Job ID = 11293684 sra ファイルのダウンロード中... Completed: 606889K bytes transferred in 28 seconds (175574K 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 17926342 spots for /home/okishinya/chipatlas/results/dm3/SRX4375846/SRR7506500.sra Written 17926342 spots for /home/okishinya/chipatlas/results/dm3/SRX4375846/SRR7506500.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: 00:04:56 17926342 reads; of these: 17926342 (100.00%) were unpaired; of these: 3120346 (17.41%) aligned 0 times 12029979 (67.11%) aligned exactly 1 time 2776017 (15.49%) aligned >1 times 82.59% overall alignment rate Time searching: 00:04:56 Overall time: 00:04:56 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] 3934145 / 14805996 = 0.2657 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 17:57:21: # Command line: callpeak -t SRX4375846.bam -f BAM -g dm -n SRX4375846.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4375846.20 # format = BAM # ChIP-seq file = ['SRX4375846.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 17:57:21: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:57:21: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:57:21: # Command line: callpeak -t SRX4375846.bam -f BAM -g dm -n SRX4375846.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4375846.05 # format = BAM # ChIP-seq file = ['SRX4375846.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 17:57:21: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:57:21: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:57:21: # Command line: callpeak -t SRX4375846.bam -f BAM -g dm -n SRX4375846.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4375846.10 # format = BAM # ChIP-seq file = ['SRX4375846.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 17:57:21: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:57:21: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:57:27: 1000000 INFO @ Sun, 04 Nov 2018 17:57:27: 1000000 INFO @ Sun, 04 Nov 2018 17:57:27: 1000000 INFO @ Sun, 04 Nov 2018 17:57:33: 2000000 INFO @ Sun, 04 Nov 2018 17:57:33: 2000000 INFO @ Sun, 04 Nov 2018 17:57:34: 2000000 INFO @ Sun, 04 Nov 2018 17:57:40: 3000000 INFO @ Sun, 04 Nov 2018 17:57:40: 3000000 INFO @ Sun, 04 Nov 2018 17:57:40: 3000000 INFO @ Sun, 04 Nov 2018 17:57:46: 4000000 INFO @ Sun, 04 Nov 2018 17:57:46: 4000000 INFO @ Sun, 04 Nov 2018 17:57:46: 4000000 INFO @ Sun, 04 Nov 2018 17:57:52: 5000000 INFO @ Sun, 04 Nov 2018 17:57:52: 5000000 INFO @ Sun, 04 Nov 2018 17:57:53: 5000000 INFO @ Sun, 04 Nov 2018 17:57:58: 6000000 INFO @ Sun, 04 Nov 2018 17:57:59: 6000000 INFO @ Sun, 04 Nov 2018 17:57:59: 6000000 INFO @ Sun, 04 Nov 2018 17:58:05: 7000000 INFO @ Sun, 04 Nov 2018 17:58:05: 7000000 INFO @ Sun, 04 Nov 2018 17:58:06: 7000000 INFO @ Sun, 04 Nov 2018 17:58:11: 8000000 INFO @ Sun, 04 Nov 2018 17:58:12: 8000000 INFO @ Sun, 04 Nov 2018 17:58:12: 8000000 INFO @ Sun, 04 Nov 2018 17:58:17: 9000000 INFO @ Sun, 04 Nov 2018 17:58:18: 9000000 INFO @ Sun, 04 Nov 2018 17:58:19: 9000000 INFO @ Sun, 04 Nov 2018 17:58:24: 10000000 INFO @ Sun, 04 Nov 2018 17:58:25: 10000000 INFO @ Sun, 04 Nov 2018 17:58:25: 10000000 INFO @ Sun, 04 Nov 2018 17:58:29: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:58:29: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:58:29: #1 total tags in treatment: 10871851 INFO @ Sun, 04 Nov 2018 17:58:29: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:58:29: #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 17:58:29: #1 tags after filtering in treatment: 10871851 INFO @ Sun, 04 Nov 2018 17:58:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:58:29: #1 finished! INFO @ Sun, 04 Nov 2018 17:58:29: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:58:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:58:30: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:58:30: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:58:30: #1 total tags in treatment: 10871851 INFO @ Sun, 04 Nov 2018 17:58:30: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:58:30: #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 17:58:31: #1 tags after filtering in treatment: 10871851 INFO @ Sun, 04 Nov 2018 