Job ID = 10609100 sra ファイルのダウンロード中... Completed: 521318K bytes transferred in 67 seconds (63478K 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 16428120 spots for /home/okishinya/chipatlas/results/dm3/SRX3011238/SRR5834715.sra Written 16428120 spots for /home/okishinya/chipatlas/results/dm3/SRX3011238/SRR5834715.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: 00:05:38 16428120 reads; of these: 16428120 (100.00%) were unpaired; of these: 483869 (2.95%) aligned 0 times 13473325 (82.01%) aligned exactly 1 time 2470926 (15.04%) aligned >1 times 97.05% overall alignment rate Time searching: 00:05:38 Overall time: 00:05:38 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_sort_core] merging from 8 files... [bam_rmdupse_core] 8088962 / 15944251 = 0.5073 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 @ Fri, 04 May 2018 07:13:31: # Command line: callpeak -t SRX3011238.bam -f BAM -g dm -n SRX3011238.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3011238.05 # format = BAM # ChIP-seq file = ['SRX3011238.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 @ Fri, 04 May 2018 07:13:31: #1 read tag files... INFO @ Fri, 04 May 2018 07:13:31: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:13:31: # Command line: callpeak -t SRX3011238.bam -f BAM -g dm -n SRX3011238.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3011238.20 # format = BAM # ChIP-seq file = ['SRX3011238.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 @ Fri, 04 May 2018 07:13:31: #1 read tag files... INFO @ Fri, 04 May 2018 07:13:31: # Command line: callpeak -t SRX3011238.bam -f BAM -g dm -n SRX3011238.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3011238.10 # format = BAM # ChIP-seq file = ['SRX3011238.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 @ Fri, 04 May 2018 07:13:31: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:13:31: #1 read tag files... INFO @ Fri, 04 May 2018 07:13:31: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:13:39: 1000000 INFO @ Fri, 04 May 2018 07:13:40: 1000000 INFO @ Fri, 04 May 2018 07:13:40: 1000000 INFO @ Fri, 04 May 2018 07:13:46: 2000000 INFO @ Fri, 04 May 2018 07:13:48: 2000000 INFO @ Fri, 04 May 2018 07:13:48: 2000000 INFO @ Fri, 04 May 2018 07:13:54: 3000000 INFO @ Fri, 04 May 2018 07:13:57: 3000000 INFO @ Fri, 04 May 2018 07:13:57: 3000000 INFO @ Fri, 04 May 2018 07:14:02: 4000000 INFO @ Fri, 04 May 2018 07:14:06: 4000000 INFO @ Fri, 04 May 2018 07:14:06: 4000000 INFO @ Fri, 04 May 2018 07:14:09: 5000000 INFO @ Fri, 04 May 2018 07:14:15: 5000000 INFO @ Fri, 04 May 2018 07:14:15: 5000000 INFO @ Fri, 04 May 2018 07:14:17: 6000000 INFO @ Fri, 04 May 2018 07:14:24: 6000000 INFO @ Fri, 04 May 2018 07:14:24: 6000000 INFO @ Fri, 04 May 2018 07:14:25: 7000000 INFO @ Fri, 04 May 2018 07:14:32: #1 tag size is determined as 80 bps INFO @ Fri, 04 May 2018 07:14:32: #1 tag size = 80 INFO @ Fri, 04 May 2018 07:14:32: #1 total tags in treatment: 7855289 INFO @ Fri, 04 May 2018 07:14:32: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:14:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:14:32: #1 tags after filtering in treatment: 7855289 INFO @ Fri, 04 May 2018 07:14:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:14:32: #1 finished! INFO @ Fri, 04 May 2018 07:14:32: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:14:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:14:33: #2 number of paired peaks: 5201 INFO @ Fri, 04 May 2018 07:14:33: start model_add_line... INFO @ Fri, 04 May 2018 07:14:33: 7000000 INFO @ Fri, 04 May 2018 07:14:33: 7000000 INFO @ Fri, 04 May 2018 07:14:33: start X-correlation... INFO @ Fri, 04 May 2018 07:14:33: end of X-cor INFO @ Fri, 04 May 2018 07:14:33: #2 finished! INFO @ Fri, 04 May 2018 07:14:33: #2 predicted fragment length is 188 bps INFO @ Fri, 04 May 2018 07:14:33: #2 alternative fragment length(s) may be 188 bps INFO @ Fri, 04 May 2018 07:14:33: #2.2 Generate R script for model : SRX3011238.05_model.r INFO @ Fri, 04 May 2018 