Job ID = 10714574 sra ファイルのダウンロード中... Completed: 404334K bytes transferred in 6 seconds (498873K 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 23079625 spots for /home/okishinya/chipatlas/results/dm3/SRX4053308/SRR7132405.sra Written 23079625 spots for /home/okishinya/chipatlas/results/dm3/SRX4053308/SRR7132405.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: 00:07:34 23079625 reads; of these: 23079625 (100.00%) were unpaired; of these: 3504603 (15.18%) aligned 0 times 15772276 (68.34%) aligned exactly 1 time 3802746 (16.48%) aligned >1 times 84.82% overall alignment rate Time searching: 00:07:34 Overall time: 00:07:34 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] 9834045 / 19575022 = 0.5024 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, 03 Jun 2018 13:43:18: # Command line: callpeak -t SRX4053308.bam -f BAM -g dm -n SRX4053308.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4053308.20 # format = BAM # ChIP-seq file = ['SRX4053308.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, 03 Jun 2018 13:43:18: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:43:18: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:43:18: # Command line: callpeak -t SRX4053308.bam -f BAM -g dm -n SRX4053308.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4053308.10 # format = BAM # ChIP-seq file = ['SRX4053308.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, 03 Jun 2018 13:43:18: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:43:18: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:43:18: # Command line: callpeak -t SRX4053308.bam -f BAM -g dm -n SRX4053308.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4053308.05 # format = BAM # ChIP-seq file = ['SRX4053308.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, 03 Jun 2018 13:43:18: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:43:18: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:43:24: 1000000 INFO @ Sun, 03 Jun 2018 13:43:24: 1000000 INFO @ Sun, 03 Jun 2018 13:43:25: 1000000 INFO @ Sun, 03 Jun 2018 13:43:31: 2000000 INFO @ Sun, 03 Jun 2018 13:43:31: 2000000 INFO @ Sun, 03 Jun 2018 13:43:32: 2000000 INFO @ Sun, 03 Jun 2018 13:43:38: 3000000 INFO @ Sun, 03 Jun 2018 13:43:38: 3000000 INFO @ Sun, 03 Jun 2018 13:43:38: 3000000 INFO @ Sun, 03 Jun 2018 13:43:44: 4000000 INFO @ Sun, 03 Jun 2018 13:43:45: 4000000 INFO @ Sun, 03 Jun 2018 13:43:45: 4000000 INFO @ Sun, 03 Jun 2018 13:43:51: 5000000 INFO @ Sun, 03 Jun 2018 13:43:52: 5000000 INFO @ Sun, 03 Jun 2018 13:43:52: 5000000 INFO @ Sun, 03 Jun 2018 13:43:58: 6000000 INFO @ Sun, 03 Jun 2018 13:43:59: 6000000 INFO @ Sun, 03 Jun 2018 13:43:59: 6000000 INFO @ Sun, 03 Jun 2018 13:44:04: 7000000 INFO @ Sun, 03 Jun 2018 13:44:06: 7000000 INFO @ Sun, 03 Jun 2018 13:44:06: 7000000 INFO @ Sun, 03 Jun 2018 13:44:11: 8000000 INFO @ Sun, 03 Jun 2018 13:44:12: 8000000 INFO @ Sun, 03 Jun 2018 13:44:13: 8000000 INFO @ Sun, 03 Jun 2018 13:44:18: 9000000 INFO @ Sun, 03 Jun 2018 13:44:19: 9000000 INFO @ Sun, 03 Jun 2018 13:44:20: 9000000 INFO @ Sun, 03 Jun 2018 13:44:23: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:44:23: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:44:23: #1 total tags in treatment: 9740977 INFO @ Sun, 03 Jun 2018 13:44:23: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:44:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:44:23: #1 tags after filtering in treatment: 9740977 INFO @ Sun, 03 Jun 2018 13:44:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:44:23: #1 finished! INFO @ Sun, 03 Jun 2018 13:44:23: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:44:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:44:24: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:44:24: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:44:24: #1 total tags in treatment: 9740977 INFO @ Sun, 03 Jun 2018 13:44:24: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:44:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:44:25: #1 tags after filtering in treatment: 9740977 INFO @ Sun, 03 Jun 2018 13:44:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:44:25: #1 