Job ID = 11240728 sra ファイルのダウンロード中... Completed: 339540K bytes transferred in 13 seconds (201035K 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 10429706 spots for /home/okishinya/chipatlas/results/dm3/SRX4639147/SRR7784128.sra Written 10429706 spots for /home/okishinya/chipatlas/results/dm3/SRX4639147/SRR7784128.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: 00:02:38 10429706 reads; of these: 10429706 (100.00%) were unpaired; of these: 4564478 (43.76%) aligned 0 times 4442521 (42.59%) aligned exactly 1 time 1422707 (13.64%) aligned >1 times 56.24% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 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] 863224 / 5865228 = 0.1472 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, 07 Oct 2018 20:33:14: # Command line: callpeak -t SRX4639147.bam -f BAM -g dm -n SRX4639147.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4639147.10 # format = BAM # ChIP-seq file = ['SRX4639147.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, 07 Oct 2018 20:33:14: # Command line: callpeak -t SRX4639147.bam -f BAM -g dm -n SRX4639147.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4639147.05 # format = BAM # ChIP-seq file = ['SRX4639147.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, 07 Oct 2018 20:33:14: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:33:14: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:33:14: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:33:14: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:33:14: # Command line: callpeak -t SRX4639147.bam -f BAM -g dm -n SRX4639147.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4639147.20 # format = BAM # ChIP-seq file = ['SRX4639147.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, 07 Oct 2018 20:33:14: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:33:14: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:33:21: 1000000 INFO @ Sun, 07 Oct 2018 20:33:21: 1000000 INFO @ Sun, 07 Oct 2018 20:33:21: 1000000 INFO @ Sun, 07 Oct 2018 20:33:27: 2000000 INFO @ Sun, 07 Oct 2018 20:33:28: 2000000 INFO @ Sun, 07 Oct 2018 20:33:28: 2000000 INFO @ Sun, 07 Oct 2018 20:33:34: 3000000 INFO @ Sun, 07 Oct 2018 20:33:34: 3000000 INFO @ Sun, 07 Oct 2018 20:33:35: 3000000 INFO @ Sun, 07 Oct 2018 20:33:41: 4000000 INFO @ Sun, 07 Oct 2018 20:33:41: 4000000 INFO @ Sun, 07 Oct 2018 20:33:41: 4000000 INFO @ Sun, 07 Oct 2018 20:33:47: 5000000 INFO @ Sun, 07 Oct 2018 20:33:47: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:33:47: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:33:47: #1 total tags in treatment: 5002004 INFO @ Sun, 07 Oct 2018 20:33:47: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:33:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:33:47: #1 tags after filtering in treatment: 5002004 INFO @ Sun, 07 Oct 2018 20:33:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:33:47: #1 finished! INFO @ Sun, 07 Oct 2018 20:33:47: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:33:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:33:48: #2 number of paired peaks: 582 WARNING @ Sun, 07 Oct 2018 20:33:48: Fewer paired peaks (582) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 582 pairs to build model! INFO @ Sun, 07 Oct 2018 20:33:48: start model_add_line... INFO @ Sun, 07 Oct 2018 20:33:48: start X-correlation... INFO @ Sun, 07 Oct 2018 20:33:48: 5000000 INFO @ Sun, 07 Oct 2018 20:33:48: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:33:48: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:33:48: #1 total tags in treatment: 5002004 INFO @ Sun, 07 Oct 2018 20:33:48: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:33:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:33:48: #1 tags after filtering in treatment: 5002004 INFO @ Sun, 07 Oct 2018 20:33:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:33:48: #1 finished! INFO @ Sun, 07 Oct 2018 20:33:48: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:33:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:33:48: end of X-cor INFO @ Sun, 07 Oct 2018 20:33:48: #2 finished! INFO @ Sun, 07 Oct 2018 20:33:48: #2 predicted fragment length is 205 bps INFO @ Sun, 07 Oct 2018 20:33:48: #2 alternative fragment length(s) may be 205 bps INFO @ Sun, 07 Oct 2018 20:33:48: #2.2 Generate R script for model : SRX4639147.10_model.r INFO @ Sun, 07 Oct 2018 20:33:48: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:33:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:33:48: 5000000 INFO @ Sun, 07 Oct 2018 20:33:48: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:33:48: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:33:48: #1 total tags in treatment: 5002004 INFO @ Sun, 07 Oct 2018 20:33:48: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:33:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:33:48: #1 tags after filtering in treatment: 5002004 INFO @ Sun, 07 Oct 2018 20:33:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:33:48: #1 finished! INFO @ Sun, 07 Oct 2018 20:33:48: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:33:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:33:48: #2 number of paired peaks: 582 WARNING @ Sun, 07 Oct 2018 20:33:48: Fewer paired peaks (582) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 582 pairs to build model! INFO @ Sun, 07 Oct 2018 20:33:48: start model_add_line... INFO @ Sun, 07 Oct 2018 20:33:48: start X-correlation... INFO @ Sun, 07 Oct 2018 20:33:48: end of X-cor INFO @ Sun, 07 Oct 2018 20:33:48: #2 finished! INFO @ Sun, 07 Oct 2018 20:33:48: #2 predicted fragment length is 205 bps INFO @ Sun, 07 Oct 2018 20:33:48: #2 alternative fragment length(s) may be 205 bps INFO @ Sun, 07 Oct 2018 20:33:48: #2.2 Generate R script for model : SRX4639147.05_model.r INFO @ Sun, 07 Oct 2018 20:33:48: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:33:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:33:49: #2 number of paired peaks: 582 WARNING @ Sun, 07 Oct 2018 20:33:49: Fewer paired peaks (582) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 582 pairs to build model! INFO @ Sun, 07 Oct 2018 20:33:49: start model_add_line... INFO @ Sun, 07 Oct 2018 20:33:49: start X-correlation... INFO @ Sun, 07 Oct 2018 20:33:49: end of X-cor INFO @ Sun, 07 Oct 2018 20:33:49: #2 finished! INFO @ Sun, 07 Oct 2018 20:33:49: #2 predicted fragment length is 205 bps INFO @ Sun, 07 Oct 2018 20:33:49: #2 alternative fragment length(s) may be 205 bps INFO @ Sun, 07 Oct 2018 20:33:49: #2.2 Generate R script for model : SRX4639147.20_model.r INFO @ Sun, 07 Oct 2018 20:33:49: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:33:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:34:00: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:34:01: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:34:01: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:34:06: #4 Write output xls file... SRX4639147.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:34:06: #4 Write peak in narrowPeak format file... SRX4639147.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:34:07: #4 Write summits bed file... SRX4639147.20_summits.bed INFO @ Sun, 07 Oct 2018 20:34:07: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (692 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:34:08: #4 Write output xls file... SRX4639147.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:34:08: #4 Write peak in narrowPeak format file... SRX4639147.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:34:08: #4 Write summits bed file... SRX4639147.10_summits.bed INFO @ Sun, 07 Oct 2018 20:34:08: Done! INFO @ Sun, 07 Oct 2018 20:34:08: #4 Write output xls file... SRX4639147.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:34:08: #4 Write peak in narrowPeak format file... SRX4639147.05_peaks.narrowPeak pass1 - making usageList (13 chroms): 1 millis INFO @ Sun, 07 Oct 2018 20:34:08: #4 Write summits bed file... SRX4639147.05_summits.bed INFO @ Sun, 07 Oct 2018 20:34:08: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2574 records, 4 fields): 6 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (1406 records, 4 fields): 457 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。