Job ID = 11240799 sra ファイルのダウンロード中... Completed: 453524K bytes transferred in 9 seconds (402172K 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 14342870 spots for /home/okishinya/chipatlas/results/dm3/SRX4798846/SRR7965223.sra Written 14342870 spots for /home/okishinya/chipatlas/results/dm3/SRX4798846/SRR7965223.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: 00:03:26 14342870 reads; of these: 14342870 (100.00%) were unpaired; of these: 2272363 (15.84%) aligned 0 times 11384376 (79.37%) aligned exactly 1 time 686131 (4.78%) aligned >1 times 84.16% overall alignment rate Time searching: 00:03:26 Overall time: 00:03:26 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] 2657155 / 12070507 = 0.2201 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 20:47:48: # Command line: callpeak -t SRX4798846.bam -f BAM -g dm -n SRX4798846.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4798846.10 # format = BAM # ChIP-seq file = ['SRX4798846.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 20:47:48: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:47:48: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:47:48: # Command line: callpeak -t SRX4798846.bam -f BAM -g dm -n SRX4798846.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4798846.20 # format = BAM # ChIP-seq file = ['SRX4798846.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 20:47:48: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:47:48: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:47:48: # Command line: callpeak -t SRX4798846.bam -f BAM -g dm -n SRX4798846.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4798846.05 # format = BAM # ChIP-seq file = ['SRX4798846.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 20:47:48: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:47:48: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:47:55: 1000000 INFO @ Sun, 07 Oct 2018 20:47:56: 1000000 INFO @ Sun, 07 Oct 2018 20:47:56: 1000000 INFO @ Sun, 07 Oct 2018 20:48:03: 2000000 INFO @ Sun, 07 Oct 2018 20:48:04: 2000000 INFO @ Sun, 07 Oct 2018 20:48:04: 2000000 INFO @ Sun, 07 Oct 2018 20:48:10: 3000000 INFO @ Sun, 07 Oct 2018 20:48:11: 3000000 INFO @ Sun, 07 Oct 2018 20:48:12: 3000000 INFO @ Sun, 07 Oct 2018 20:48:17: 4000000 INFO @ Sun, 07 Oct 2018 20:48:19: 4000000 INFO @ Sun, 07 Oct 2018 20:48:19: 4000000 INFO @ Sun, 07 Oct 2018 20:48:24: 5000000 INFO @ Sun, 07 Oct 2018 20:48:26: 5000000 INFO @ Sun, 07 Oct 2018 20:48:26: 5000000 INFO @ Sun, 07 Oct 2018 20:48:31: 6000000 INFO @ Sun, 07 Oct 2018 20:48:33: 6000000 INFO @ Sun, 07 Oct 2018 20:48:33: 6000000 INFO @ Sun, 07 Oct 2018 20:48:38: 7000000 INFO @ Sun, 07 Oct 2018 20:48:40: 7000000 INFO @ Sun, 07 Oct 2018 20:48:40: 7000000 INFO @ Sun, 07 Oct 2018 20:48:45: 8000000 INFO @ Sun, 07 Oct 2018 20:48:47: 8000000 INFO @ Sun, 07 Oct 2018 20:48:48: 8000000 INFO @ Sun, 07 Oct 2018 20:48:52: 9000000 INFO @ Sun, 07 Oct 2018 20:48:53: 9000000 INFO @ Sun, 07 Oct 2018 20:48:55: 9000000 INFO @ Sun, 07 Oct 2018 20:48:55: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:48:55: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:48:55: #1 total tags in treatment: 9413352 INFO @ Sun, 07 Oct 2018 20:48:55: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:48:55: #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 20:48:55: #1 tags after filtering in treatment: 9413352 INFO @ Sun, 07 Oct 2018 20:48:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:48:55: #1 finished! INFO @ Sun, 07 Oct 2018 20:48:55: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:48:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:48:56: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:48:56: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:48:56: #1 total tags in treatment: 9413352 INFO @ Sun, 07 Oct 2018 20:48:56: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:48:56: #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 20:48:56: #2 number of paired peaks: 8896 INFO @ Sun, 07 Oct 2018 20:48:56: start model_add_line... INFO @ Sun, 07 Oct 2018 20:48:56: #1 tags after filtering in treatment: 9413352 