Job ID = 11293692 sra ファイルのダウンロード中... Completed: 582379K bytes transferred in 26 seconds (176864K 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 17532108 spots for /home/okishinya/chipatlas/results/dm3/SRX4375854/SRR7506508.sra Written 17532108 spots for /home/okishinya/chipatlas/results/dm3/SRX4375854/SRR7506508.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: 00:05:07 17532108 reads; of these: 17532108 (100.00%) were unpaired; of these: 1621972 (9.25%) aligned 0 times 13046441 (74.41%) aligned exactly 1 time 2863695 (16.33%) aligned >1 times 90.75% overall alignment rate Time searching: 00:05:08 Overall time: 00:05:08 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] 5644983 / 15910136 = 0.3548 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 @ Sun, 04 Nov 2018 17:57:44: # Command line: callpeak -t SRX4375854.bam -f BAM -g dm -n SRX4375854.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4375854.05 # format = BAM # ChIP-seq file = ['SRX4375854.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 @ Sun, 04 Nov 2018 17:57:44: # Command line: callpeak -t SRX4375854.bam -f BAM -g dm -n SRX4375854.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4375854.10 # format = BAM # ChIP-seq file = ['SRX4375854.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 @ Sun, 04 Nov 2018 17:57:44: # Command line: callpeak -t SRX4375854.bam -f BAM -g dm -n SRX4375854.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4375854.20 # format = BAM # ChIP-seq file = ['SRX4375854.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 @ Sun, 04 Nov 2018 17:57:44: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:57:44: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:57:44: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:57:44: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:57:44: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:57:44: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:57:50: 1000000 INFO @ Sun, 04 Nov 2018 17:57:50: 1000000 INFO @ Sun, 04 Nov 2018 17:57:50: 1000000 INFO @ Sun, 04 Nov 2018 17:57:56: 2000000 INFO @ Sun, 04 Nov 2018 17:57:56: 2000000 INFO @ Sun, 04 Nov 2018 17:57:56: 2000000 INFO @ Sun, 04 Nov 2018 17:58:02: 3000000 INFO @ Sun, 04 Nov 2018 17:58:02: 3000000 INFO @ Sun, 04 Nov 2018 17:58:03: 3000000 INFO @ Sun, 04 Nov 2018 17:58:08: 4000000 INFO @ Sun, 04 Nov 2018 17:58:08: 4000000 INFO @ Sun, 04 Nov 2018 17:58:09: 4000000 INFO @ Sun, 04 Nov 2018 17:58:14: 5000000 INFO @ Sun, 04 Nov 2018 17:58:14: 5000000 INFO @ Sun, 04 Nov 2018 17:58:15: 5000000 INFO @ Sun, 04 Nov 2018 17:58:20: 6000000 INFO @ Sun, 04 Nov 2018 17:58:20: 6000000 INFO @ Sun, 04 Nov 2018 17:58:21: 6000000 INFO @ Sun, 04 Nov 2018 17:58:26: 7000000 INFO @ Sun, 04 Nov 2018 17:58:27: 7000000 INFO @ Sun, 04 Nov 2018 17:58:27: 7000000 INFO @ Sun, 04 Nov 2018 17:58:32: 8000000 INFO @ Sun, 04 Nov 2018 17:58:33: 8000000 INFO @ Sun, 04 Nov 2018 17:58:33: 8000000 INFO @ Sun, 04 Nov 2018 17:58:38: 9000000 INFO @ Sun, 04 Nov 2018 17:58:39: 9000000 INFO @ Sun, 04 Nov 2018 17:58:39: 9000000 INFO @ Sun, 04 Nov 2018 17:58:43: 10000000 INFO @ Sun, 04 Nov 2018 17:58:45: 10000000 INFO @ Sun, 04 Nov 2018 17:58:45: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:58:45: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:58:45: #1 total tags in treatment: 10265153 INFO @ Sun, 04 Nov 2018 17:58:45: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:58:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:58:45: 10000000 INFO @ Sun, 04 Nov 2018 17:58:45: #1 tags after filtering in treatment: 10265153 INFO @ Sun, 04 Nov 2018 17:58:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:58:45: #1 finished! INFO @ Sun, 04 Nov 2018 17:58:45: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:58:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:58:47: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:58:47: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:58:47: #1 total tags in treatment: 10265153 INFO @ Sun, 04 Nov 2018 17:58:47: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:58:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:58:47: #2 number of paired peaks: 8429 INFO @ Sun, 04 Nov 2018 