Job ID = 10714575 sra ファイルのダウンロード中... Completed: 76156K bytes transferred in 3 seconds (169673K 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 4782793 spots for /home/okishinya/chipatlas/results/dm3/SRX4053329/SRR7132384.sra Written 4782793 spots for /home/okishinya/chipatlas/results/dm3/SRX4053329/SRR7132384.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: 00:01:32 4782793 reads; of these: 4782793 (100.00%) were unpaired; of these: 638358 (13.35%) aligned 0 times 3341598 (69.87%) aligned exactly 1 time 802837 (16.79%) aligned >1 times 86.65% overall alignment rate Time searching: 00:01:32 Overall time: 00:01:32 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] 663833 / 4144435 = 0.1602 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 13:33:27: # Command line: callpeak -t SRX4053329.bam -f BAM -g dm -n SRX4053329.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4053329.20 # format = BAM # ChIP-seq file = ['SRX4053329.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, 03 Jun 2018 13:33:27: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:33:27: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:33:27: # Command line: callpeak -t SRX4053329.bam -f BAM -g dm -n SRX4053329.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4053329.05 # format = BAM # ChIP-seq file = ['SRX4053329.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, 03 Jun 2018 13:33:27: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:33:27: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:33:27: # Command line: callpeak -t SRX4053329.bam -f BAM -g dm -n SRX4053329.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4053329.10 # format = BAM # ChIP-seq file = ['SRX4053329.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, 03 Jun 2018 13:33:27: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:33:27: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:33:33: 1000000 INFO @ Sun, 03 Jun 2018 13:33:33: 1000000 INFO @ Sun, 03 Jun 2018 13:33:33: 1000000 INFO @ Sun, 03 Jun 2018 13:33:39: 2000000 INFO @ Sun, 03 Jun 2018 13:33:39: 2000000 INFO @ Sun, 03 Jun 2018 13:33:39: 2000000 INFO @ Sun, 03 Jun 2018 13:33:45: 3000000 INFO @ Sun, 03 Jun 2018 13:33:45: 3000000 INFO @ Sun, 03 Jun 2018 13:33:45: 3000000 INFO @ Sun, 03 Jun 2018 13:33:48: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:33:48: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:33:48: #1 total tags in treatment: 3480602 INFO @ Sun, 03 Jun 2018 13:33:48: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:33:48: #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 13:33:48: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:33:48: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:33:48: #1 total tags in treatment: 3480602 INFO @ Sun, 03 Jun 2018 13:33:48: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:33:48: #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 13:33:48: #1 tags after filtering in treatment: 3480602 INFO @ Sun, 03 Jun 2018 13:33:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:33:48: #1 finished! INFO @ Sun, 03 Jun 2018 13:33:48: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:33:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:33:48: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:33:48: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:33:48: #1 total tags in treatment: 3480602 INFO @ Sun, 03 Jun 2018 13:33:48: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:33:48: #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 13:33:48: #1 tags after filtering in treatment: 3480602 INFO @ Sun, 03 Jun 2018 13:33:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:33:48: #1 finished! INFO @ Sun, 03 Jun 2018 13:33:48: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:33:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:33:48: #1 tags after filtering in treatment: 3480602 INFO @ Sun, 03 Jun 2018 13:33:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:33:48: #1 finished! INFO @ Sun, 03 Jun 2018 13:33:48: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:33:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:33:48: #2 number of paired peaks: 6268 INFO @ Sun, 03 Jun 2018 13:33:48: start model_add_line... INFO @ Sun, 03 Jun 2018 13:33:49: #2 number of paired peaks: 6268 INFO @ Sun, 03 Jun 2018 13:33:49: start model_add_line... INFO @ Sun, 03 Jun 2018 13:33:49: #2 number of paired peaks: 6268 INFO @ Sun, 03 Jun 2018 13:33:49: start model_add_line... INFO @ Sun, 03 Jun 2018 13:33:49: start X-correlation... INFO @ Sun, 03 Jun 2018 13:33:49: end of X-cor INFO @ Sun, 03 Jun 2018 13:33:49: #2 finished! INFO @ Sun, 03 Jun 2018 13:33:49: #2 predicted fragment length is 261 bps INFO @ Sun, 03 Jun 2018 13:33:49: #2 alternative fragment length(s) may be 4,261 bps INFO @ Sun, 03 Jun 2018 13:33:49: #2.2 Generate R script for model : SRX4053329.20_model.r INFO @ Sun, 03 Jun 2018 13:33:49: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:33:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:33:49: start X-correlation... INFO @ Sun, 03 Jun 2018 13:33:49: end of X-cor INFO @ Sun, 03 Jun 2018 13:33:49: #2 finished! INFO @ Sun, 03 Jun 2018 13:33:49: #2 predicted fragment length is 261 bps INFO @ Sun, 03 Jun 2018 13:33:49: #2 alternative fragment length(s) may be 4,261 bps INFO @ Sun, 03 Jun 2018 13:33:49: #2.2 Generate R script for model : SRX4053329.10_model.r INFO @ Sun, 03 Jun 2018 13:33:49: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:33:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:33:49: start X-correlation... INFO @ Sun, 03 Jun 2018 13:33:49: end of X-cor INFO @ Sun, 03 Jun 2018 13:33:49: #2 finished! INFO @ Sun, 03 Jun 2018 13:33:49: #2 predicted fragment length is 261 bps INFO @ Sun, 03 Jun 2018 13:33:49: #2 alternative fragment length(s) may be 4,261 bps INFO @ Sun, 03 Jun 2018 13:33:49: #2.2 Generate R script for model : SRX4053329.05_model.r INFO @ Sun, 03 Jun 2018 13:33:49: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:33:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:34:00: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:34:01: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:34:01: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:34:05: #4 Write output xls file... SRX4053329.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:34:05: #4 Write peak in narrowPeak format file... SRX4053329.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:34:05: #4 Write summits bed file... SRX4053329.05_summits.bed INFO @ Sun, 03 Jun 2018 13:34:05: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (968 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:34:05: #4 Write output xls file... SRX4053329.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:34:05: #4 Write peak in narrowPeak format file... SRX4053329.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:34:05: #4 Write summits bed file... SRX4053329.10_summits.bed INFO @ Sun, 03 Jun 2018 13:34:05: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (452 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:34:05: #4 Write output xls file... SRX4053329.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:34:05: #4 Write peak in narrowPeak format file... SRX4053329.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:34:05: #4 Write summits bed file... SRX4053329.20_summits.bed INFO @ Sun, 03 Jun 2018 13:34:05: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (181 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。