Job ID = 11293683 sra ファイルのダウンロード中... Completed: 732210K bytes transferred in 27 seconds (220633K 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 21703675 spots for /home/okishinya/chipatlas/results/dm3/SRX4375845/SRR7506499.sra Written 21703675 spots for /home/okishinya/chipatlas/results/dm3/SRX4375845/SRR7506499.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: 00:05:24 21703675 reads; of these: 21703675 (100.00%) were unpaired; of these: 5487060 (25.28%) aligned 0 times 13481973 (62.12%) aligned exactly 1 time 2734642 (12.60%) aligned >1 times 74.72% overall alignment rate Time searching: 00:05:24 Overall time: 00:05:24 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] 4535884 / 16216615 = 0.2797 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 17:58:19: # Command line: callpeak -t SRX4375845.bam -f BAM -g dm -n SRX4375845.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4375845.05 # format = BAM # ChIP-seq file = ['SRX4375845.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 17:58:19: # Command line: callpeak -t SRX4375845.bam -f BAM -g dm -n SRX4375845.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4375845.10 # format = BAM # ChIP-seq file = ['SRX4375845.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 17:58:19: # Command line: callpeak -t SRX4375845.bam -f BAM -g dm -n SRX4375845.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4375845.20 # format = BAM # ChIP-seq file = ['SRX4375845.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 17:58:19: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:58:19: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:58:19: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:58:19: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:58:19: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:58:19: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:58:25: 1000000 INFO @ Sun, 04 Nov 2018 17:58:25: 1000000 INFO @ Sun, 04 Nov 2018 17:58:25: 1000000 INFO @ Sun, 04 Nov 2018 17:58:31: 2000000 INFO @ Sun, 04 Nov 2018 17:58:31: 2000000 INFO @ Sun, 04 Nov 2018 17:58:32: 2000000 INFO @ Sun, 04 Nov 2018 17:58:37: 3000000 INFO @ Sun, 04 Nov 2018 17:58:38: 3000000 INFO @ Sun, 04 Nov 2018 17:58:38: 3000000 INFO @ Sun, 04 Nov 2018 17:58:43: 4000000 INFO @ Sun, 04 Nov 2018 17:58:44: 4000000 INFO @ Sun, 04 Nov 2018 17:58:45: 4000000 INFO @ Sun, 04 Nov 2018 17:58:50: 5000000 INFO @ Sun, 04 Nov 2018 17:58:51: 5000000 INFO @ Sun, 04 Nov 2018 17:58:52: 5000000 INFO @ Sun, 04 Nov 2018 17:58:56: 6000000 INFO @ Sun, 04 Nov 2018 17:58:57: 6000000 INFO @ Sun, 04 Nov 2018 17:58:59: 6000000 INFO @ Sun, 04 Nov 2018 17:59:02: 7000000 INFO @ Sun, 04 Nov 2018 17:59:04: 7000000 INFO @ Sun, 04 Nov 2018 17:59:05: 7000000 INFO @ Sun, 04 Nov 2018 17:59:08: 8000000 INFO @ Sun, 04 Nov 2018 17:59:10: 8000000 INFO @ Sun, 04 Nov 2018 17:59:12: 8000000 INFO @ Sun, 04 Nov 2018 17:59:14: 9000000 INFO @ Sun, 04 Nov 2018 17:59:17: 9000000 INFO @ Sun, 04 Nov 2018 17:59:19: 9000000 INFO @ Sun, 04 Nov 2018 17:59:20: 10000000 INFO @ Sun, 04 Nov 2018 17:59:23: 10000000 INFO @ Sun, 04 Nov 2018 17:59:25: 10000000 INFO @ Sun, 04 Nov 2018 17:59:26: 11000000 INFO @ Sun, 04 Nov 2018 17:59:30: 11000000 INFO @ Sun, 04 Nov 2018 17:59:30: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:59:30: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:59:30: #1 total tags in treatment: 11680731 INFO @ Sun, 04 Nov 2018 17:59:30: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:59:30: #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 17:59:31: #1 tags after filtering in treatment: 11680731 INFO @ Sun, 04 Nov 2018 17:59:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:59:31: #1 finished! INFO @ Sun, 04 Nov 2018 17:59:31: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:59:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:59:32: 11000000 INFO @ Sun, 04 Nov 2018 17:59:32: #2 number of paired peaks: 8035 INFO @ Sun, 04 Nov 2018 17:59:32: start model_add_line... INFO @ Sun, 04 Nov 2018 17:59:32: start X-correlation... INFO @ Sun, 04 Nov 2018 17:59:33: end of X-cor INFO @ Sun, 04 Nov 2018 17:59:33: #2 finished! INFO @ Sun, 04 Nov 2018 17:59:33: #2 predicted fragment length is 192 bps INFO @ Sun, 04 Nov 2018 17:59:33: #2 