17:58:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:58:31: #1 finished! INFO @ Sun, 04 Nov 2018 17:58:31: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:58:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:58:31: #2 number of paired peaks: 7525 INFO @ Sun, 04 Nov 2018 17:58:31: start model_add_line... INFO @ Sun, 04 Nov 2018 17:58:31: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:58:31: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:58:31: #1 total tags in treatment: 10871851 INFO @ Sun, 04 Nov 2018 17:58:31: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:58:31: #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 17:58:31: start X-correlation... INFO @ Sun, 04 Nov 2018 17:58:31: end of X-cor INFO @ Sun, 04 Nov 2018 17:58:31: #2 finished! INFO @ Sun, 04 Nov 2018 17:58:31: #2 predicted fragment length is 179 bps INFO @ Sun, 04 Nov 2018 17:58:31: #2 alternative fragment length(s) may be 179 bps INFO @ Sun, 04 Nov 2018 17:58:31: #2.2 Generate R script for model : SRX4375846.20_model.r INFO @ Sun, 04 Nov 2018 17:58:31: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:58:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:58:31: #1 tags after filtering in treatment: 10871851 INFO @ Sun, 04 Nov 2018 17:58:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:58:31: #1 finished! INFO @ Sun, 04 Nov 2018 17:58:31: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:58:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:58:32: #2 number of paired peaks: 7525 INFO @ Sun, 04 Nov 2018 17:58:32: start model_add_line... INFO @ Sun, 04 Nov 2018 17:58:32: start X-correlation... INFO @ Sun, 04 Nov 2018 17:58:32: end of X-cor INFO @ Sun, 04 Nov 2018 17:58:32: #2 finished! INFO @ Sun, 04 Nov 2018 17:58:32: #2 predicted fragment length is 179 bps INFO @ Sun, 04 Nov 2018 17:58:32: #2 alternative fragment length(s) may be 179 bps INFO @ Sun, 04 Nov 2018 17:58:32: #2.2 Generate R script for model : SRX4375846.10_model.r INFO @ Sun, 04 Nov 2018 17:58:32: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:58:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:58:33: #2 number of paired peaks: 7525 INFO @ Sun, 04 Nov 2018 17:58:33: start model_add_line... INFO @ Sun, 04 Nov 2018 17:58:33: start X-correlation... INFO @ Sun, 04 Nov 2018 17:58:33: end of X-cor INFO @ Sun, 04 Nov 2018 17:58:33: #2 finished! INFO @ Sun, 04 Nov 2018 17:58:33: #2 predicted fragment length is 179 bps INFO @ Sun, 04 Nov 2018 17:58:33: #2 alternative fragment length(s) may be 179 bps INFO @ Sun, 04 Nov 2018 17:58:33: #2.2 Generate R script for model : SRX4375846.05_model.r INFO @ Sun, 04 Nov 2018 17:58:33: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:58:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:59:10: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:59:11: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:59:11: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:59:26: #4 Write output xls file... SRX4375846.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:59:26: #4 Write output xls file... SRX4375846.05_peaks.xls INFO @ Sun, 04 Nov 2018 17:59:26: #4 Write peak in narrowPeak format file... SRX4375846.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:59:26: #4 Write peak in narrowPeak format file... SRX4375846.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:59:26: #4 Write summits bed file... SRX4375846.10_summits.bed INFO @ Sun, 04 Nov 2018 17:59:26: Done! INFO @ Sun, 04 Nov 2018 17:59:26: #4 Write summits bed file... SRX4375846.05_summits.bed INFO @ Sun, 04 Nov 2018 17:59:26: Done! INFO @ Sun, 04 Nov 2018 17:59:26: #4 Write output xls file... SRX4375846.20_peaks.xls pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8592 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:59:26: #4 Write peak in narrowPeak format file... SRX4375846.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:59:26: #4 Write summits bed file... SRX4375846.20_summits.bed INFO @ Sun, 04 Nov 2018 17:59:26: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11485 records, 4 fields): 15 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5830 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。