Job ID = 11240729 sra ファイルのダウンロード中... Completed: 332190K bytes transferred in 14 seconds (190890K 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 9407890 spots for /home/okishinya/chipatlas/results/dm3/SRX4639148/SRR7784129.sra Written 9407890 spots for /home/okishinya/chipatlas/results/dm3/SRX4639148/SRR7784129.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:23 9407890 reads; of these: 9407890 (100.00%) were unpaired; of these: 1170381 (12.44%) aligned 0 times 5911161 (62.83%) aligned exactly 1 time 2326348 (24.73%) aligned >1 times 87.56% overall alignment rate Time searching: 00:03:24 Overall time: 00:03:24 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] 1322665 / 8237509 = 0.1606 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 20:34:37: # Command line: callpeak -t SRX4639148.bam -f BAM -g dm -n SRX4639148.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4639148.20 # format = BAM # ChIP-seq file = ['SRX4639148.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 20:34:37: # Command line: callpeak -t SRX4639148.bam -f BAM -g dm -n SRX4639148.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4639148.10 # format = BAM # ChIP-seq file = ['SRX4639148.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 20:34:37: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:34:37: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:34:37: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:34:37: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:34:37: # Command line: callpeak -t SRX4639148.bam -f BAM -g dm -n SRX4639148.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4639148.05 # format = BAM # ChIP-seq file = ['SRX4639148.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 20:34:37: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:34:37: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:34:44: 1000000 INFO @ Sun, 07 Oct 2018 20:34:44: 1000000 INFO @ Sun, 07 Oct 2018 20:34:44: 1000000 INFO @ Sun, 07 Oct 2018 20:34:50: 2000000 INFO @ Sun, 07 Oct 2018 20:34:51: 2000000 INFO @ Sun, 07 Oct 2018 20:34:51: 2000000 INFO @ Sun, 07 Oct 2018 20:34:57: 3000000 INFO @ Sun, 07 Oct 2018 20:34:57: 3000000 INFO @ Sun, 07 Oct 2018 20:34:58: 3000000 INFO @ Sun, 07 Oct 2018 20:35:04: 4000000 INFO @ Sun, 07 Oct 2018 20:35:04: 4000000 INFO @ Sun, 07 Oct 2018 20:35:05: 4000000 INFO @ Sun, 07 Oct 2018 20:35:11: 5000000 INFO @ Sun, 07 Oct 2018 20:35:12: 5000000 INFO @ Sun, 07 Oct 2018 20:35:12: 5000000 INFO @ Sun, 07 Oct 2018 20:35:18: 6000000 INFO @ Sun, 07 Oct 2018 20:35:18: 6000000 INFO @ Sun, 07 Oct 2018 20:35:19: 6000000 INFO @ Sun, 07 Oct 2018 20:35:24: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:35:24: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:35:24: #1 total tags in treatment: 6914844 INFO @ Sun, 07 Oct 2018 20:35:24: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:35:24: #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 20:35:25: #1 tags after filtering in treatment: 6914844 INFO @ Sun, 07 Oct 2018 20:35:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:35:25: #1 finished! INFO @ Sun, 07 Oct 2018 20:35:25: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:35:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:35:25: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:35:25: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:35:25: #1 total tags in treatment: 6914844 INFO @ Sun, 07 Oct 2018 20:35:25: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:35:25: #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 20:35:25: #1 tags after filtering in treatment: 6914844 INFO @ Sun, 07 Oct 2018 20:35:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:35:25: #1 finished! INFO @ Sun, 07 Oct 2018 20:35:25: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:35:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:35:25: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:35:25: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:35:25: #1 total tags in treatment: 6914844 INFO @ Sun, 07 Oct 2018 20:35:25: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:35:25: #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 20:35:25: #2 number of paired peaks: 219 WARNING @ Sun, 07 Oct 2018 20:35:25: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Sun, 07 Oct 2018 20:35:25: start model_add_line... INFO @ Sun, 07 Oct 2018 20:35:25: start X-correlation... INFO @ Sun, 07 Oct 2018 20:35:25: end of X-cor INFO @ Sun, 07 Oct 2018 20:35:25: #2 finished! INFO @ Sun, 07 Oct 2018 20:35:25: #2 predicted fragment length is 158 bps INFO @ Sun, 07 Oct 2018 20:35:25: #2 alternative fragment length(s) may be 158 bps INFO @ Sun, 07 Oct 2018 20:35:25: #2.2 Generate R script for model : SRX4639148.05_model.r INFO @ Sun, 07 Oct 2018 20:35:25: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:35:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:35:25: #1 tags after filtering in treatment: 6914844 INFO @ Sun, 07 Oct 2018 20:35:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:35:25: #1 finished! INFO @ Sun, 07 Oct 2018 20:35:25: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:35:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:35:26: #2 number of paired peaks: 219 WARNING @ Sun, 07 Oct 2018 20:35:26: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Sun, 07 Oct 2018 20:35:26: start model_add_line... INFO @ Sun, 07 Oct 2018 20:35:26: start X-correlation... INFO @ Sun, 07 Oct 2018 20:35:26: end of X-cor INFO @ Sun, 07 Oct 2018 20:35:26: #2 finished! INFO @ Sun, 07 Oct 2018 20:35:26: #2 predicted fragment length is 158 bps INFO @ Sun, 07 Oct 2018 20:35:26: #2 alternative fragment length(s) may be 158 bps INFO @ Sun, 07 Oct 2018 20:35:26: #2.2 Generate R script for model : SRX4639148.20_model.r INFO @ Sun, 07 Oct 2018 20:35:26: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:35:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:35:26: #2 number of paired peaks: 219 WARNING @ Sun, 07 Oct 2018 20:35:26: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Sun, 07 Oct 2018 20:35:26: start model_add_line... INFO @ Sun, 07 Oct 2018 20:35:26: start X-correlation... INFO @ Sun, 07 Oct 2018 20:35:26: end of X-cor INFO @ Sun, 07 Oct 2018 20:35:26: #2 finished! INFO @ Sun, 07 Oct 2018 20:35:26: #2 predicted fragment length is 158 bps INFO @ Sun, 07 Oct 2018 20:35:26: #2 alternative fragment length(s) may be 158 bps INFO @ Sun, 07 Oct 2018 20:35:26: #2.2 Generate R script for model : SRX4639148.10_model.r INFO @ Sun, 07 Oct 2018 20:35:26: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:35:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:35:40: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:35:41: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:35:41: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:35:49: #4 Write output xls file... SRX4639148.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:35:49: #4 Write peak in narrowPeak format file... SRX4639148.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:35:49: #4 Write summits bed file... SRX4639148.05_summits.bed INFO @ Sun, 07 Oct 2018 20:35:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1607 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:35:49: #4 Write output xls file... SRX4639148.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:35:49: #4 Write peak in narrowPeak format file... SRX4639148.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:35:49: #4 Write summits bed file... SRX4639148.10_summits.bed INFO @ Sun, 07 Oct 2018 20:35:50: Done! INFO @ Sun, 07 Oct 2018 20:35:50: #4 Write output xls file... SRX4639148.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:35:50: #4 Write peak in narrowPeak format file... SRX4639148.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:35:50: #4 Write summits bed file... SRX4639148.20_summits.bed pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (942 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:35:50: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (404 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。