Job ID = 11240738 sra ファイルのダウンロード中... Completed: 598195K bytes transferred in 20 seconds (240117K 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 33363817 spots for /home/okishinya/chipatlas/results/dm3/SRX4669022/SRR7817547.sra Written 33363817 spots for /home/okishinya/chipatlas/results/dm3/SRX4669022/SRR7817547.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: 00:10:22 33363817 reads; of these: 33363817 (100.00%) were unpaired; of these: 2188490 (6.56%) aligned 0 times 23201117 (69.54%) aligned exactly 1 time 7974210 (23.90%) aligned >1 times 93.44% overall alignment rate Time searching: 00:10:22 Overall time: 00:10:22 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 16 files... [bam_rmdupse_core] 11928768 / 31175327 = 0.3826 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, 07 Oct 2018 20:47:35: # Command line: callpeak -t SRX4669022.bam -f BAM -g dm -n SRX4669022.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669022.05 # format = BAM # ChIP-seq file = ['SRX4669022.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, 07 Oct 2018 20:47:35: # Command line: callpeak -t SRX4669022.bam -f BAM -g dm -n SRX4669022.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669022.10 # format = BAM # ChIP-seq file = ['SRX4669022.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, 07 Oct 2018 20:47:35: # Command line: callpeak -t SRX4669022.bam -f BAM -g dm -n SRX4669022.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669022.20 # format = BAM # ChIP-seq file = ['SRX4669022.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, 07 Oct 2018 20:47:35: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:47:35: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:47:35: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:47:35: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:47:35: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:47:35: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:47:40: 1000000 INFO @ Sun, 07 Oct 2018 20:47:40: 1000000 INFO @ Sun, 07 Oct 2018 20:47:40: 1000000 INFO @ Sun, 07 Oct 2018 20:47:46: 2000000 INFO @ Sun, 07 Oct 2018 20:47:46: 2000000 INFO @ Sun, 07 Oct 2018 20:47:46: 2000000 INFO @ Sun, 07 Oct 2018 20:47:52: 3000000 INFO @ Sun, 07 Oct 2018 20:47:52: 3000000 INFO @ Sun, 07 Oct 2018 20:47:52: 3000000 INFO @ Sun, 07 Oct 2018 20:47:57: 4000000 INFO @ Sun, 07 Oct 2018 20:47:58: 4000000 INFO @ Sun, 07 Oct 2018 20:47:58: 4000000 INFO @ Sun, 07 Oct 2018 20:48:03: 5000000 INFO @ Sun, 07 Oct 2018 20:48:04: 5000000 INFO @ Sun, 07 Oct 2018 20:48:04: 5000000 INFO @ Sun, 07 Oct 2018 20:48:09: 6000000 INFO @ Sun, 07 Oct 2018 20:48:09: 6000000 INFO @ Sun, 07 Oct 2018 20:48:10: 6000000 INFO @ Sun, 07 Oct 2018 20:48:15: 7000000 INFO @ Sun, 07 Oct 2018 20:48:15: 7000000 INFO @ Sun, 07 Oct 2018 20:48:17: 7000000 INFO @ Sun, 07 Oct 2018 20:48:21: 8000000 INFO @ Sun, 07 Oct 2018 20:48:21: 8000000 INFO @ Sun, 07 Oct 2018 20:48:23: 8000000 INFO @ Sun, 07 Oct 2018 20:48:26: 9000000 INFO @ Sun, 07 Oct 2018 20:48:27: 9000000 INFO @ Sun, 07 Oct 2018 20:48:29: 9000000 INFO @ Sun, 07 Oct 2018 20:48:32: 10000000 INFO @ Sun, 07 Oct 2018 20:48:33: 10000000 INFO @ Sun, 07 Oct 2018 20:48:35: 10000000 INFO @ Sun, 07 Oct 2018 20:48:38: 11000000 INFO @ Sun, 07 Oct 2018 20:48:38: 11000000 INFO @ Sun, 07 Oct 2018 20:48:41: 11000000 INFO @ Sun, 07 Oct 2018 20:48:43: 12000000 INFO @ Sun, 07 Oct 2018 20:48:44: 12000000 INFO @ Sun, 07 Oct 2018 20:48:47: 12000000 INFO @ Sun, 07 Oct 2018 20:48:49: 13000000 INFO @ Sun, 07 Oct 2018 20:48:50: 13000000 INFO @ Sun, 07 Oct 2018 20:48:53: 13000000 INFO @ Sun, 07 Oct 2018 20:48:55: 14000000 INFO @ Sun, 07 Oct 2018 20:48:56: 14000000 INFO @ Sun, 07 Oct 2018 20:48:59: 14000000 INFO @ Sun, 07 Oct 2018 20:49:01: 15000000 INFO @ Sun, 07 Oct 2018 20:49:02: 15000000 INFO @ Sun, 07 Oct 2018 20:49:05: 15000000 INFO @ Sun, 07 Oct 2018 20:49:06: 16000000 INFO @ Sun, 07 Oct 2018 20:49:08: 16000000 INFO @ Sun, 07 Oct 2018 20:49:11: 16000000 INFO @ Sun, 07 Oct 2018 20:49:12: 17000000 INFO @ Sun, 07 Oct 2018 20:49:14: 17000000 INFO @ Sun, 07 Oct 2018 20:49:17: 17000000 INFO @ Sun, 07 Oct 2018 20:49:18: 18000000 INFO @ Sun, 07 Oct 2018 20:49:19: 18000000 INFO @ Sun, 07 Oct 2018 20:49:23: 19000000 INFO @ Sun, 07 Oct 2018 20:49:23: 18000000 INFO @ Sun, 07 Oct 2018 20:49:25: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:49:25: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:49:25: #1 total tags in treatment: 19246559 INFO @ Sun, 07 Oct 2018 20:49:25: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:49:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:49:25: #1 tags after filtering in treatment: 19246559 INFO @ Sun, 07 Oct 2018 20:49:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:49:25: #1 finished! INFO @ Sun, 07 Oct 2018 20:49:25: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:49:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:49:25: 19000000 INFO @ Sun, 07 Oct 2018 20:49:27: #2 number of paired peaks: 825 