Job ID = 10609569 sra ファイルのダウンロード中... Completed: 522427K bytes transferred in 50 seconds (84103K 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 16215395 spots for /home/okishinya/chipatlas/results/dm3/SRX3011240/SRR5834717.sra Written 16215395 spots for /home/okishinya/chipatlas/results/dm3/SRX3011240/SRR5834717.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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:47 16215395 reads; of these: 16215395 (100.00%) were unpaired; of these: 465293 (2.87%) aligned 0 times 13068804 (80.60%) aligned exactly 1 time 2681298 (16.54%) aligned >1 times 97.13% overall alignment rate Time searching: 00:05:48 Overall time: 00:05:48 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] 5586731 / 15750102 = 0.3547 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 @ Mon, 07 May 2018 12:15:01: # Command line: callpeak -t SRX3011240.bam -f BAM -g dm -n SRX3011240.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3011240.10 # format = BAM # ChIP-seq file = ['SRX3011240.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 @ Mon, 07 May 2018 12:15:01: #1 read tag files... INFO @ Mon, 07 May 2018 12:15:01: #1 read treatment tags... INFO @ Mon, 07 May 2018 12:15:01: # Command line: callpeak -t SRX3011240.bam -f BAM -g dm -n SRX3011240.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3011240.05 # format = BAM # ChIP-seq file = ['SRX3011240.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 @ Mon, 07 May 2018 12:15:01: #1 read tag files... INFO @ Mon, 07 May 2018 12:15:01: #1 read treatment tags... INFO @ Mon, 07 May 2018 12:15:01: # Command line: callpeak -t SRX3011240.bam -f BAM -g dm -n SRX3011240.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3011240.20 # format = BAM # ChIP-seq file = ['SRX3011240.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 @ Mon, 07 May 2018 12:15:01: #1 read tag files... INFO @ Mon, 07 May 2018 12:15:01: #1 read treatment tags... INFO @ Mon, 07 May 2018 12:15:09: 1000000 INFO @ Mon, 07 May 2018 12:15:10: 1000000 INFO @ Mon, 07 May 2018 12:15:10: 1000000 INFO @ Mon, 07 May 2018 12:15:18: 2000000 INFO @ Mon, 07 May 2018 12:15:19: 2000000 INFO @ Mon, 07 May 2018 12:15:20: 2000000 INFO @ Mon, 07 May 2018 12:15:27: 3000000 INFO @ Mon, 07 May 2018 12:15:28: 3000000 INFO @ Mon, 07 May 2018 12:15:29: 3000000 INFO @ Mon, 07 May 2018 12:15:36: 4000000 INFO @ Mon, 07 May 2018 12:15:36: 4000000 INFO @ Mon, 07 May 2018 12:15:39: 4000000 INFO @ Mon, 07 May 2018 12:15:45: 5000000 INFO @ Mon, 07 May 2018 12:15:46: 5000000 INFO @ Mon, 07 May 2018 12:15:48: 5000000 INFO @ Mon, 07 May 2018 12:15:54: 6000000 INFO @ Mon, 07 May 2018 12:15:55: 6000000 INFO @ Mon, 07 May 2018 12:15:58: 6000000 INFO @ Mon, 07 May 2018 12:16:03: 7000000 INFO @ Mon, 07 May 2018 12:16:04: 7000000 INFO @ Mon, 07 May 2018 12:16:07: 7000000 INFO @ Mon, 07 May 2018 12:16:12: 8000000 INFO @ Mon, 07 May 2018 12:16:13: 8000000 INFO @ Mon, 07 May 2018 12:16:17: 8000000 INFO @ Mon, 07 May 2018 12:16:21: 9000000 INFO @ Mon, 07 May 2018 12:16:22: 9000000 INFO @ Mon, 07 May 2018 12:16:26: 9000000 INFO @ Mon, 07 May 2018 12:16:30: 10000000 INFO @ Mon, 07 May 2018 12:16:31: 10000000 INFO @ Mon, 07 May 2018 12:16:32: #1 tag size is determined as 80 bps INFO @ Mon, 07 May 2018 12:16:32: #1 tag size = 80 INFO @ Mon, 07 May 2018 12:16:32: #1 total tags in treatment: 10163371 INFO @ Mon, 07 May 2018 12:16:32: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 12:16:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 12:16:32: #1 tags after filtering in treatment: 10163371 INFO @ Mon, 07 May 2018 12:16:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 12:16:32: #1 finished! INFO @ Mon, 07 May 2018 12:16:32: #2 Build Peak Model... INFO @ Mon, 07 May 2018 12:16:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 12:16:33: #1 tag size is determined as 80 bps INFO @ Mon, 07 May 2018 12:16:33: #1 tag size = 80 INFO @ Mon, 07 May 2018 12:16:33: #1 total tags in treatment: 10163371 INFO @ Mon, 07 May 2018 12:16:33: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 12:16:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 12:16:33: #2 number of paired peaks: 3903 INFO @ Mon, 07 May 2018 12:16:33: start