Job ID = 11171393 sra ファイルのダウンロード中... Completed: 150551K bytes transferred in 15 seconds (77249K 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 9215339 spots for /home/okishinya/chipatlas/results/dm3/SRX4315040/SRR7444501.sra Written 9215339 spots for /home/okishinya/chipatlas/results/dm3/SRX4315040/SRR7444501.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: 00:03:54 9215339 reads; of these: 9215339 (100.00%) were unpaired; of these: 2405 (0.03%) aligned 0 times 7825572 (84.92%) aligned exactly 1 time 1387362 (15.05%) aligned >1 times 99.97% overall alignment rate Time searching: 00:03:54 Overall time: 00:03:54 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] 5270017 / 9212934 = 0.5720 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 14:14:24: # Command line: callpeak -t SRX4315040.bam -f BAM -g dm -n SRX4315040.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4315040.10 # format = BAM # ChIP-seq file = ['SRX4315040.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 14:14:24: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:14:24: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:14:24: # Command line: callpeak -t SRX4315040.bam -f BAM -g dm -n SRX4315040.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4315040.05 # format = BAM # ChIP-seq file = ['SRX4315040.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 14:14:24: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:14:24: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:14:24: # Command line: callpeak -t SRX4315040.bam -f BAM -g dm -n SRX4315040.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4315040.20 # format = BAM # ChIP-seq file = ['SRX4315040.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 14:14:24: #1 read tag files... INFO @ Sat, 08 Sep 2018 14:14:24: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 14:14:32: 1000000 INFO @ Sat, 08 Sep 2018 14:14:32: 1000000 INFO @ Sat, 08 Sep 2018 14:14:32: 1000000 INFO @ Sat, 08 Sep 2018 14:14:39: 2000000 INFO @ Sat, 08 Sep 2018 14:14:40: 2000000 INFO @ Sat, 08 Sep 2018 14:14:40: 2000000 INFO @ Sat, 08 Sep 2018 14:14:47: 3000000 INFO @ Sat, 08 Sep 2018 14:14:47: 3000000 INFO @ Sat, 08 Sep 2018 14:14:47: 3000000 INFO @ Sat, 08 Sep 2018 14:14:54: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:14:54: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:14:54: #1 total tags in treatment: 3942917 INFO @ Sat, 08 Sep 2018 14:14:54: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:14:54: #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 14:14:54: #1 tags after filtering in treatment: 3942917 INFO @ Sat, 08 Sep 2018 14:14:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:14:54: #1 finished! INFO @ Sat, 08 Sep 2018 14:14:54: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:14:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:14:54: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:14:54: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:14:54: #1 total tags in treatment: 3942917 INFO @ Sat, 08 Sep 2018 14:14:54: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:14:54: #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 14:14:54: #2 number of paired peaks: 804 WARNING @ Sat, 08 Sep 2018 14:14:54: Fewer paired peaks (804) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 804 pairs to build model! INFO @ Sat, 08 Sep 2018 14:14:54: start model_add_line... INFO @ Sat, 08 Sep 2018 14:14:54: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 14:14:54: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 14:14:54: #1 total tags in treatment: 3942917 INFO @ Sat, 08 Sep 2018 14:14:54: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 14:14:54: #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 14:14:54: #1 tags after filtering in treatment: 3942917 INFO @ Sat, 08 Sep 2018 14:14:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:14:54: #1 finished! INFO @ Sat, 08 Sep 2018 14:14:54: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:14:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:14:54: start X-correlation... INFO @ Sat, 08 Sep 2018 14:14:54: end of X-cor INFO @ Sat, 08 Sep 2018 14:14:54: #2 finished! INFO @ Sat, 08 Sep 2018 14:14:54: #2 predicted fragment length is 92 bps INFO @ Sat, 08 Sep 2018 14:14:54: #2 alternative fragment length(s) may be 92 bps INFO @ Sat, 08 Sep 2018 14:14:54: #2.2 Generate R script for model : SRX4315040.05_model.r WARNING @ Sat, 08 Sep 2018 14:14:54: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:14:54: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Sat, 08 Sep 2018 14:14:54: #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 14:14:54: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:14:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:14:54: #1 tags after filtering in treatment: 3942917 INFO @ Sat, 08 Sep 2018 14:14:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 14:14:54: #1 finished! INFO @ Sat, 08 Sep 2018 14:14:54: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 14:14:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 14:14:55: #2 number of paired peaks: 804 WARNING @ Sat, 08 Sep 2018 14:14:55: Fewer paired peaks (804) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 804 pairs to build model! INFO @ Sat, 08 Sep 2018 14:14:55: start model_add_line... INFO @ Sat, 08 Sep 2018 14:14:55: start X-correlation... INFO @ Sat, 08 Sep 2018 14:14:55: end of X-cor INFO @ Sat, 08 Sep 2018 14:14:55: #2 finished! INFO @ Sat, 08 Sep 2018 14:14:55: #2 predicted fragment length is 92 bps INFO @ Sat, 08 Sep 2018 14:14:55: #2 alternative fragment length(s) may be 92 bps INFO @ Sat, 08 Sep 2018 14:14:55: #2.2 Generate R script for model : SRX4315040.20_model.r INFO @ Sat, 08 Sep 2018 14:14:55: #2 number of paired peaks: 804 WARNING @ Sat, 08 Sep 2018 14:14:55: Fewer paired peaks (804) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 804 pairs to build model! INFO @ Sat, 08 Sep 2018 14:14:55: start model_add_line... WARNING @ Sat, 08 Sep 2018 14:14:55: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:14:55: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Sat, 08 Sep 2018 14:14:55: #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 14:14:55: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:14:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:14:55: start X-correlation... INFO @ Sat, 08 Sep 2018 14:14:55: end of X-cor INFO @ Sat, 08 Sep 2018 14:14:55: #2 finished! INFO @ Sat, 08 Sep 2018 14:14:55: #2 predicted fragment length is 92 bps INFO @ Sat, 08 Sep 2018 14:14:55: #2 alternative fragment length(s) may be 92 bps INFO @ Sat, 08 Sep 2018 14:14:55: #2.2 Generate R script for model : SRX4315040.10_model.r WARNING @ Sat, 08 Sep 2018 14:14:55: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 14:14:55: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Sat, 08 Sep 2018 14:14:55: #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 14:14:55: #3 Call peaks... INFO @ Sat, 08 Sep 2018 14:14:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 14:15:04: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:15:04: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:15:05: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 14:15:09: #4 Write output xls file... SRX4315040.05_peaks.xls INFO @ Sat, 08 Sep 2018 14:15:09: #4 Write peak in narrowPeak format file... SRX4315040.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:15:09: #4 Write summits bed file... SRX4315040.05_summits.bed INFO @ Sat, 08 Sep 2018 14:15:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2551 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:15:10: #4 Write output xls file... SRX4315040.10_peaks.xls INFO @ Sat, 08 Sep 2018 14:15:10: #4 Write peak in narrowPeak format file... SRX4315040.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:15:10: #4 Write summits bed file... SRX4315040.10_summits.bed INFO @ Sat, 08 Sep 2018 14:15:10: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1126 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 14:15:10: #4 Write output xls file... SRX4315040.20_peaks.xls INFO @ Sat, 08 Sep 2018 14:15:10: #4 Write peak in narrowPeak format file... SRX4315040.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 14:15:10: #4 Write summits bed file... SRX4315040.20_summits.bed INFO @ Sat, 08 Sep 2018 14:15:10: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (489 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。