Job ID = 10175273 sra ファイルのダウンロード中... Completed: 483580K bytes transferred in 17 seconds (221688K 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... Written 28358405 spots for /home/okishinya/chipatlas/results/dm3/SRX3159474/SRR6004204.sra Written 28358405 spots total 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: 00:08:09 28358405 reads; of these: 28358405 (100.00%) were unpaired; of these: 4801334 (16.93%) aligned 0 times 20103873 (70.89%) aligned exactly 1 time 3453198 (12.18%) aligned >1 times 83.07% overall alignment rate Time searching: 00:08:09 Overall time: 00:08:09 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 12 files... [bam_rmdupse_core] 4393500 / 23557071 = 0.1865 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 @ Mon, 06 Nov 2017 12:37:50: # Command line: callpeak -t SRX3159474.bam -f BAM -g dm -n SRX3159474.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3159474.20 # format = BAM # ChIP-seq file = ['SRX3159474.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 @ Mon, 06 Nov 2017 12:37:50: # Command line: callpeak -t SRX3159474.bam -f BAM -g dm -n SRX3159474.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3159474.05 # format = BAM # ChIP-seq file = ['SRX3159474.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 @ Mon, 06 Nov 2017 12:37:50: # Command line: callpeak -t SRX3159474.bam -f BAM -g dm -n SRX3159474.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3159474.10 # format = BAM # ChIP-seq file = ['SRX3159474.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 @ Mon, 06 Nov 2017 12:37:50: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:37:50: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:37:50: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:37:50: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:37:50: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:37:50: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:37:56: 1000000 INFO @ Mon, 06 Nov 2017 12:37:56: 1000000 INFO @ Mon, 06 Nov 2017 12:37:56: 1000000 INFO @ Mon, 06 Nov 2017 12:38:02: 2000000 INFO @ Mon, 06 Nov 2017 12:38:02: 2000000 INFO @ Mon, 06 Nov 2017 12:38:02: 2000000 INFO @ Mon, 06 Nov 2017 12:38:08: 3000000 INFO @ Mon, 06 Nov 2017 12:38:08: 3000000 INFO @ Mon, 06 Nov 2017 12:38:08: 3000000 INFO @ Mon, 06 Nov 2017 12:38:14: 4000000 INFO @ Mon, 06 Nov 2017 12:38:14: 4000000 INFO @ Mon, 06 Nov 2017 12:38:14: 4000000 INFO @ Mon, 06 Nov 2017 12:38:20: 5000000 INFO @ Mon, 06 Nov 2017 12:38:20: 5000000 INFO @ Mon, 06 Nov 2017 12:38:20: 5000000 INFO @ Mon, 06 Nov 2017 12:38:26: 6000000 INFO @ Mon, 06 Nov 2017 12:38:26: 6000000 INFO @ Mon, 06 Nov 2017 12:38:27: 6000000 INFO @ Mon, 06 Nov 2017 12:38:32: 7000000 INFO @ Mon, 06 Nov 2017 12:38:33: 7000000 INFO @ Mon, 06 Nov 2017 12:38:33: 7000000 INFO @ Mon, 06 Nov 2017 12:38:38: 8000000 INFO @ Mon, 06 Nov 2017 12:38:39: 8000000 INFO @ Mon, 06 Nov 2017 12:38:39: 8000000 INFO @ Mon, 06 Nov 2017 12:38:45: 9000000 INFO @ Mon, 06 Nov 2017 12:38:45: 9000000 INFO @ Mon, 06 Nov 2017 12:38:46: 9000000 INFO @ Mon, 06 Nov 2017 12:38:51: 10000000 INFO @ Mon, 06 Nov 2017 12:38:52: 10000000 INFO @ Mon, 06 Nov 2017 12:38:52: 10000000 INFO @ Mon, 06 Nov 2017 12:38:58: 11000000 INFO @ Mon, 06 Nov 2017 12:38:59: 11000000 INFO @ Mon, 06 Nov 2017 12:38:59: 11000000 INFO @ Mon, 06 Nov 2017 12:39:04: 12000000 INFO @ Mon, 06 Nov 2017 12:39:05: 12000000 INFO @ Mon, 06 Nov 2017 12:39:05: 12000000 INFO @ Mon, 06 Nov 2017 12:39:10: 13000000 INFO @ Mon, 06 Nov 2017 12:39:11: 13000000 INFO @ Mon, 06 Nov 2017 12:39:11: 13000000 INFO @ Mon, 06 Nov 2017 12:39:16: 14000000 INFO @ Mon, 06 Nov 2017 12:39:17: 14000000 INFO @ Mon, 06 Nov 2017 12:39:17: 14000000 INFO @ Mon, 06 Nov 2017 12:39:22: 15000000 INFO @ Mon, 06 Nov 2017 12:39:23: 15000000 INFO @ Mon, 06 Nov 2017 12:39:23: 15000000 INFO @ Mon, 06 Nov 2017 12:39:29: 16000000 INFO @ Mon, 06 Nov 2017 12:39:29: 16000000 INFO @ Mon, 06 Nov 2017 12:39:29: 16000000 INFO @ Mon, 06 Nov 2017 12:39:35: 17000000 INFO @ Mon, 06 Nov 2017 12:39:35: 17000000 INFO @ Mon, 06 Nov 2017 12:39:35: 17000000 INFO @ Mon, 06 Nov 2017 12:39:41: 18000000 INFO @ Mon, 06 Nov 2017 12:39:41: 18000000 INFO @ Mon, 06 Nov 2017 12:39:41: 18000000 INFO @ Mon, 06 Nov 2017 12:39:47: 19000000 INFO @ Mon, 06 Nov 2017 12:39:47: 19000000 INFO @ Mon, 06 Nov 2017 12:39:47: 19000000 INFO @ Mon, 06 Nov 2017 12:39:48: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:39:48: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:39:48: #1 total tags in treatment: 19163571 INFO @ Mon, 06 Nov 2017 12:39:48: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:39:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:39:48: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:39:48: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:39:48: #1 total tags in treatment: 19163571 INFO @ Mon, 06 Nov 2017 12:39:48: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:39:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:39:48: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:39:48: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:39:48: #1 total tags in treatment: 19163571 INFO @ Mon, 06 Nov 2017 12:39:48: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:39:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:39:49: #1 tags after filtering in treatment: 19163571 INFO @ Mon, 06 Nov 2017 12:39:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:39:49: #1 finished! INFO @ Mon, 06 Nov 2017 12:39:49: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:39:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:39:49: #1 tags after filtering in treatment: 19163571 INFO @ Mon, 06 Nov 2017 12:39:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:39:49: #1 finished! INFO @ Mon, 06 Nov 2017 12:39:49: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:39:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:39:49: #1 tags after filtering in treatment: 19163571 INFO @ Mon, 06 Nov 2017 12:39:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:39:49: #1 finished! INFO @ Mon, 06 Nov 2017 12:39:49: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:39:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:39:51: #2 number of paired peaks: 4457 INFO @ Mon, 06 Nov 2017 12:39:51: start model_add_line... INFO @ Mon, 06 Nov 2017 12:39:51: #2 number of paired peaks: 4457 INFO @ Mon, 06 Nov 2017 12:39:51: start model_add_line... INFO @ Mon, 06 Nov 2017 12:39:51: #2 number of paired peaks: 4457 INFO @ Mon, 06 Nov 2017 12:39:51: start model_add_line... INFO @ Mon, 06 Nov 2017 12:39:51: start X-correlation... INFO @ Mon, 06 Nov 2017 12:39:51: start X-correlation... INFO @ Mon, 06 Nov 2017 12:39:51: start X-correlation... INFO @ Mon, 06 Nov 2017 12:39:51: end of X-cor INFO @ Mon, 06 Nov 2017 12:39:51: end of X-cor INFO @ Mon, 06 Nov 2017 12:39:51: end of X-cor INFO @ Mon, 06 Nov 2017 12:39:51: #2 finished! INFO @ Mon, 06 Nov 2017 12:39:51: #2 finished! INFO @ Mon, 06 Nov 2017 12:39:51: #2 finished! INFO @ Mon, 06 Nov 2017 12:39:51: #2 predicted fragment length is 222 bps INFO @ Mon, 06 Nov 2017 12:39:51: #2 predicted fragment length is 222 bps INFO @ Mon, 06 Nov 2017 12:39:51: #2 predicted fragment length is 222 bps INFO @ Mon, 06 Nov 2017 12:39:51: #2 alternative fragment length(s) may be 3,222 bps INFO @ Mon, 06 Nov 2017 12:39:51: #2 alternative fragment length(s) may be 3,222 bps INFO @ Mon, 06 Nov 2017 12:39:51: #2 alternative fragment length(s) may be 3,222 bps INFO @ Mon, 06 Nov 2017 12:39:51: #2.2 Generate R script for model : SRX3159474.10_model.r INFO @ Mon, 06 Nov 2017 12:39:51: #2.2 Generate R script for model : SRX3159474.05_model.r INFO @ Mon, 06 Nov 2017 12:39:51: #2.2 Generate R script for model : SRX3159474.20_model.r INFO @ Mon, 06 Nov 2017 12:39:51: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:39:51: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:39:51: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:39:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:39:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:39:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:40:51: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:40:52: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:40:53: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:41:13: #4 Write output xls file... SRX3159474.20_peaks.xls INFO @ Mon, 06 Nov 2017 12:41:13: #4 Write peak in narrowPeak format file... SRX3159474.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:41:13: #4 Write summits bed file... SRX3159474.20_summits.bed INFO @ Mon, 06 Nov 2017 12:41:13: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2775 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:41:16: #4 Write output xls file... SRX3159474.10_peaks.xls INFO @ Mon, 06 Nov 2017 12:41:16: #4 Write peak in narrowPeak format file... SRX3159474.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:41:17: #4 Write summits bed file... SRX3159474.10_summits.bed INFO @ Mon, 06 Nov 2017 12:41:17: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4783 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:41:18: #4 Write output xls file... SRX3159474.05_peaks.xls INFO @ Mon, 06 Nov 2017 12:41:18: #4 Write peak in narrowPeak format file... SRX3159474.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:41:18: #4 Write summits bed file... SRX3159474.05_summits.bed INFO @ Mon, 06 Nov 2017 12:41:18: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6529 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。