Job ID = 9371915 sra ファイルのダウンロード中... Completed: 708346K bytes transferred in 28 seconds (202584K bits/sec), in 1 file, 2 directories. 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... Written 29327337 spots for /home/okishinya/chipatlas/results/dm3/SRX2520639/SRR5206758.sra Written 29327337 spots total 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: 00:06:58 29327337 reads; of these: 29327337 (100.00%) were unpaired; of these: 16664731 (56.82%) aligned 0 times 9602686 (32.74%) aligned exactly 1 time 3059920 (10.43%) aligned >1 times 43.18% overall alignment rate Time searching: 00:06:58 Overall time: 00:06:58 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] 3556321 / 12662606 = 0.2809 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 Aug 2017 15:01:05: # Command line: callpeak -t SRX2520639.bam -f BAM -g dm -n SRX2520639.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2520639.05 # format = BAM # ChIP-seq file = ['SRX2520639.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 Aug 2017 15:01:05: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:01:05: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:01:05: # Command line: callpeak -t SRX2520639.bam -f BAM -g dm -n SRX2520639.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2520639.20 # format = BAM # ChIP-seq file = ['SRX2520639.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 Aug 2017 15:01:05: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:01:05: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:01:05: # Command line: callpeak -t SRX2520639.bam -f BAM -g dm -n SRX2520639.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2520639.10 # format = BAM # ChIP-seq file = ['SRX2520639.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 Aug 2017 15:01:05: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:01:05: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:01:12: 1000000 INFO @ Fri, 04 Aug 2017 15:01:13: 1000000 INFO @ Fri, 04 Aug 2017 15:01:13: 1000000 INFO @ Fri, 04 Aug 2017 15:01:19: 2000000 INFO @ Fri, 04 Aug 2017 15:01:21: 2000000 INFO @ Fri, 04 Aug 2017 15:01:21: 2000000 INFO @ Fri, 04 Aug 2017 15:01:27: 3000000 INFO @ Fri, 04 Aug 2017 15:01:29: 3000000 INFO @ Fri, 04 Aug 2017 15:01:29: 3000000 INFO @ Fri, 04 Aug 2017 15:01:34: 4000000 INFO @ Fri, 04 Aug 2017 15:01:37: 4000000 INFO @ Fri, 04 Aug 2017 15:01:37: 4000000 INFO @ Fri, 04 Aug 2017 15:01:41: 5000000 INFO @ Fri, 04 Aug 2017 15:01:45: 5000000 INFO @ Fri, 04 Aug 2017 15:01:45: 5000000 INFO @ Fri, 04 Aug 2017 15:01:49: 6000000 INFO @ Fri, 04 Aug 2017 15:01:53: 6000000 INFO @ Fri, 04 Aug 2017 15:01:53: 6000000 INFO @ Fri, 04 Aug 2017 15:01:56: 7000000 INFO @ Fri, 04 Aug 2017 15:02:00: 7000000 INFO @ Fri, 04 Aug 2017 15:02:00: 7000000 INFO @ Fri, 04 Aug 2017 15:02:03: 8000000 INFO @ Fri, 04 Aug 2017 15:02:08: 8000000 INFO @ Fri, 04 Aug 2017 15:02:08: 8000000 INFO @ Fri, 04 Aug 2017 15:02:10: 9000000 INFO @ Fri, 04 Aug 2017 15:02:11: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:02:11: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:02:11: #1 total tags in treatment: 9106285 INFO @ Fri, 04 Aug 2017 15:02:11: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:02:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 15:02:11: #1 tags after filtering in treatment: 9106285 INFO @ Fri, 04 Aug 2017 15:02:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:02:11: #1 finished! INFO @ Fri, 04 Aug 2017 15:02:11: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:02:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:02:12: #2 number of paired peaks: 1362 INFO @ Fri, 04 Aug 2017 15:02:12: start model_add_line... INFO @ Fri, 04 Aug 2017 15:02:12: start X-correlation... INFO @ Fri, 04 Aug 2017 15:02:12: end of X-cor INFO @ Fri, 04 Aug 2017 15:02:12: #2 finished! INFO @ Fri, 04 Aug 2017 15:02:12: #2 predicted fragment length is 154 bps INFO @ Fri, 04 Aug 2017 15:02:12: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 04 Aug 2017 15:02:12: #2.2 Generate R script for model : SRX2520639.20_model.r INFO @ Fri, 04 Aug 2017 