INFO @ Sun, 07 Oct 2018 20:48:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:48:56: #1 finished! INFO @ Sun, 07 Oct 2018 20:48:56: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:48:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:48:57: start X-correlation... INFO @ Sun, 07 Oct 2018 20:48:57: end of X-cor INFO @ Sun, 07 Oct 2018 20:48:57: #2 finished! INFO @ Sun, 07 Oct 2018 20:48:57: #2 predicted fragment length is 175 bps INFO @ Sun, 07 Oct 2018 20:48:57: #2 alternative fragment length(s) may be 4,175 bps INFO @ Sun, 07 Oct 2018 20:48:57: #2.2 Generate R script for model : SRX4798846.20_model.r INFO @ Sun, 07 Oct 2018 20:48:57: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:48:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:48:58: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:48:58: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:48:58: #1 total tags in treatment: 9413352 INFO @ Sun, 07 Oct 2018 20:48:58: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:48:58: #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 20:48:58: #1 tags after filtering in treatment: 9413352 INFO @ Sun, 07 Oct 2018 20:48:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:48:58: #1 finished! INFO @ Sun, 07 Oct 2018 20:48:58: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:48:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:48:58: #2 number of paired peaks: 8896 INFO @ Sun, 07 Oct 2018 20:48:58: start model_add_line... INFO @ Sun, 07 Oct 2018 20:48:58: start X-correlation... INFO @ Sun, 07 Oct 2018 20:48:58: end of X-cor INFO @ Sun, 07 Oct 2018 20:48:58: #2 finished! INFO @ Sun, 07 Oct 2018 20:48:58: #2 predicted fragment length is 175 bps INFO @ Sun, 07 Oct 2018 20:48:58: #2 alternative fragment length(s) may be 4,175 bps INFO @ Sun, 07 Oct 2018 20:48:58: #2.2 Generate R script for model : SRX4798846.10_model.r INFO @ Sun, 07 Oct 2018 20:48:58: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:48:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:48:59: #2 number of paired peaks: 8896 INFO @ Sun, 07 Oct 2018 20:48:59: start model_add_line... INFO @ Sun, 07 Oct 2018 20:48:59: start X-correlation... INFO @ Sun, 07 Oct 2018 20:48:59: end of X-cor INFO @ Sun, 07 Oct 2018 20:48:59: #2 finished! INFO @ Sun, 07 Oct 2018 20:48:59: #2 predicted fragment length is 175 bps INFO @ Sun, 07 Oct 2018 20:48:59: #2 alternative fragment length(s) may be 4,175 bps INFO @ Sun, 07 Oct 2018 20:48:59: #2.2 Generate R script for model : SRX4798846.05_model.r INFO @ Sun, 07 Oct 2018 20:48:59: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:48:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:49:21: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:49:24: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:49:24: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:49:33: #4 Write output xls file... SRX4798846.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:49:33: #4 Write peak in narrowPeak format file... SRX4798846.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:49:33: #4 Write summits bed file... SRX4798846.20_summits.bed INFO @ Sun, 07 Oct 2018 20:49:33: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1829 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:49:36: #4 Write output xls file... SRX4798846.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:49:37: #4 Write peak in narrowPeak format file... SRX4798846.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:49:37: #4 Write summits bed file... SRX4798846.10_summits.bed INFO @ Sun, 07 Oct 2018 20:49:37: #4 Write output xls file... SRX4798846.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:49:37: Done! INFO @ Sun, 07 Oct 2018 20:49:37: #4 Write peak in narrowPeak format file... SRX4798846.05_peaks.narrowPeak pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4889 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:49:37: #4 Write summits bed file... SRX4798846.05_summits.bed INFO @ Sun, 07 Oct 2018 20:49:37: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8066 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。