Job ID = 10480693 sra ファイルのダウンロード中... Completed: 331570K bytes transferred in 27 seconds (99725K 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 10743895 spots for /home/okishinya/chipatlas/results/dm3/SRX3068964/SRR5907440.sra Written 10743895 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:50 10743895 reads; of these: 10743895 (100.00%) were unpaired; of these: 1854988 (17.27%) aligned 0 times 7838117 (72.95%) aligned exactly 1 time 1050790 (9.78%) aligned >1 times 82.73% overall alignment rate Time searching: 00:02:51 Overall time: 00:02:51 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_rmdupse_core] 2807233 / 8888907 = 0.3158 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 07:43:05: # Command line: callpeak -t SRX3068964.bam -f BAM -g dm -n SRX3068964.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3068964.10 # format = BAM # ChIP-seq file = ['SRX3068964.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 07:43:05: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:43:05: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:43:05: # Command line: callpeak -t SRX3068964.bam -f BAM -g dm -n SRX3068964.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3068964.20 # format = BAM # ChIP-seq file = ['SRX3068964.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 07:43:05: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:43:05: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:43:05: # Command line: callpeak -t SRX3068964.bam -f BAM -g dm -n SRX3068964.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3068964.05 # format = BAM # ChIP-seq file = ['SRX3068964.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 07:43:05: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:43:05: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:43:11: 1000000 INFO @ Fri, 16 Mar 2018 07:43:12: 1000000 INFO @ Fri, 16 Mar 2018 07:43:12: 1000000 INFO @ Fri, 16 Mar 2018 07:43:18: 2000000 INFO @ Fri, 16 Mar 2018 07:43:18: 2000000 INFO @ Fri, 16 Mar 2018 07:43:19: 2000000 INFO @ Fri, 16 Mar 2018 07:43:25: 3000000 INFO @ Fri, 16 Mar 2018 07:43:25: 3000000 INFO @ Fri, 16 Mar 2018 07:43:25: 3000000 INFO @ Fri, 16 Mar 2018 07:43:32: 4000000 INFO @ Fri, 16 Mar 2018 07:43:32: 4000000 INFO @ Fri, 16 Mar 2018 07:43:32: 4000000 INFO @ Fri, 16 Mar 2018 07:43:38: 5000000 INFO @ Fri, 16 Mar 2018 07:43:39: 5000000 INFO @ Fri, 16 Mar 2018 07:43:39: 5000000 INFO @ Fri, 16 Mar 2018 07:43:45: 6000000 INFO @ Fri, 16 Mar 2018 07:43:46: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:43:46: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:43:46: #1 total tags in treatment: 6081674 INFO @ Fri, 16 Mar 2018 07:43:46: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:43:46: #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 07:43:46: 6000000 INFO @ Fri, 16 Mar 2018 07:43:46: #1 tags after filtering in treatment: 6081674 INFO @ Fri, 16 Mar 2018 07:43:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:43:46: #1 finished! INFO @ Fri, 16 Mar 2018 07:43:46: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:43:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:43:46: 6000000 INFO @ Fri, 16 Mar 2018 07:43:46: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:43:46: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:43:46: #1 total tags in treatment: 6081674 INFO @ Fri, 16 Mar 2018 07:43:46: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:43:46: #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 07:43:46: #1 tags after filtering in treatment: 6081674 INFO @ Fri, 16 Mar 2018 07:43:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:43:46: #1 finished! INFO @ Fri, 16 Mar 2018 07:43:46: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:43:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:43:46: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:43:46: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:43:46: #1 total tags in treatment: 6081674 INFO @ Fri, 16 Mar 2018 07:43:46: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:43:46: #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 07:43:46: #2 number of paired peaks: 2726 INFO @ Fri, 16 Mar 2018 07:43:46: start model_add_line... INFO @ Fri, 16 Mar 2018 07:43:46: start X-correlation... INFO @ Fri, 16 Mar 2018 07:43:46: end of X-cor INFO @ Fri, 16 Mar 2018 07:43:46: #2 finished! INFO @ Fri, 16 Mar 2018 07:43:46: #2 predicted fragment length is 167 bps INFO @ Fri, 16 Mar 2018 07:43:46: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 16 Mar 2018 07:43:46: #2.2 Generate R script for model : SRX3068964.20_model.r INFO @ Fri, 16 Mar 2018 07:43:46: #1 tags after filtering in treatment: 6081674 INFO @ Fri, 16 Mar 2018 07:43:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:43:46: #1 finished! INFO @ Fri, 16 Mar 2018 07:43:46: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:43:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:43:46: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:43:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:43:47: #2 number of paired peaks: 2726 INFO @ Fri, 16 Mar 2018 07:43:47: start model_add_line... INFO @ Fri, 16 Mar 2018 07:43:47: start X-correlation... INFO @ Fri, 16 Mar 2018 07:43:47: end of X-cor INFO @ Fri, 16 Mar 2018 07:43:47: #2 finished! INFO @ Fri, 16 Mar 2018 07:43:47: #2 predicted fragment length is 167 bps INFO @ Fri, 16 Mar 2018 07:43:47: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 16 Mar 2018 07:43:47: #2.2 Generate R script for model : SRX3068964.10_model.r INFO @ Fri, 16 Mar 2018 07:43:47: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:43:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:43:47: #2 number of paired peaks: 2726 INFO @ Fri, 16 Mar 2018 07:43:47: start model_add_line... INFO @ Fri, 16 Mar 2018 07:43:47: start X-correlation... INFO @ Fri, 16 Mar 2018 07:43:47: end of X-cor INFO @ Fri, 16 Mar 2018 07:43:47: #2 finished! INFO @ Fri, 16 Mar 2018 07:43:47: #2 predicted fragment length is 167 bps INFO @ Fri, 16 Mar 2018 07:43:47: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 16 Mar 2018 07:43:47: #2.2 Generate R script for model : SRX3068964.05_model.r INFO @ Fri, 16 Mar 2018 07:43:47: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:43:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:44:01: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:44:02: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:44:02: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:44:09: #4 Write output xls file... SRX3068964.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:44:09: #4 Write peak in narrowPeak format file... SRX3068964.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:44:09: #4 Write summits bed file... SRX3068964.20_summits.bed INFO @ Fri, 16 Mar 2018 07:44:09: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2682 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:44:11: #4 Write output xls file... SRX3068964.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:44:11: #4 Write peak in narrowPeak format file... SRX3068964.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:44:11: #4 Write summits bed file... SRX3068964.10_summits.bed INFO @ Fri, 16 Mar 2018 07:44:11: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5919 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:44:11: #4 Write output xls file... SRX3068964.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:44:11: #4 Write peak in narrowPeak format file... SRX3068964.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:44:11: #4 Write summits bed file... SRX3068964.05_summits.bed INFO @ Fri, 16 Mar 2018 07:44:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9258 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。