Job ID = 10480718 sra ファイルのダウンロード中... Completed: 631375K bytes transferred in 65 seconds (79340K 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... Written 20673809 spots for /home/okishinya/chipatlas/results/dm3/SRX3068989/SRR5907465.sra Written 20673809 spots total 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: 00:05:55 20673809 reads; of these: 20673809 (100.00%) were unpaired; of these: 2997480 (14.50%) aligned 0 times 15366930 (74.33%) aligned exactly 1 time 2309399 (11.17%) aligned >1 times 85.50% overall alignment rate Time searching: 00:05:55 Overall time: 00:05:55 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] 9192068 / 17676329 = 0.5200 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 @ Fri, 16 Mar 2018 07:53:58: # Command line: callpeak -t SRX3068989.bam -f BAM -g dm -n SRX3068989.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3068989.10 # format = BAM # ChIP-seq file = ['SRX3068989.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 @ Fri, 16 Mar 2018 07:53:58: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:53:58: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:53:58: # Command line: callpeak -t SRX3068989.bam -f BAM -g dm -n SRX3068989.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3068989.20 # format = BAM # ChIP-seq file = ['SRX3068989.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 @ Fri, 16 Mar 2018 07:53:58: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:53:58: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:53:58: # Command line: callpeak -t SRX3068989.bam -f BAM -g dm -n SRX3068989.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3068989.05 # format = BAM # ChIP-seq file = ['SRX3068989.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 @ Fri, 16 Mar 2018 07:53:58: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:53:58: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:54:04: 1000000 INFO @ Fri, 16 Mar 2018 07:54:04: 1000000 INFO @ Fri, 16 Mar 2018 07:54:04: 1000000 INFO @ Fri, 16 Mar 2018 07:54:10: 2000000 INFO @ Fri, 16 Mar 2018 07:54:10: 2000000 INFO @ Fri, 16 Mar 2018 07:54:10: 2000000 INFO @ Fri, 16 Mar 2018 07:54:16: 3000000 INFO @ Fri, 16 Mar 2018 07:54:17: 3000000 INFO @ Fri, 16 Mar 2018 07:54:17: 3000000 INFO @ Fri, 16 Mar 2018 07:54:22: 4000000 INFO @ Fri, 16 Mar 2018 07:54:23: 4000000 INFO @ Fri, 16 Mar 2018 07:54:23: 4000000 INFO @ Fri, 16 Mar 2018 07:54:28: 5000000 INFO @ Fri, 16 Mar 2018 07:54:29: 5000000 INFO @ Fri, 16 Mar 2018 07:54:29: 5000000 INFO @ Fri, 16 Mar 2018 07:54:34: 6000000 INFO @ Fri, 16 Mar 2018 07:54:35: 6000000 INFO @ Fri, 16 Mar 2018 07:54:36: 6000000 INFO @ Fri, 16 Mar 2018 07:54:40: 7000000 INFO @ Fri, 16 Mar 2018 07:54:42: 7000000 INFO @ Fri, 16 Mar 2018 07:54:42: 7000000 INFO @ Fri, 16 Mar 2018 07:54:46: 8000000 INFO @ Fri, 16 Mar 2018 07:54:48: 8000000 INFO @ Fri, 16 Mar 2018 07:54:48: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:54:48: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:54:48: #1 total tags in treatment: 8484261 INFO @ Fri, 16 Mar 2018 07:54:48: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:54:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:54:49: #1 tags after filtering in treatment: 8484261 INFO @ Fri, 16 Mar 2018 07:54:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:54:49: #1 finished! INFO @ Fri, 16 Mar 2018 07:54:49: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:54:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:54:49: 8000000 INFO @ Fri, 16 Mar 2018 07:54:49: #2 number of paired peaks: 2592 INFO @ Fri, 16 Mar 2018 07:54:49: start model_add_line... INFO @ Fri, 16 Mar 2018 07:54:50: start X-correlation... INFO @ Fri, 16 Mar 2018 07:54:50: end of X-cor INFO @ Fri, 16 Mar 2018 07:54:50: #2 finished! INFO @ Fri, 16 Mar 2018 07:54:50: #2 predicted fragment length is 206 bps INFO @ Fri, 16 Mar 2018 07:54:50: #2 alternative fragment length(s) may be 206 bps INFO @ Fri, 16 Mar 2018 07:54:50: #2.2 Generate R script for model : SRX3068989.10_model.r INFO @ Fri, 16 Mar 2018 07:54:50: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:54:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:54:52: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:54:52: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:54:52: #1 total tags in treatment: 8484261 INFO @ Fri, 16 Mar 2018 07:54:52: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:54:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:54:52: #1 tags after filtering in treatment: 8484261 INFO @ Fri, 16 Mar 2018 07:54:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:54:52: #1 finished! INFO @ Fri, 16 Mar 2018 07:54:52: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:54:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:54:52: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:54:52: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:54:52: #1 total tags in treatment: 8484261 INFO @ Fri, 16 Mar 2018 07:54:52: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:54:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:54:52: #1 tags after filtering in treatment: 8484261 INFO @ Fri, 16 Mar 2018 07:54:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:54:52: #1 finished! INFO @ Fri, 16 Mar 2018 07:54:52: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:54:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:54:53: #2 number of paired peaks: 2592 INFO @ Fri, 16 Mar 2018 07:54:53: start model_add_line... INFO @ Fri, 16 Mar 2018 07:54:53: start X-correlation... INFO @ Fri, 16 Mar 2018 07:54:53: end of X-cor INFO @ Fri, 16 Mar 2018 07:54:53: #2 finished! INFO @ Fri, 16 Mar 2018 07:54:53: #2 predicted fragment length is 206 bps INFO @ Fri, 16 Mar 2018 07:54:53: #2 alternative fragment length(s) may be 206 bps INFO @ Fri, 16 Mar 2018 07:54:53: #2.2 Generate R script for model : SRX3068989.20_model.r INFO @ Fri, 16 Mar 2018 07:54:53: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:54:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:54:53: #2 number of paired peaks: 2592 INFO @ Fri, 16 Mar 2018 07:54:53: start model_add_line... INFO @ Fri, 16 Mar 2018 07:54:53: start X-correlation... INFO @ Fri, 16 Mar 2018 07:54:53: end of X-cor INFO @ Fri, 16 Mar 2018 07:54:53: #2 finished! INFO @ Fri, 16 Mar 2018 07:54:53: #2 predicted fragment length is 206 bps INFO @ Fri, 16 Mar 2018 07:54:53: #2 alternative fragment length(s) may be 206 bps INFO @ Fri, 16 Mar 2018 07:54:53: #2.2 Generate R script for model : SRX3068989.05_model.r INFO @ Fri, 16 Mar 2018 07:54:53: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:54:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:55:12: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:55:16: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:55:16: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:55:24: #4 Write output xls file... SRX3068989.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:55:24: #4 Write peak in narrowPeak format file... SRX3068989.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:55:24: #4 Write summits bed file... SRX3068989.10_summits.bed INFO @ Fri, 16 Mar 2018 07:55:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5546 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:55:27: #4 Write output xls file... SRX3068989.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:55:27: #4 Write peak in narrowPeak format file... SRX3068989.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:55:27: #4 Write summits bed file... SRX3068989.05_summits.bed INFO @ Fri, 16 Mar 2018 07:55:27: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8496 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:55:29: #4 Write output xls file... SRX3068989.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:55:29: #4 Write peak in narrowPeak format file... SRX3068989.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:55:29: #4 Write summits bed file... SRX3068989.20_summits.bed INFO @ Fri, 16 Mar 2018 07:55:29: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (3079 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。