Job ID = 10714398 sra ファイルのダウンロード中... Completed: 154409K bytes transferred in 6 seconds (183733K 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 14511367 spots for /home/okishinya/chipatlas/results/ce10/SRX4082358/SRR7164176.sra Written 14511367 spots for /home/okishinya/chipatlas/results/ce10/SRX4082358/SRR7164176.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: 00:01:38 14511367 reads; of these: 14511367 (100.00%) were unpaired; of these: 5469833 (37.69%) aligned 0 times 8054108 (55.50%) aligned exactly 1 time 987426 (6.80%) aligned >1 times 62.31% overall alignment rate Time searching: 00:01:38 Overall time: 00:01:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1705289 / 9041534 = 0.1886 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, 03 Jun 2018 12:32:24: # Command line: callpeak -t SRX4082358.bam -f BAM -g ce -n SRX4082358.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082358.10 # format = BAM # ChIP-seq file = ['SRX4082358.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 03 Jun 2018 12:32:24: # Command line: callpeak -t SRX4082358.bam -f BAM -g ce -n SRX4082358.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082358.05 # format = BAM # ChIP-seq file = ['SRX4082358.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 03 Jun 2018 12:32:24: # Command line: callpeak -t SRX4082358.bam -f BAM -g ce -n SRX4082358.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082358.20 # format = BAM # ChIP-seq file = ['SRX4082358.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 03 Jun 2018 12:32:24: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:32:24: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:32:24: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:32:24: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:32:24: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:32:24: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:32:30: 1000000 INFO @ Sun, 03 Jun 2018 12:32:31: 1000000 INFO @ Sun, 03 Jun 2018 12:32:31: 1000000 INFO @ Sun, 03 Jun 2018 12:32:37: 2000000 INFO @ Sun, 03 Jun 2018 12:32:38: 2000000 INFO @ Sun, 03 Jun 2018 12:32:39: 2000000 INFO @ Sun, 03 Jun 2018 12:32:44: 3000000 INFO @ Sun, 03 Jun 2018 12:32:45: 3000000 INFO @ Sun, 03 Jun 2018 12:32:46: 3000000 INFO @ Sun, 03 Jun 2018 12:32:51: 4000000 INFO @ Sun, 03 Jun 2018 12:32:52: 4000000 INFO @ Sun, 03 Jun 2018 12:32:54: 4000000 INFO @ Sun, 03 Jun 2018 12:32:58: 5000000 INFO @ Sun, 03 Jun 2018 12:32:59: 5000000 INFO @ Sun, 03 Jun 2018 12:33:01: 5000000 INFO @ Sun, 03 Jun 2018 12:33:05: 6000000 INFO @ Sun, 03 Jun 2018 12:33:05: 6000000 INFO @ Sun, 03 Jun 2018 12:33:08: 6000000 INFO @ Sun, 03 Jun 2018 12:33:12: 7000000 INFO @ Sun, 03 Jun 2018 12:33:12: 7000000 INFO @ Sun, 03 Jun 2018 12:33:14: #1 tag size is determined as 32 bps INFO @ Sun, 03 Jun 2018 12:33:14: #1 tag size = 32 INFO @ Sun, 03 Jun 2018 12:33:14: #1 total tags in treatment: 7336245 INFO @ Sun, 03 Jun 2018 12:33:14: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:33:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:33:14: #1 tags after filtering in treatment: 7336245 INFO @ Sun, 03 Jun 2018 12:33:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:33:14: #1 finished! INFO @ Sun, 03 Jun 2018 12:33:14: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:33:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:33:14: #1 tag size is determined as 32 bps INFO @ Sun, 03 Jun 2018 12:33:14: #1 tag size = 32 INFO @ Sun, 03 Jun 2018 12:33:14: #1 total tags in treatment: 7336245 INFO @ Sun, 03 Jun 2018 12:33:14: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:33:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:33:14: #1 tags after filtering in treatment: 7336245 INFO @ Sun, 03 Jun 2018 12:33:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:33:14: #1 finished! INFO @ Sun, 03 Jun 2018 12:33:14: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:33:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:33:15: #2 number of