Job ID = 11597961 sra ファイルのダウンロード中... Completed: 652195K bytes transferred in 11 seconds (467171K 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 40590256 spots for /home/okishinya/chipatlas/results/dm3/SRX3049401/SRR5883312.sra Written 40590256 spots for /home/okishinya/chipatlas/results/dm3/SRX3049401/SRR5883312.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: 00:05:25 40590256 reads; of these: 40590256 (100.00%) were unpaired; of these: 37132660 (91.48%) aligned 0 times 2566087 (6.32%) aligned exactly 1 time 891509 (2.20%) aligned >1 times 8.52% overall alignment rate Time searching: 00:05:25 Overall time: 00:05:25 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] 1426791 / 3457596 = 0.4127 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 @ Wed, 30 Jan 2019 16:37:07: # Command line: callpeak -t SRX3049401.bam -f BAM -g dm -n SRX3049401.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3049401.05 # format = BAM # ChIP-seq file = ['SRX3049401.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 @ Wed, 30 Jan 2019 16:37:07: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:37:07: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:37:07: # Command line: callpeak -t SRX3049401.bam -f BAM -g dm -n SRX3049401.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3049401.10 # format = BAM # ChIP-seq file = ['SRX3049401.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 @ Wed, 30 Jan 2019 16:37:07: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:37:07: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:37:07: # Command line: callpeak -t SRX3049401.bam -f BAM -g dm -n SRX3049401.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3049401.20 # format = BAM # ChIP-seq file = ['SRX3049401.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 @ Wed, 30 Jan 2019 16:37:07: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:37:07: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:37:13: 1000000 INFO @ Wed, 30 Jan 2019 16:37:14: 1000000 INFO @ Wed, 30 Jan 2019 16:37:14: 1000000 INFO @ Wed, 30 Jan 2019 16:37:19: 2000000 INFO @ Wed, 30 Jan 2019 16:37:19: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:37:19: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:37:19: #1 total tags in treatment: 2030805 INFO @ Wed, 30 Jan 2019 16:37:19: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:37:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:37:19: #1 tags after filtering in treatment: 2030805 INFO @ Wed, 30 Jan 2019 16:37:19: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:37:19: #1 finished! INFO @ Wed, 30 Jan 2019 16:37:19: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:37:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:37:20: #2 number of paired peaks: 1358 INFO @ Wed, 30 Jan 2019 16:37:20: start model_add_line... INFO @ Wed, 30 Jan 2019 16:37:20: start X-correlation... INFO @ Wed, 30 Jan 2019 16:37:20: end of X-cor INFO @ Wed, 30 Jan 2019 16:37:20: #2 finished! INFO @ Wed, 30 Jan 2019 16:37:20: #2 predicted fragment length is 115 bps INFO @ Wed, 30 Jan 2019 16:37:20: #2 alternative fragment length(s) may be 115 bps INFO @ Wed, 30 Jan 2019 16:37:20: #2.2 Generate R script for model : SRX3049401.05_model.r INFO @ Wed, 30 Jan 2019 16:37:20: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:37:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:37:20: 2000000 INFO @ Wed, 30 Jan 2019 16:37:20: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:37:20: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:37:20: #1 total tags in treatment: 2030805 INFO @ Wed, 30 Jan 2019 16:37:20: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:37:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:37:20: #1 tags after filtering in treatment: 2030805 INFO @ Wed, 30 Jan 2019 16:37:20: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:37:20: #1 finished! INFO @ Wed, 30 Jan 2019 16:37:20: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:37:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:37:20: #2 number of paired peaks: 1358 INFO @ Wed, 30 Jan 2019 16:37:20: start model_add_line... INFO @ Wed, 30 Jan 2019 16:37:20: start X-correlation... INFO @ Wed, 30 Jan 2019 16:37:20: end of X-cor INFO @ Wed, 30 Jan 2019 16:37:20: #2 finished! INFO @ Wed, 30 Jan 2019 16:37:20: #2 predicted fragment length is 115 bps INFO @ Wed, 30 Jan 2019 16:37:20: #2 alternative fragment length(s) may be 115 bps INFO @ Wed, 30 Jan 2019 16:37:20: #2.2 Generate R script for model : SRX3049401.20_model.r INFO @ Wed, 30 Jan 2019 16:37:20: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:37:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:37:21: 2000000 INFO @ Wed, 30 Jan 2019 16:37:21: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:37:21: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:37:21: #1 total tags in treatment: 2030805 INFO @ Wed, 30 Jan 2019 16:37:21: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:37:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:37:21: #1 tags after filtering in treatment: 2030805 INFO @ Wed, 30 Jan 2019 16:37:21: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:37:21: #1 finished! INFO @ Wed, 30 Jan 2019 16:37:21: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:37:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:37:21: #2 number of paired peaks: 1358 INFO @ Wed, 30 Jan 2019 16:37:21: start model_add_line... INFO @ Wed, 30 Jan 2019 16:37:21: start X-correlation... INFO @ Wed, 30 Jan 2019 16:37:21: end of X-cor INFO @ Wed, 30 Jan 2019 16:37:21: #2 finished! INFO @ Wed, 30 Jan 2019 16:37:21: #2 predicted fragment length is 115 bps INFO @ Wed, 30 Jan 2019 16:37:21: #2 alternative fragment length(s) may be 115 bps INFO @ Wed, 30 Jan 2019 16:37:21: #2.2 Generate R script for model : SRX3049401.10_model.r INFO @ Wed, 30 Jan 2019 16:37:21: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:37:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:37:25: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:37:25: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:37:26: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:37:27: #4 Write output xls file... SRX3049401.05_peaks.xls INFO @ Wed, 30 Jan 2019 16:37:27: #4 Write peak in narrowPeak format file... SRX3049401.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:37:27: #4 Write summits bed file... SRX3049401.05_summits.bed INFO @ Wed, 30 Jan 2019 16:37:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2253 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 16:37:28: #4 Write output xls file... SRX3049401.20_peaks.xls INFO @ Wed, 30 Jan 2019 16:37:28: #4 Write peak in narrowPeak format file... SRX3049401.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:37:28: #4 Write summits bed file... SRX3049401.20_summits.bed INFO @ Wed, 30 Jan 2019 16:37:28: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (583 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 16:37:29: #4 Write output xls file... SRX3049401.10_peaks.xls INFO @ Wed, 30 Jan 2019 16:37:29: #4 Write peak in narrowPeak format file... SRX3049401.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:37:29: #4 Write summits bed file... SRX3049401.10_summits.bed INFO @ Wed, 30 Jan 2019 16:37:29: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1363 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。