finished! INFO @ Sun, 03 Jun 2018 13:44:25: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:44:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:44:25: #2 number of paired peaks: 5876 INFO @ Sun, 03 Jun 2018 13:44:25: start model_add_line... INFO @ Sun, 03 Jun 2018 13:44:25: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:44:25: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:44:25: #1 total tags in treatment: 9740977 INFO @ Sun, 03 Jun 2018 13:44:25: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:44:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:44:25: #1 tags after filtering in treatment: 9740977 INFO @ Sun, 03 Jun 2018 13:44:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:44:25: #1 finished! INFO @ Sun, 03 Jun 2018 13:44:25: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:44:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:44:25: start X-correlation... INFO @ Sun, 03 Jun 2018 13:44:25: end of X-cor INFO @ Sun, 03 Jun 2018 13:44:25: #2 finished! INFO @ Sun, 03 Jun 2018 13:44:25: #2 predicted fragment length is 191 bps INFO @ Sun, 03 Jun 2018 13:44:25: #2 alternative fragment length(s) may be 2,191 bps INFO @ Sun, 03 Jun 2018 13:44:25: #2.2 Generate R script for model : SRX4053308.20_model.r INFO @ Sun, 03 Jun 2018 13:44:25: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:44:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:44:26: #2 number of paired peaks: 5876 INFO @ Sun, 03 Jun 2018 13:44:26: start model_add_line... INFO @ Sun, 03 Jun 2018 13:44:26: start X-correlation... INFO @ Sun, 03 Jun 2018 13:44:26: end of X-cor INFO @ Sun, 03 Jun 2018 13:44:26: #2 finished! INFO @ Sun, 03 Jun 2018 13:44:26: #2 predicted fragment length is 191 bps INFO @ Sun, 03 Jun 2018 13:44:26: #2 alternative fragment length(s) may be 2,191 bps INFO @ Sun, 03 Jun 2018 13:44:26: #2.2 Generate R script for model : SRX4053308.05_model.r INFO @ Sun, 03 Jun 2018 13:44:26: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:44:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:44:26: #2 number of paired peaks: 5876 INFO @ Sun, 03 Jun 2018 13:44:26: start model_add_line... INFO @ Sun, 03 Jun 2018 13:44:27: start X-correlation... INFO @ Sun, 03 Jun 2018 13:44:27: end of X-cor INFO @ Sun, 03 Jun 2018 13:44:27: #2 finished! INFO @ Sun, 03 Jun 2018 13:44:27: #2 predicted fragment length is 191 bps INFO @ Sun, 03 Jun 2018 13:44:27: #2 alternative fragment length(s) may be 2,191 bps INFO @ Sun, 03 Jun 2018 13:44:27: #2.2 Generate R script for model : SRX4053308.10_model.r INFO @ Sun, 03 Jun 2018 13:44:27: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:44:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:44:56: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:44:56: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:44:56: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:45:07: #4 Write output xls file... SRX4053308.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:45:07: #4 Write peak in narrowPeak format file... SRX4053308.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:45:07: #4 Write summits bed file... SRX4053308.20_summits.bed INFO @ Sun, 03 Jun 2018 13:45:07: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (671 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:45:08: #4 Write output xls file... SRX4053308.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:45:08: #4 Write peak in narrowPeak format file... SRX4053308.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:45:08: #4 Write summits bed file... SRX4053308.05_summits.bed INFO @ Sun, 03 Jun 2018 13:45:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2274 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:45:09: #4 Write output xls file... SRX4053308.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:45:09: #4 Write peak in narrowPeak format file... SRX4053308.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:45:09: #4 Write summits bed file... SRX4053308.10_summits.bed INFO @ Sun, 03 Jun 2018 13:45:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1254 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。