17:58:47: start model_add_line... INFO @ Sun, 04 Nov 2018 17:58:47: #1 tags after filtering in treatment: 10265153 INFO @ Sun, 04 Nov 2018 17:58:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:58:47: #1 finished! INFO @ Sun, 04 Nov 2018 17:58:47: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:58:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:58:47: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:58:47: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:58:47: #1 total tags in treatment: 10265153 INFO @ Sun, 04 Nov 2018 17:58:47: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:58:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:58:47: start X-correlation... INFO @ Sun, 04 Nov 2018 17:58:47: #1 tags after filtering in treatment: 10265153 INFO @ Sun, 04 Nov 2018 17:58:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:58:47: #1 finished! INFO @ Sun, 04 Nov 2018 17:58:47: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:58:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:58:47: end of X-cor INFO @ Sun, 04 Nov 2018 17:58:47: #2 finished! INFO @ Sun, 04 Nov 2018 17:58:47: #2 predicted fragment length is 202 bps INFO @ Sun, 04 Nov 2018 17:58:47: #2 alternative fragment length(s) may be 202 bps INFO @ Sun, 04 Nov 2018 17:58:47: #2.2 Generate R script for model : SRX4375854.20_model.r INFO @ Sun, 04 Nov 2018 17:58:47: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:58:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:58:48: #2 number of paired peaks: 8429 INFO @ Sun, 04 Nov 2018 17:58:48: start model_add_line... INFO @ Sun, 04 Nov 2018 17:58:49: start X-correlation... INFO @ Sun, 04 Nov 2018 17:58:49: end of X-cor INFO @ Sun, 04 Nov 2018 17:58:49: #2 finished! INFO @ Sun, 04 Nov 2018 17:58:49: #2 predicted fragment length is 202 bps INFO @ Sun, 04 Nov 2018 17:58:49: #2 alternative fragment length(s) may be 202 bps INFO @ Sun, 04 Nov 2018 17:58:49: #2.2 Generate R script for model : SRX4375854.05_model.r INFO @ Sun, 04 Nov 2018 17:58:49: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:58:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:58:49: #2 number of paired peaks: 8429 INFO @ Sun, 04 Nov 2018 17:58:49: start model_add_line... INFO @ Sun, 04 Nov 2018 17:58:49: start X-correlation... INFO @ Sun, 04 Nov 2018 17:58:49: end of X-cor INFO @ Sun, 04 Nov 2018 17:58:49: #2 finished! INFO @ Sun, 04 Nov 2018 17:58:49: #2 predicted fragment length is 202 bps INFO @ Sun, 04 Nov 2018 17:58:49: #2 alternative fragment length(s) may be 202 bps INFO @ Sun, 04 Nov 2018 17:58:49: #2.2 Generate R script for model : SRX4375854.10_model.r INFO @ Sun, 04 Nov 2018 17:58:49: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:58:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:59:27: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:59:28: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:59:28: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:59:43: #4 Write output xls file... SRX4375854.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:59:43: #4 Write peak in narrowPeak format file... SRX4375854.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:59:43: #4 Write summits bed file... SRX4375854.10_summits.bed INFO @ Sun, 04 Nov 2018 17:59:43: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8259 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:59:44: #4 Write output xls file... SRX4375854.05_peaks.xls INFO @ Sun, 04 Nov 2018 17:59:44: #4 Write peak in narrowPeak format file... SRX4375854.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:59:44: #4 Write summits bed file... SRX4375854.05_summits.bed INFO @ Sun, 04 Nov 2018 17:59:44: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9972 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:59:46: #4 Write output xls file... SRX4375854.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:59:46: #4 Write peak in narrowPeak format file... SRX4375854.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:59:46: #4 Write summits bed file... SRX4375854.20_summits.bed INFO @ Sun, 04 Nov 2018 17:59:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6358 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。