Job ID = 9157548 sra ファイルのダウンロード中... Completed: 616869K bytes transferred in 7 seconds (696915K bits/sec), in 1 file, 2 directories. 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 18668481 spots for /home/okishinya/chipatlas/results/ce10/SRX257660/SRR800671.sra Written 18668481 spots total 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: 00:04:47 18668481 reads; of these: 18668481 (100.00%) were unpaired; of these: 696998 (3.73%) aligned 0 times 14977962 (80.23%) aligned exactly 1 time 2993521 (16.04%) aligned >1 times 96.27% overall alignment rate Time searching: 00:04:47 Overall time: 00:04:47 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 12306468 / 17971483 = 0.6848 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 @ Tue, 27 Jun 2017 12:19:27: # Command line: callpeak -t SRX257660.bam -f BAM -g ce -n SRX257660.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX257660.20 # format = BAM # ChIP-seq file = ['SRX257660.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 27 Jun 2017 12:19:27: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:19:27: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:19:27: # Command line: callpeak -t SRX257660.bam -f BAM -g ce -n SRX257660.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX257660.05 # format = BAM # ChIP-seq file = ['SRX257660.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 27 Jun 2017 12:19:27: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:19:27: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:19:27: # Command line: callpeak -t SRX257660.bam -f BAM -g ce -n SRX257660.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX257660.10 # format = BAM # ChIP-seq file = ['SRX257660.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 27 Jun 2017 12:19:27: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:19:27: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:19:34: 1000000 INFO @ Tue, 27 Jun 2017 12:19:34: 1000000 INFO @ Tue, 27 Jun 2017 12:19:34: 1000000 INFO @ Tue, 27 Jun 2017 12:19:41: 2000000 INFO @ Tue, 27 Jun 2017 12:19:41: 2000000 INFO @ Tue, 27 Jun 2017 12:19:41: 2000000 INFO @ Tue, 27 Jun 2017 12:19:48: 3000000 INFO @ Tue, 27 Jun 2017 12:19:48: 3000000 INFO @ Tue, 27 Jun 2017 12:19:48: 3000000 INFO @ Tue, 27 Jun 2017 12:19:55: 4000000 INFO @ Tue, 27 Jun 2017 12:19:55: 4000000 INFO @ Tue, 27 Jun 2017 12:19:55: 4000000 INFO @ Tue, 27 Jun 2017 12:20:01: 5000000 INFO @ Tue, 27 Jun 2017 12:20:02: 5000000 INFO @ Tue, 27 Jun 2017 12:20:02: 5000000 INFO @ Tue, 27 Jun 2017 12:20:06: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 12:20:06: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 12:20:06: #1 total tags in treatment: 5665015 INFO @ Tue, 27 Jun 2017 12:20:06: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:20:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 12:20:06: #1 tags after filtering in treatment: 5665015 INFO @ Tue, 27 Jun 2017 12:20:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:20:06: #1 finished! INFO @ Tue, 27 Jun 2017 12:20:06: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:20:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:20:06: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 12:20:06: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 12:20:06: #1 total tags in treatment: 5665015 INFO @ Tue, 27 Jun 2017 12:20:06: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:20:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 12:20:06: #1 tags after filtering in treatment: 5665015 INFO @ Tue, 27 Jun 2017 12:20:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:20:06: #1 finished! INFO @ Tue, 27 Jun 2017 12:20:06: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:20:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:20:06: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 12:20:06: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 12:20:06: #1 total tags in treatment: 5665015 INFO @ Tue, 27 Jun 2017 12:20:06: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:20:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 12:20:06: #2 number of paired peaks: 1037 INFO @ Tue, 27 Jun 2017 12:20:06: start model_add_line... INFO @ Tue, 27 Jun 2017 12:20:07: start X-correlation... INFO @ Tue, 27 Jun 2017 12:20:07: #1 tags after filtering in treatment: 5665015 INFO @ Tue, 27 Jun 2017 12:20:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:20:07: #1 finished! INFO @ Tue, 27 Jun 2017 12:20:07: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:20:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:20:07: end of X-cor INFO @ Tue, 27 Jun 2017 12:20:07: #2 finished! INFO @ Tue, 27 Jun 2017 12:20:07: #2 predicted fragment length is 132 bps INFO @ Tue, 27 Jun 2017 12:20:07: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 27 Jun 2017 12:20:07: #2.2 Generate R script for model : SRX257660.05_model.r INFO @ Tue, 27 Jun 2017 12:20:07: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:20:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:20:07: #2 number of paired peaks: 1037 INFO @ Tue, 27 Jun 2017 12:20:07: start model_add_line... INFO @ Tue, 27 Jun 2017 12:20:07: start X-correlation... INFO @ Tue, 27 Jun 2017 12:20:07: end of X-cor INFO @ Tue, 27 Jun 2017 12:20:07: #2 finished! INFO @ Tue, 27 Jun 2017 12:20:07: #2 predicted fragment length is 132 bps INFO @ Tue, 27 Jun 2017 12:20:07: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 27 Jun 2017 12:20:07: #2.2 Generate R script for model : SRX257660.20_model.r INFO @ Tue, 27 Jun 2017 12:20:07: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:20:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:20:07: #2 number of paired peaks: 1037 INFO @ Tue, 27 Jun 2017 12:20:07: start model_add_line... INFO @ Tue, 27 Jun 2017 12:20:07: start X-correlation... INFO @ Tue, 27 Jun 2017 12:20:07: end of X-cor INFO @ Tue, 27 Jun 2017 12:20:07: #2 finished! INFO @ Tue, 27 Jun 2017 12:20:07: #2 predicted fragment length is 132 bps INFO @ Tue, 27 Jun 2017 12:20:07: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 27 Jun 2017 12:20:07: #2.2 Generate R script for model : SRX257660.10_model.r INFO @ Tue, 27 Jun 2017 12:20:07: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:20:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:20:21: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:20:22: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:20:23: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:20:28: #4 Write output xls file... SRX257660.20_peaks.xls INFO @ Tue, 27 Jun 2017 12:20:28: #4 Write peak in narrowPeak format file... SRX257660.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:20:28: #4 Write summits bed file... SRX257660.20_summits.bed INFO @ Tue, 27 Jun 2017 12:20:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (649 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 12:20:30: #4 Write output xls file... SRX257660.05_peaks.xls INFO @ Tue, 27 Jun 2017 12:20:30: #4 Write peak in narrowPeak format file... SRX257660.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:20:30: #4 Write summits bed file... SRX257660.05_summits.bed INFO @ Tue, 27 Jun 2017 12:20:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1629 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 12:20:31: #4 Write output xls file... SRX257660.10_peaks.xls INFO @ Tue, 27 Jun 2017 12:20:31: #4 Write peak in narrowPeak format file... SRX257660.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:20:31: #4 Write summits bed file... SRX257660.10_summits.bed INFO @ Tue, 27 Jun 2017 12:20:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1054 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。