Job ID = 11293667 sra ファイルのダウンロード中... Completed: 396928K bytes transferred in 17 seconds (185921K 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 12528023 spots for /home/okishinya/chipatlas/results/dm3/SRX4375829/SRR7506483.sra Written 12528023 spots for /home/okishinya/chipatlas/results/dm3/SRX4375829/SRR7506483.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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:22 12528023 reads; of these: 12528023 (100.00%) were unpaired; of these: 4176992 (33.34%) aligned 0 times 6304387 (50.32%) aligned exactly 1 time 2046644 (16.34%) aligned >1 times 66.66% 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] 1279416 / 8351031 = 0.1532 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, 04 Nov 2018 17:53:16: # Command line: callpeak -t SRX4375829.bam -f BAM -g dm -n SRX4375829.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4375829.05 # format = BAM # ChIP-seq file = ['SRX4375829.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 @ Sun, 04 Nov 2018 17:53:16: # Command line: callpeak -t SRX4375829.bam -f BAM -g dm -n SRX4375829.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4375829.20 # format = BAM # ChIP-seq file = ['SRX4375829.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 @ Sun, 04 Nov 2018 17:53:16: # Command line: callpeak -t SRX4375829.bam -f BAM -g dm -n SRX4375829.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4375829.10 # format = BAM # ChIP-seq file = ['SRX4375829.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 @ Sun, 04 Nov 2018 17:53:16: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:53:16: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:53:16: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:53:16: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:53:16: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:53:16: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:53:23: 1000000 INFO @ Sun, 04 Nov 2018 17:53:23: 1000000 INFO @ Sun, 04 Nov 2018 17:53:23: 1000000 INFO @ Sun, 04 Nov 2018 17:53:30: 2000000 INFO @ Sun, 04 Nov 2018 17:53:30: 2000000 INFO @ Sun, 04 Nov 2018 17:53:31: 2000000 INFO @ Sun, 04 Nov 2018 17:53:37: 3000000 INFO @ Sun, 04 Nov 2018 17:53:38: 3000000 INFO @ Sun, 04 Nov 2018 17:53:38: 3000000 INFO @ Sun, 04 Nov 2018 17:53:44: 4000000 INFO @ Sun, 04 Nov 2018 17:53:45: 4000000 INFO @ Sun, 04 Nov 2018 17:53:46: 4000000 INFO @ Sun, 04 Nov 2018 17:53:51: 5000000 INFO @ Sun, 04 Nov 2018 17:53:53: 5000000 INFO @ Sun, 04 Nov 2018 17:53:53: 5000000 INFO @ Sun, 04 Nov 2018 17:53:58: 6000000 INFO @ Sun, 04 Nov 2018 17:54:00: 6000000 INFO @ Sun, 04 Nov 2018 17:54:00: 6000000 INFO @ Sun, 04 Nov 2018 17:54:05: 7000000 INFO @ Sun, 04 Nov 2018 17:54:05: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:54:05: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:54:05: #1 total tags in treatment: 7071615 INFO @ Sun, 04 Nov 2018 17:54:05: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:54:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:54:06: #1 tags after filtering in treatment: 7071615 INFO @ Sun, 04 Nov 2018 17:54:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:54:06: #1 finished! INFO @ Sun, 04 Nov 2018 17:54:06: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:54:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:54:06: #2 number of paired peaks: 384 WARNING @ Sun, 04 Nov 2018 17:54:06: Fewer paired peaks (384) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 384 pairs to build model! INFO @ Sun, 04 Nov 2018 17:54:06: start model_add_line... INFO @ Sun, 04 Nov 2018 17:54:06: start X-correlation... INFO @ Sun, 04 Nov 2018 17:54:06: end of X-cor INFO @ Sun, 04 Nov 2018 17:54:06: #2 finished! INFO @ Sun, 04 Nov 2018 17:54:06: #2 predicted fragment length is 66 bps INFO @ Sun, 04 Nov 2018 17:54:06: #2 alternative fragment length(s) may be 66 bps INFO @ Sun, 04 Nov 2018 17:54:06: #2.2 Generate R script for model : SRX4375829.20_model.r WARNING @ Sun, 04 Nov 2018 17:54:06: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:54:06: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sun, 04 Nov 2018 17:54:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 17:54:06: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:54:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:54:07: 7000000 INFO @ Sun, 04 Nov 2018 17:54:08: 7000000 INFO @ Sun, 04 Nov 2018 17:54:08: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:54:08: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:54:08: #1 total tags in treatment: 7071615 INFO @ Sun, 04 Nov 2018 17:54:08: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:54:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:54:08: #1 tags after filtering in treatment: 7071615 INFO @ Sun, 04 Nov 2018 17:54:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:54:08: #1 finished! INFO @ Sun, 04 Nov 2018 17:54:08: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:54:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:54:08: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:54:08: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:54:08: #1 total tags in treatment: 7071615 INFO @ Sun, 04 Nov 2018 17:54:08: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:54:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:54:08: #1 tags after filtering in treatment: 7071615 INFO @ Sun, 04 Nov 2018 17:54:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:54:08: #1 finished! INFO @ Sun, 04 Nov 2018 17:54:08: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:54:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:54:09: #2 number of paired peaks: 384 WARNING @ Sun, 04 Nov 2018 17:54:09: Fewer paired peaks (384) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 384 pairs to build model! INFO @ Sun, 04 Nov 2018 17:54:09: start model_add_line... INFO @ Sun, 04 Nov 2018 17:54:09: start X-correlation... INFO @ Sun, 04 Nov 2018 17:54:09: end of X-cor INFO @ Sun, 04 Nov 2018 17:54:09: #2 finished! INFO @ Sun, 04 Nov 2018 17:54:09: #2 predicted fragment length is 66 bps INFO @ Sun, 04 Nov 2018 17:54:09: #2 alternative fragment length(s) may be 66 bps INFO @ Sun, 04 Nov 2018 17:54:09: #2.2 Generate R script for model : SRX4375829.10_model.r WARNING @ Sun, 04 Nov 2018 17:54:09: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:54:09: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sun, 04 Nov 2018 17:54:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 17:54:09: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:54:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:54:09: #2 number of paired peaks: 384 WARNING @ Sun, 04 Nov 2018 17:54:09: Fewer paired peaks (384) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 384 pairs to build model! INFO @ Sun, 04 Nov 2018 17:54:09: start model_add_line... INFO @ Sun, 04 Nov 2018 17:54:09: start X-correlation... INFO @ Sun, 04 Nov 2018 17:54:09: end of X-cor INFO @ Sun, 04 Nov 2018 17:54:09: #2 finished! INFO @ Sun, 04 Nov 2018 17:54:09: #2 predicted fragment length is 66 bps INFO @ Sun, 04 Nov 2018 17:54:09: #2 alternative fragment length(s) may be 66 bps INFO @ Sun, 04 Nov 2018 17:54:09: #2.2 Generate R script for model : SRX4375829.05_model.r WARNING @ Sun, 04 Nov 2018 17:54:09: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:54:09: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sun, 04 Nov 2018 17:54:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 17:54:09: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:54:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:54:22: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:54:25: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:54:26: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:54:32: #4 Write output xls file... SRX4375829.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:54:32: #4 Write peak in narrowPeak format file... SRX4375829.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:54:32: #4 Write summits bed file... SRX4375829.20_summits.bed INFO @ Sun, 04 Nov 2018 17:54:32: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (245 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:54:33: #4 Write output xls file... SRX4375829.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:54:33: #4 Write peak in narrowPeak format file... SRX4375829.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:54:33: #4 Write summits bed file... SRX4375829.10_summits.bed INFO @ Sun, 04 Nov 2018 17:54:33: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (562 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:54:35: #4 Write output xls file... SRX4375829.05_peaks.xls INFO @ Sun, 04 Nov 2018 17:54:35: #4 Write peak in narrowPeak format file... SRX4375829.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:54:35: #4 Write summits bed file... SRX4375829.05_summits.bed INFO @ Sun, 04 Nov 2018 17:54:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1436 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。