model_add_line... INFO @ Mon, 07 May 2018 12:16:33: #1 tags after filtering in treatment: 10163371 INFO @ Mon, 07 May 2018 12:16:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 12:16:33: #1 finished! INFO @ Mon, 07 May 2018 12:16:33: #2 Build Peak Model... INFO @ Mon, 07 May 2018 12:16:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 12:16:33: start X-correlation... INFO @ Mon, 07 May 2018 12:16:33: end of X-cor INFO @ Mon, 07 May 2018 12:16:33: #2 finished! INFO @ Mon, 07 May 2018 12:16:33: #2 predicted fragment length is 200 bps INFO @ Mon, 07 May 2018 12:16:33: #2 alternative fragment length(s) may be 200 bps INFO @ Mon, 07 May 2018 12:16:33: #2.2 Generate R script for model : SRX3011240.20_model.r INFO @ Mon, 07 May 2018 12:16:33: #3 Call peaks... INFO @ Mon, 07 May 2018 12:16:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 12:16:34: #2 number of paired peaks: 3903 INFO @ Mon, 07 May 2018 12:16:34: start model_add_line... INFO @ Mon, 07 May 2018 12:16:34: start X-correlation... INFO @ Mon, 07 May 2018 12:16:34: end of X-cor INFO @ Mon, 07 May 2018 12:16:34: #2 finished! INFO @ Mon, 07 May 2018 12:16:34: #2 predicted fragment length is 200 bps INFO @ Mon, 07 May 2018 12:16:34: #2 alternative fragment length(s) may be 200 bps INFO @ Mon, 07 May 2018 12:16:34: #2.2 Generate R script for model : SRX3011240.10_model.r INFO @ Mon, 07 May 2018 12:16:34: #3 Call peaks... INFO @ Mon, 07 May 2018 12:16:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 12:16:35: 10000000 INFO @ Mon, 07 May 2018 12:16:37: #1 tag size is determined as 80 bps INFO @ Mon, 07 May 2018 12:16:37: #1 tag size = 80 INFO @ Mon, 07 May 2018 12:16:37: #1 total tags in treatment: 10163371 INFO @ Mon, 07 May 2018 12:16:37: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 12:16:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 12:16:37: #1 tags after filtering in treatment: 10163371 INFO @ Mon, 07 May 2018 12:16:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 12:16:37: #1 finished! INFO @ Mon, 07 May 2018 12:16:37: #2 Build Peak Model... INFO @ Mon, 07 May 2018 12:16:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 12:16:38: #2 number of paired peaks: 3903 INFO @ Mon, 07 May 2018 12:16:38: start model_add_line... INFO @ Mon, 07 May 2018 12:16:38: start X-correlation... INFO @ Mon, 07 May 2018 12:16:38: end of X-cor INFO @ Mon, 07 May 2018 12:16:38: #2 finished! INFO @ Mon, 07 May 2018 12:16:38: #2 predicted fragment length is 200 bps INFO @ Mon, 07 May 2018 12:16:38: #2 alternative fragment length(s) may be 200 bps INFO @ Mon, 07 May 2018 12:16:38: #2.2 Generate R script for model : SRX3011240.05_model.r INFO @ Mon, 07 May 2018 12:16:38: #3 Call peaks... INFO @ Mon, 07 May 2018 12:16:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 12:17:04: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 12:17:07: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 12:17:08: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 12:17:21: #4 Write output xls file... SRX3011240.20_peaks.xls INFO @ Mon, 07 May 2018 12:17:21: #4 Write peak in narrowPeak format file... SRX3011240.20_peaks.narrowPeak INFO @ Mon, 07 May 2018 12:17:21: #4 Write summits bed file... SRX3011240.20_summits.bed INFO @ Mon, 07 May 2018 12:17:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4287 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 07 May 2018 12:17:22: #4 Write output xls file... SRX3011240.10_peaks.xls INFO @ Mon, 07 May 2018 12:17:22: #4 Write peak in narrowPeak format file... SRX3011240.10_peaks.narrowPeak INFO @ Mon, 07 May 2018 12:17:22: #4 Write summits bed file... SRX3011240.10_summits.bed INFO @ Mon, 07 May 2018 12:17:22: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6241 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 07 May 2018 12:17:23: #4 Write output xls file... SRX3011240.05_peaks.xls INFO @ Mon, 07 May 2018 12:17:23: #4 Write peak in narrowPeak format file... SRX3011240.05_peaks.narrowPeak INFO @ Mon, 07 May 2018 12:17:23: #4 Write summits bed file... SRX3011240.05_summits.bed INFO @ Mon, 07 May 2018 12:17:23: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8373 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。