @ Sat, 08 Sep 2018 13:49:20: #2 alternative fragment length(s) may be 2,133,204 bps INFO @ Sat, 08 Sep 2018 13:49:20: #2.2 Generate R script for model : SRX3511959.20_model.r WARNING @ Sat, 08 Sep 2018 13:49:20: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:49:20: #2 You may need to consider one of the other alternative d(s): 2,133,204 WARNING @ Sat, 08 Sep 2018 13:49:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:49:20: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:49:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:49:26: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:49:28: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:49:29: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:49:30: #4 Write output xls file... SRX3511959.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:49:30: #4 Write peak in narrowPeak format file... SRX3511959.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:49:30: #4 Write summits bed file... SRX3511959.10_summits.bed INFO @ Sat, 08 Sep 2018 13:49:30: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (45 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:49:32: #4 Write output xls file... SRX3511959.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:49:32: #4 Write peak in narrowPeak format file... SRX3511959.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:49:32: #4 Write summits bed file... SRX3511959.05_summits.bed INFO @ Sat, 08 Sep 2018 13:49:32: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (144 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:49:33: #4 Write output xls file... SRX3511959.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:49:33: #4 Write peak in narrowPeak format file... SRX3511959.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:49:33: #4 Write summits bed file... SRX3511959.20_summits.bed INFO @ Sat, 08 Sep 2018 13:49:33: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (17 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。