Job ID = 9156955 sra ファイルのダウンロード中... Completed: 188608K bytes transferred in 4 seconds (317471K 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 6196375 spots for /home/okishinya/chipatlas/results/ce10/SRX2228855/SRR4380311.sra Written 6196375 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: 00:01:56 6196375 reads; of these: 6196375 (100.00%) were unpaired; of these: 453040 (7.31%) aligned 0 times 4839568 (78.10%) aligned exactly 1 time 903767 (14.59%) aligned >1 times 92.69% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 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_rmdupse_core] 1528001 / 5743335 = 0.2660 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 10:30:51: # Command line: callpeak -t SRX2228855.bam -f BAM -g ce -n SRX2228855.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228855.10 # format = BAM # ChIP-seq file = ['SRX2228855.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 10:30:51: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:30:51: # Command line: callpeak -t SRX2228855.bam -f BAM -g ce -n SRX2228855.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228855.20 # format = BAM # ChIP-seq file = ['SRX2228855.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 10:30:51: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:30:51: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:30:51: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:30:51: # Command line: callpeak -t SRX2228855.bam -f BAM -g ce -n SRX2228855.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228855.05 # format = BAM # ChIP-seq file = ['SRX2228855.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 10:30:51: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:30:51: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:30:58: 1000000 INFO @ Tue, 27 Jun 2017 10:30:58: 1000000 INFO @ Tue, 27 Jun 2017 10:30:58: 1000000 INFO @ Tue, 27 Jun 2017 10:31:06: 2000000 INFO @ Tue, 27 Jun 2017 10:31:06: 2000000 INFO @ Tue, 27 Jun 2017 10:31:06: 2000000 INFO @ Tue, 27 Jun 2017 10:31:14: 3000000 INFO @ Tue, 27 Jun 2017 10:31:14: 3000000 INFO @ Tue, 27 Jun 2017 10:31:14: 3000000 INFO @ Tue, 27 Jun 2017 10:31:22: 4000000 INFO @ Tue, 27 Jun 2017 10:31:22: 4000000 INFO @ Tue, 27 Jun 2017 10:31:22: 4000000 INFO @ Tue, 27 Jun 2017 10:31:24: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:31:24: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:31:24: #1 total tags in treatment: 4215334 INFO @ Tue, 27 Jun 2017 10:31:24: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:31:24: #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 10:31:24: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:31:24: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:31:24: #1 total tags in treatment: 4215334 INFO @ Tue, 27 Jun 2017 10:31:24: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:31:24: #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 10:31:24: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:31:24: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:31:24: #1 total tags in treatment: 4215334 INFO @ Tue, 27 Jun 2017 10:31:24: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:31:24: #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 10:31:24: #1 tags after filtering in treatment: 4215334 INFO @ Tue, 27 Jun 2017 10:31:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:31:24: #1 finished! INFO @ Tue, 27 Jun 2017 10:31:24: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:31:24: #1 tags after filtering in treatment: 4215334 INFO @ Tue, 27 Jun 2017 10:31:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:31:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:31:24: #1 finished! INFO @ Tue, 27 Jun 2017 10:31:24: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:31:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:31:24: #1 tags after filtering in treatment: 4215334 INFO @ Tue, 27 Jun 2017 10:31:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:31:24: #1 finished! INFO @ Tue, 27 Jun 2017 10:31:24: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:31:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:31:24: #2 number of paired peaks: 706 WARNING @ Tue, 27 Jun 2017 10:31:24: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Tue, 27 Jun 2017 10:31:24: start model_add_line... INFO @ Tue, 27 Jun 2017 10:31:24: #2 number of paired peaks: 706 WARNING @ Tue, 27 Jun 2017 10:31:24: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Tue, 27 Jun 2017 10:31:24: start model_add_line... INFO @ Tue, 27 Jun 2017 10:31:24: #2 number of paired peaks: 706 WARNING @ Tue, 27 Jun 2017 10:31:24: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Tue, 27 Jun 2017 10:31:24: start model_add_line... INFO @ Tue, 27 Jun 2017 10:31:24: start X-correlation... INFO @ Tue, 27 Jun 2017 10:31:24: end of X-cor INFO @ Tue, 27 Jun 2017 10:31:24: #2 finished! INFO @ Tue, 27 Jun 2017 10:31:24: #2 predicted fragment length is 213 bps INFO @ Tue, 27 Jun 2017 10:31:24: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 27 Jun 2017 10:31:24: #2.2 Generate R script for model : SRX2228855.05_model.r INFO @ Tue, 27 Jun 2017 10:31:24: start X-correlation... INFO @ Tue, 27 Jun 2017 10:31:24: end of X-cor INFO @ Tue, 27 Jun 2017 10:31:24: #2 finished! INFO @ Tue, 27 Jun 2017 10:31:24: #2 predicted fragment length is 213 bps INFO @ Tue, 27 Jun 2017 10:31:24: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 27 Jun 2017 10:31:24: #2.2 Generate R script for model : SRX2228855.20_model.r INFO @ Tue, 27 Jun 2017 10:31:24: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:31:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:31:24: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:31:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:31:24: start X-correlation... INFO @ Tue, 27 Jun 2017 10:31:24: end of X-cor INFO @ Tue, 27 Jun 2017 10:31:24: #2 finished! INFO @ Tue, 27 Jun 2017 10:31:24: #2 predicted fragment length is 213 bps INFO @ Tue, 27 Jun 2017 10:31:24: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 27 Jun 2017 10:31:24: #2.2 Generate R script for model : SRX2228855.10_model.r INFO @ Tue, 27 Jun 2017 10:31:24: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:31:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:31:36: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:31:36: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:31:36: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:31:42: #4 Write output xls file... SRX2228855.20_peaks.xls INFO @ Tue, 27 Jun 2017 10:31:42: #4 Write peak in narrowPeak format file... SRX2228855.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:31:42: #4 Write summits bed file... SRX2228855.20_summits.bed INFO @ Tue, 27 Jun 2017 10:31:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (364 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:31:42: #4 Write output xls file... SRX2228855.05_peaks.xls INFO @ Tue, 27 Jun 2017 10:31:42: #4 Write peak in narrowPeak format file... SRX2228855.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:31:42: #4 Write summits bed file... SRX2228855.05_summits.bed INFO @ Tue, 27 Jun 2017 10:31:42: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1305 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:31:42: #4 Write output xls file... SRX2228855.10_peaks.xls INFO @ Tue, 27 Jun 2017 10:31:42: #4 Write peak in narrowPeak format file... SRX2228855.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:31:42: #4 Write summits bed file... SRX2228855.10_summits.bed INFO @ Tue, 27 Jun 2017 10:31:42: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (721 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。