15:02:12: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:02:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:02:16: 9000000 INFO @ Fri, 04 Aug 2017 15:02:16: 9000000 INFO @ Fri, 04 Aug 2017 15:02:17: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:02:17: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:02:17: #1 total tags in treatment: 9106285 INFO @ Fri, 04 Aug 2017 15:02:17: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:02:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 15:02:17: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:02:17: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:02:17: #1 total tags in treatment: 9106285 INFO @ Fri, 04 Aug 2017 15:02:17: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:02:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 15:02:17: #1 tags after filtering in treatment: 9106285 INFO @ Fri, 04 Aug 2017 15:02:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:02:17: #1 finished! INFO @ Fri, 04 Aug 2017 15:02:17: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:02:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:02:17: #1 tags after filtering in treatment: 9106285 INFO @ Fri, 04 Aug 2017 15:02:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:02:17: #1 finished! INFO @ Fri, 04 Aug 2017 15:02:17: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:02:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:02:18: #2 number of paired peaks: 1362 INFO @ Fri, 04 Aug 2017 15:02:18: start model_add_line... INFO @ Fri, 04 Aug 2017 15:02:18: #2 number of paired peaks: 1362 INFO @ Fri, 04 Aug 2017 15:02:18: start model_add_line... INFO @ Fri, 04 Aug 2017 15:02:18: start X-correlation... INFO @ Fri, 04 Aug 2017 15:02:18: end of X-cor INFO @ Fri, 04 Aug 2017 15:02:18: #2 finished! INFO @ Fri, 04 Aug 2017 15:02:18: #2 predicted fragment length is 154 bps INFO @ Fri, 04 Aug 2017 15:02:18: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 04 Aug 2017 15:02:18: #2.2 Generate R script for model : SRX2520639.05_model.r INFO @ Fri, 04 Aug 2017 15:02:18: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:02:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:02:18: start X-correlation... INFO @ Fri, 04 Aug 2017 15:02:18: end of X-cor INFO @ Fri, 04 Aug 2017 15:02:18: #2 finished! INFO @ Fri, 04 Aug 2017 15:02:18: #2 predicted fragment length is 154 bps INFO @ Fri, 04 Aug 2017 15:02:18: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 04 Aug 2017 15:02:18: #2.2 Generate R script for model : SRX2520639.10_model.r INFO @ Fri, 04 Aug 2017 15:02:18: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:02:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:02:34: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:02:40: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:02:42: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:02:47: #4 Write output xls file... SRX2520639.20_peaks.xls INFO @ Fri, 04 Aug 2017 15:02:47: #4 Write peak in narrowPeak format file... SRX2520639.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:02:47: #4 Write summits bed file... SRX2520639.20_summits.bed INFO @ Fri, 04 Aug 2017 15:02:47: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1680 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:02:52: #4 Write output xls file... SRX2520639.10_peaks.xls INFO @ Fri, 04 Aug 2017 15:02:52: #4 Write peak in narrowPeak format file... SRX2520639.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:02:52: #4 Write summits bed file... SRX2520639.10_summits.bed INFO @ Fri, 04 Aug 2017 15:02:52: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3067 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:02:55: #4 Write output xls file... SRX2520639.05_peaks.xls INFO @ Fri, 04 Aug 2017 15:02:55: #4 Write peak in narrowPeak format file... SRX2520639.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:02:55: #4 Write summits bed file... SRX2520639.05_summits.bed INFO @ Fri, 04 Aug 2017 15:02:55: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4899 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。