paired peaks: 3080 INFO @ Sun, 03 Jun 2018 12:33:15: start model_add_line... INFO @ Sun, 03 Jun 2018 12:33:15: start X-correlation... INFO @ Sun, 03 Jun 2018 12:33:15: #2 number of paired peaks: 3080 INFO @ Sun, 03 Jun 2018 12:33:15: start model_add_line... INFO @ Sun, 03 Jun 2018 12:33:15: end of X-cor INFO @ Sun, 03 Jun 2018 12:33:15: #2 finished! INFO @ Sun, 03 Jun 2018 12:33:15: #2 predicted fragment length is 185 bps INFO @ Sun, 03 Jun 2018 12:33:15: #2 alternative fragment length(s) may be 3,185 bps INFO @ Sun, 03 Jun 2018 12:33:15: #2.2 Generate R script for model : SRX4082358.20_model.r INFO @ Sun, 03 Jun 2018 12:33:15: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:33:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:33:15: start X-correlation... INFO @ Sun, 03 Jun 2018 12:33:15: end of X-cor INFO @ Sun, 03 Jun 2018 12:33:15: #2 finished! INFO @ Sun, 03 Jun 2018 12:33:15: #2 predicted fragment length is 185 bps INFO @ Sun, 03 Jun 2018 12:33:15: #2 alternative fragment length(s) may be 3,185 bps INFO @ Sun, 03 Jun 2018 12:33:15: #2.2 Generate R script for model : SRX4082358.10_model.r INFO @ Sun, 03 Jun 2018 12:33:15: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:33:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:33:15: 7000000 INFO @ Sun, 03 Jun 2018 12:33:18: #1 tag size is determined as 32 bps INFO @ Sun, 03 Jun 2018 12:33:18: #1 tag size = 32 INFO @ Sun, 03 Jun 2018 12:33:18: #1 total tags in treatment: 7336245 INFO @ Sun, 03 Jun 2018 12:33:18: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:33:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:33:18: #1 tags after filtering in treatment: 7336245 INFO @ Sun, 03 Jun 2018 12:33:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:33:18: #1 finished! INFO @ Sun, 03 Jun 2018 12:33:18: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:33:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:33:19: #2 number of paired peaks: 3080 INFO @ Sun, 03 Jun 2018 12:33:19: start model_add_line... INFO @ Sun, 03 Jun 2018 12:33:19: start X-correlation... INFO @ Sun, 03 Jun 2018 12:33:19: end of X-cor INFO @ Sun, 03 Jun 2018 12:33:19: #2 finished! INFO @ Sun, 03 Jun 2018 12:33:19: #2 predicted fragment length is 185 bps INFO @ Sun, 03 Jun 2018 12:33:19: #2 alternative fragment length(s) may be 3,185 bps INFO @ Sun, 03 Jun 2018 12:33:19: #2.2 Generate R script for model : SRX4082358.05_model.r INFO @ Sun, 03 Jun 2018 12:33:19: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:33:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:33:34: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:33:35: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:33:39: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:33:45: #4 Write output xls file... SRX4082358.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:33:45: #4 Write peak in narrowPeak format file... SRX4082358.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:33:45: #4 Write summits bed file... SRX4082358.10_summits.bed INFO @ Sun, 03 Jun 2018 12:33:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3283 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:33:45: #4 Write output xls file... SRX4082358.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:33:45: #4 Write peak in narrowPeak format file... SRX4082358.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:33:45: #4 Write summits bed file... SRX4082358.20_summits.bed INFO @ Sun, 03 Jun 2018 12:33:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (901 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:33:49: #4 Write output xls file... SRX4082358.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:33:49: #4 Write peak in narrowPeak format file... SRX4082358.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:33:49: #4 Write summits bed file... SRX4082358.05_summits.bed INFO @ Sun, 03 Jun 2018 12:33:49: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6365 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。