WARNING @ Sun, 07 Oct 2018 20:49:27: Fewer paired peaks (825) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 825 pairs to build model! INFO @ Sun, 07 Oct 2018 20:49:27: start model_add_line... INFO @ Sun, 07 Oct 2018 20:49:27: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:49:27: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:49:27: #1 total tags in treatment: 19246559 INFO @ Sun, 07 Oct 2018 20:49:27: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:49:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:49:27: start X-correlation... INFO @ Sun, 07 Oct 2018 20:49:27: end of X-cor INFO @ Sun, 07 Oct 2018 20:49:27: #2 finished! INFO @ Sun, 07 Oct 2018 20:49:27: #2 predicted fragment length is 148 bps INFO @ Sun, 07 Oct 2018 20:49:27: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 07 Oct 2018 20:49:27: #2.2 Generate R script for model : SRX4669022.10_model.r INFO @ Sun, 07 Oct 2018 20:49:27: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:49:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:49:27: #1 tags after filtering in treatment: 19246559 INFO @ Sun, 07 Oct 2018 20:49:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:49:27: #1 finished! INFO @ Sun, 07 Oct 2018 20:49:27: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:49:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:49:29: #2 number of paired peaks: 825 WARNING @ Sun, 07 Oct 2018 20:49:29: Fewer paired peaks (825) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 825 pairs to build model! INFO @ Sun, 07 Oct 2018 20:49:29: start model_add_line... INFO @ Sun, 07 Oct 2018 20:49:29: start X-correlation... INFO @ Sun, 07 Oct 2018 20:49:29: end of X-cor INFO @ Sun, 07 Oct 2018 20:49:29: #2 finished! INFO @ Sun, 07 Oct 2018 20:49:29: #2 predicted fragment length is 148 bps INFO @ Sun, 07 Oct 2018 20:49:29: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 07 Oct 2018 20:49:29: #2.2 Generate R script for model : SRX4669022.20_model.r INFO @ Sun, 07 Oct 2018 20:49:29: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:49:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:49:29: 19000000 INFO @ Sun, 07 Oct 2018 20:49:31: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:49:31: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:49:31: #1 total tags in treatment: 19246559 INFO @ Sun, 07 Oct 2018 20:49:31: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:49:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:49:31: #1 tags after filtering in treatment: 19246559 INFO @ Sun, 07 Oct 2018 20:49:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:49:31: #1 finished! INFO @ Sun, 07 Oct 2018 20:49:31: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:49:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:49:33: #2 number of paired peaks: 825 WARNING @ Sun, 07 Oct 2018 20:49:33: Fewer paired peaks (825) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 825 pairs to build model! INFO @ Sun, 07 Oct 2018 20:49:33: start model_add_line... INFO @ Sun, 07 Oct 2018 20:49:33: start X-correlation... INFO @ Sun, 07 Oct 2018 20:49:33: end of X-cor INFO @ Sun, 07 Oct 2018 20:49:33: #2 finished! INFO @ Sun, 07 Oct 2018 20:49:33: #2 predicted fragment length is 148 bps INFO @ Sun, 07 Oct 2018 20:49:33: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 07 Oct 2018 20:49:33: #2.2 Generate R script for model : SRX4669022.05_model.r INFO @ Sun, 07 Oct 2018 20:49:33: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:49:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:50:15: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:50:18: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:50:20: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:50:41: #4 Write output xls file... SRX4669022.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:50:41: #4 Write peak in narrowPeak format file... SRX4669022.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:50:41: #4 Write summits bed file... SRX4669022.10_summits.bed INFO @ Sun, 07 Oct 2018 20:50:41: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7072 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:50:43: #4 Write output xls file... SRX4669022.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:50:43: #4 Write peak in narrowPeak format file... SRX4669022.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:50:43: #4 Write summits bed file... SRX4669022.20_summits.bed INFO @ Sun, 07 Oct 2018 20:50:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3020 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:50:46: #4 Write output xls file... SRX4669022.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:50:46: #4 Write peak in narrowPeak format file... SRX4669022.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:50:46: #4 Write summits bed file... SRX4669022.05_summits.bed INFO @ Sun, 07 Oct 2018 20:50:46: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (13167 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。