07:14:33: #3 Call peaks... INFO @ Fri, 04 May 2018 07:14:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:14:40: #1 tag size is determined as 80 bps INFO @ Fri, 04 May 2018 07:14:40: #1 tag size = 80 INFO @ Fri, 04 May 2018 07:14:40: #1 total tags in treatment: 7855289 INFO @ Fri, 04 May 2018 07:14:40: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:14:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:14:40: #1 tag size is determined as 80 bps INFO @ Fri, 04 May 2018 07:14:40: #1 tag size = 80 INFO @ Fri, 04 May 2018 07:14:40: #1 total tags in treatment: 7855289 INFO @ Fri, 04 May 2018 07:14:40: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:14:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:14:40: #1 tags after filtering in treatment: 7855289 INFO @ Fri, 04 May 2018 07:14:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:14:40: #1 finished! INFO @ Fri, 04 May 2018 07:14:40: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:14:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:14:40: #1 tags after filtering in treatment: 7855289 INFO @ Fri, 04 May 2018 07:14:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:14:40: #1 finished! INFO @ Fri, 04 May 2018 07:14:40: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:14:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:14:41: #2 number of paired peaks: 5201 INFO @ Fri, 04 May 2018 07:14:41: start model_add_line... INFO @ Fri, 04 May 2018 07:14:41: #2 number of paired peaks: 5201 INFO @ Fri, 04 May 2018 07:14:41: start model_add_line... INFO @ Fri, 04 May 2018 07:14:41: start X-correlation... INFO @ Fri, 04 May 2018 07:14:41: end of X-cor INFO @ Fri, 04 May 2018 07:14:41: #2 finished! INFO @ Fri, 04 May 2018 07:14:41: #2 predicted fragment length is 188 bps INFO @ Fri, 04 May 2018 07:14:41: #2 alternative fragment length(s) may be 188 bps INFO @ Fri, 04 May 2018 07:14:41: #2.2 Generate R script for model : SRX3011238.20_model.r INFO @ Fri, 04 May 2018 07:14:41: #3 Call peaks... INFO @ Fri, 04 May 2018 07:14:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:14:41: start X-correlation... INFO @ Fri, 04 May 2018 07:14:41: end of X-cor INFO @ Fri, 04 May 2018 07:14:41: #2 finished! INFO @ Fri, 04 May 2018 07:14:41: #2 predicted fragment length is 188 bps INFO @ Fri, 04 May 2018 07:14:41: #2 alternative fragment length(s) may be 188 bps INFO @ Fri, 04 May 2018 07:14:41: #2.2 Generate R script for model : SRX3011238.10_model.r INFO @ Fri, 04 May 2018 07:14:41: #3 Call peaks... INFO @ Fri, 04 May 2018 07:14:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:14:59: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:15:07: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:15:07: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:15:10: #4 Write output xls file... SRX3011238.05_peaks.xls INFO @ Fri, 04 May 2018 07:15:10: #4 Write peak in narrowPeak format file... SRX3011238.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:15:11: #4 Write summits bed file... SRX3011238.05_summits.bed INFO @ Fri, 04 May 2018 07:15:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9102 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:15:18: #4 Write output xls file... SRX3011238.20_peaks.xls INFO @ Fri, 04 May 2018 07:15:18: #4 Write peak in narrowPeak format file... SRX3011238.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:15:18: #4 Write output xls file... SRX3011238.10_peaks.xls INFO @ Fri, 04 May 2018 07:15:18: #4 Write summits bed file... SRX3011238.20_summits.bed INFO @ Fri, 04 May 2018 07:15:18: Done! INFO @ Fri, 04 May 2018 07:15:18: #4 Write peak in narrowPeak format file... SRX3011238.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:15:18: #4 Write summits bed file... SRX3011238.10_summits.bed INFO @ Fri, 04 May 2018 07:15:19: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5092 records, 4 fields): 8 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7035 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。