alternative fragment length(s) may be 192 bps INFO @ Sun, 04 Nov 2018 17:59:33: #2.2 Generate R script for model : SRX4375845.10_model.r INFO @ Sun, 04 Nov 2018 17:59:33: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:59:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:59:34: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:59:34: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:59:34: #1 total tags in treatment: 11680731 INFO @ Sun, 04 Nov 2018 17:59:34: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:59:34: #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 17:59:35: #1 tags after filtering in treatment: 11680731 INFO @ Sun, 04 Nov 2018 17:59:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:59:35: #1 finished! INFO @ Sun, 04 Nov 2018 17:59:35: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:59:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:59:36: #2 number of paired peaks: 8035 INFO @ Sun, 04 Nov 2018 17:59:36: start model_add_line... INFO @ Sun, 04 Nov 2018 17:59:36: start X-correlation... INFO @ Sun, 04 Nov 2018 17:59:36: end of X-cor INFO @ Sun, 04 Nov 2018 17:59:36: #2 finished! INFO @ Sun, 04 Nov 2018 17:59:36: #2 predicted fragment length is 192 bps INFO @ Sun, 04 Nov 2018 17:59:36: #2 alternative fragment length(s) may be 192 bps INFO @ Sun, 04 Nov 2018 17:59:36: #2.2 Generate R script for model : SRX4375845.20_model.r INFO @ Sun, 04 Nov 2018 17:59:36: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:59:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:59:37: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:59:37: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:59:37: #1 total tags in treatment: 11680731 INFO @ Sun, 04 Nov 2018 17:59:37: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:59:37: #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 17:59:37: #1 tags after filtering in treatment: 11680731 INFO @ Sun, 04 Nov 2018 17:59:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:59:37: #1 finished! INFO @ Sun, 04 Nov 2018 17:59:37: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:59:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:59:38: #2 number of paired peaks: 8035 INFO @ Sun, 04 Nov 2018 17:59:38: start model_add_line... INFO @ Sun, 04 Nov 2018 17:59:39: start X-correlation... INFO @ Sun, 04 Nov 2018 17:59:39: end of X-cor INFO @ Sun, 04 Nov 2018 17:59:39: #2 finished! INFO @ Sun, 04 Nov 2018 17:59:39: #2 predicted fragment length is 192 bps INFO @ Sun, 04 Nov 2018 17:59:39: #2 alternative fragment length(s) may be 192 bps INFO @ Sun, 04 Nov 2018 17:59:39: #2.2 Generate R script for model : SRX4375845.05_model.r INFO @ Sun, 04 Nov 2018 17:59:39: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:59:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 18:00:14: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 18:00:18: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 18:00:20: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 18:00:31: #4 Write output xls file... SRX4375845.10_peaks.xls INFO @ Sun, 04 Nov 2018 18:00:31: #4 Write peak in narrowPeak format file... SRX4375845.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 18:00:32: #4 Write summits bed file... SRX4375845.10_summits.bed INFO @ Sun, 04 Nov 2018 18:00:32: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (8917 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 18:00:35: #4 Write output xls file... SRX4375845.20_peaks.xls INFO @ Sun, 04 Nov 2018 18:00:35: #4 Write peak in narrowPeak format file... SRX4375845.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 18:00:35: #4 Write summits bed file... SRX4375845.20_summits.bed INFO @ Sun, 04 Nov 2018 18:00:35: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6240 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 18:00:36: #4 Write output xls file... SRX4375845.05_peaks.xls INFO @ Sun, 04 Nov 2018 18:00:37: #4 Write peak in narrowPeak format file... SRX4375845.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 18:00:37: #4 Write summits bed file... SRX4375845.05_summits.bed INFO @ Sun, 04 Nov 2018 18:00:37: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11559 records, 4 fields): 746 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。