Job ID = 10175271 sra ファイルのダウンロード中... Completed: 387265K bytes transferred in 14 seconds (218094K 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 21548163 spots for /home/okishinya/chipatlas/results/dm3/SRX3159472/SRR6004202.sra Written 21548163 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: 00:06:25 21548163 reads; of these: 21548163 (100.00%) were unpaired; of these: 1370655 (6.36%) aligned 0 times 17488008 (81.16%) aligned exactly 1 time 2689500 (12.48%) aligned >1 times 93.64% overall alignment rate Time searching: 00:06:25 Overall time: 00:06:25 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_sort_core] merging from 12 files... [bam_rmdupse_core] 5485873 / 20177508 = 0.2719 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 12:30:52: # Command line: callpeak -t SRX3159472.bam -f BAM -g dm -n SRX3159472.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3159472.05 # format = BAM # ChIP-seq file = ['SRX3159472.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 12:30:52: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:30:52: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:30:52: # Command line: callpeak -t SRX3159472.bam -f BAM -g dm -n SRX3159472.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3159472.20 # format = BAM # ChIP-seq file = ['SRX3159472.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 12:30:52: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:30:52: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:30:52: # Command line: callpeak -t SRX3159472.bam -f BAM -g dm -n SRX3159472.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3159472.10 # format = BAM # ChIP-seq file = ['SRX3159472.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 12:30:52: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:30:52: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:30:58: 1000000 INFO @ Mon, 06 Nov 2017 12:30:58: 1000000 INFO @ Mon, 06 Nov 2017 12:30:58: 1000000 INFO @ Mon, 06 Nov 2017 12:31:04: 2000000 INFO @ Mon, 06 Nov 2017 12:31:04: 2000000 INFO @ Mon, 06 Nov 2017 12:31:04: 2000000 INFO @ Mon, 06 Nov 2017 12:31:10: 3000000 INFO @ Mon, 06 Nov 2017 12:31:10: 3000000 INFO @ Mon, 06 Nov 2017 12:31:10: 3000000 INFO @ Mon, 06 Nov 2017 12:31:16: 4000000 INFO @ Mon, 06 Nov 2017 12:31:16: 4000000 INFO @ Mon, 06 Nov 2017 12:31:16: 4000000 INFO @ Mon, 06 Nov 2017 12:31:22: 5000000 INFO @ Mon, 06 Nov 2017 12:31:22: 5000000 INFO @ Mon, 06 Nov 2017 12:31:23: 5000000 INFO @ Mon, 06 Nov 2017 12:31:28: 6000000 INFO @ Mon, 06 Nov 2017 12:31:28: 6000000 INFO @ Mon, 06 Nov 2017 12:31:29: 6000000 INFO @ Mon, 06 Nov 2017 12:31:34: 7000000 INFO @ Mon, 06 Nov 2017 12:31:35: 7000000 INFO @ Mon, 06 Nov 2017 12:31:35: 7000000 INFO @ Mon, 06 Nov 2017 12:31:40: 8000000 INFO @ Mon, 06 Nov 2017 12:31:41: 8000000 INFO @ Mon, 06 Nov 2017 12:31:41: 8000000 INFO @ Mon, 06 Nov 2017 12:31:46: 9000000 INFO @ Mon, 06 Nov 2017 12:31:47: 9000000 INFO @ Mon, 06 Nov 2017 12:31:47: 9000000 INFO @ Mon, 06 Nov 2017 12:31:52: 10000000 INFO @ Mon, 06 Nov 2017 12:31:53: 10000000 INFO @ Mon, 06 Nov 2017 12:31:53: 10000000 INFO @ Mon, 06 Nov 2017 12:31:58: 11000000 INFO @ Mon, 06 Nov 2017 12:31:59: 11000000 INFO @ Mon, 06 Nov 2017 12:31:59: 11000000 INFO @ Mon, 06 Nov 2017 12:32:03: 12000000 INFO @ Mon, 06 Nov 2017 12:32:05: 12000000 INFO @ Mon, 06 Nov 2017 12:32:06: 12000000 INFO @ Mon, 06 Nov 2017 12:32:09: 13000000 INFO @ Mon, 06 Nov 2017 12:32:12: 13000000 INFO @ Mon, 06 Nov 2017 12:32:12: 13000000 INFO @ Mon, 06 Nov 2017 12:32:16: 14000000 INFO @ Mon, 06 Nov 2017 12:32:18: 14000000 INFO @ Mon, 06 Nov 2017 12:32:19: 14000000 INFO @ Mon, 06 Nov 2017 12:32:21: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:32:21: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:32:21: #1 total tags in treatment: 14691635 INFO @ Mon, 06 Nov 2017 12:32:21: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:32:21: #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 12:32:21: #1 tags after filtering in treatment: 14691635 INFO @ Mon, 06 Nov 2017 12:32:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:32:21: #1 finished! INFO @ Mon, 06 Nov 2017 12:32:21: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:32:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:32:22: #2 number of paired peaks: 3840 INFO @ Mon, 06 Nov 2017 12:32:22: start model_add_line... INFO @ Mon, 06 Nov 2017 12:32:23: start X-correlation... INFO @ Mon, 06 Nov 2017 12:32:23: end of X-cor INFO @ Mon, 06 Nov 2017 12:32:23: #2 finished! INFO @ Mon, 06 Nov 2017 12:32:23: #2 predicted fragment length is 149 bps INFO @ Mon, 06 Nov 2017 12:32:23: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 06 Nov 2017 12:32:23: #2.2 Generate R script for model : SRX3159472.05_model.r INFO @ Mon, 06 Nov 2017 12:32:23: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:32:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:32:23: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:32:23: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:32:23: #1 total tags in treatment: 14691635 INFO @ Mon, 06 Nov 2017 12:32:23: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:32:23: #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 12:32:23: #1 tags after filtering in treatment: 14691635 INFO @ Mon, 06 Nov 2017 12:32:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:32:23: #1 finished! INFO @ Mon, 06 Nov 2017 12:32:23: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:32:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:32:23: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:32:23: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:32:23: #1 total tags in treatment: 14691635 INFO @ Mon, 06 Nov 2017 12:32:23: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:32:23: #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 12:32:23: #1 tags after filtering in treatment: 14691635 INFO @ Mon, 06 Nov 2017 12:32:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:32:23: #1 finished! INFO @ Mon, 06 Nov 2017 12:32:23: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:32:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:32:25: #2 number of paired peaks: 3840 INFO @ Mon, 06 Nov 2017 12:32:25: start model_add_line... INFO @ Mon, 06 Nov 2017 12:32:25: start X-correlation... INFO @ Mon, 06 Nov 2017 12:32:25: end of X-cor INFO @ Mon, 06 Nov 2017 12:32:25: #2 finished! INFO @ Mon, 06 Nov 2017 12:32:25: #2 predicted fragment length is 149 bps INFO @ Mon, 06 Nov 2017 12:32:25: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 06 Nov 2017 12:32:25: #2.2 Generate R script for model : SRX3159472.10_model.r INFO @ Mon, 06 Nov 2017 12:32:25: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:32:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:32:25: #2 number of paired peaks: 3840 INFO @ Mon, 06 Nov 2017 12:32:25: start model_add_line... INFO @ Mon, 06 Nov 2017 12:32:25: start X-correlation... INFO @ Mon, 06 Nov 2017 12:32:25: end of X-cor INFO @ Mon, 06 Nov 2017 12:32:25: #2 finished! INFO @ Mon, 06 Nov 2017 12:32:25: #2 predicted fragment length is 149 bps INFO @ Mon, 06 Nov 2017 12:32:25: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 06 Nov 2017 12:32:25: #2.2 Generate R script for model : SRX3159472.20_model.r INFO @ Mon, 06 Nov 2017 12:32:25: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:32:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:33:01: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:33:02: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:33:05: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:33:22: #4 Write output xls file... SRX3159472.05_peaks.xls INFO @ Mon, 06 Nov 2017 12:33:22: #4 Write peak in narrowPeak format file... SRX3159472.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:33:23: #4 Write summits bed file... SRX3159472.05_summits.bed INFO @ Mon, 06 Nov 2017 12:33:23: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7613 records, 4 fields): 12 millis INFO @ Mon, 06 Nov 2017 12:33:23: #4 Write output xls file... SRX3159472.10_peaks.xls CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:33:23: #4 Write peak in narrowPeak format file... SRX3159472.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:33:23: #4 Write summits bed file... SRX3159472.10_summits.bed INFO @ Mon, 06 Nov 2017 12:33:23: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6450 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:33:26: #4 Write output xls file... SRX3159472.20_peaks.xls INFO @ Mon, 06 Nov 2017 12:33:26: #4 Write peak in narrowPeak format file... SRX3159472.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:33:26: #4 Write summits bed file... SRX3159472.20_summits.bed INFO @ Mon, 06 Nov 2017 12:33:26: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5293 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。