Job ID = 9156973 sra ファイルのダウンロード中... Completed: 585922K bytes transferred in 8 seconds (587024K 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 30487356 spots for /home/okishinya/chipatlas/results/ce10/SRX2228862/SRR4380318.sra Written 30487356 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: 00:00:01 Multiseed full-index search: 00:06:00 30487356 reads; of these: 30487356 (100.00%) were unpaired; of these: 2947823 (9.67%) aligned 0 times 22650155 (74.29%) aligned exactly 1 time 4889378 (16.04%) aligned >1 times 90.33% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 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] 22062562 / 27539533 = 0.8011 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 10:45:19: # Command line: callpeak -t SRX2228862.bam -f BAM -g ce -n SRX2228862.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228862.20 # format = BAM # ChIP-seq file = ['SRX2228862.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 10:45:19: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:45:19: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:45:19: # Command line: callpeak -t SRX2228862.bam -f BAM -g ce -n SRX2228862.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228862.10 # format = BAM # ChIP-seq file = ['SRX2228862.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 10:45:19: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:45:19: # Command line: callpeak -t SRX2228862.bam -f BAM -g ce -n SRX2228862.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228862.05 # format = BAM # ChIP-seq file = ['SRX2228862.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 10:45:19: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:45:19: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:45:19: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:45:27: 1000000 INFO @ Tue, 27 Jun 2017 10:45:27: 1000000 INFO @ Tue, 27 Jun 2017 10:45:27: 1000000 INFO @ Tue, 27 Jun 2017 10:45:36: 2000000 INFO @ Tue, 27 Jun 2017 10:45:36: 2000000 INFO @ Tue, 27 Jun 2017 10:45:36: 2000000 INFO @ Tue, 27 Jun 2017 10:45:44: 3000000 INFO @ Tue, 27 Jun 2017 10:45:44: 3000000 INFO @ Tue, 27 Jun 2017 10:45:44: 3000000 INFO @ Tue, 27 Jun 2017 10:45:52: 4000000 INFO @ Tue, 27 Jun 2017 10:45:52: 4000000 INFO @ Tue, 27 Jun 2017 10:45:53: 4000000 INFO @ Tue, 27 Jun 2017 10:46:00: 5000000 INFO @ Tue, 27 Jun 2017 10:46:00: 5000000 INFO @ Tue, 27 Jun 2017 10:46:02: 5000000 INFO @ Tue, 27 Jun 2017 10:46:04: #1 tag size is determined as 35 bps INFO @ Tue, 27 Jun 2017 10:46:04: #1 tag size is determined as 35 bps INFO @ Tue, 27 Jun 2017 10:46:04: #1 tag size = 35 INFO @ Tue, 27 Jun 2017 10:46:04: #1 tag size = 35 INFO @ Tue, 27 Jun 2017 10:46:04: #1 total tags in treatment: 5476971 INFO @ Tue, 27 Jun 2017 10:46:04: #1 total tags in treatment: 5476971 INFO @ Tue, 27 Jun 2017 10:46:04: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:46:04: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:46:04: #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 10:46:04: #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 10:46:04: #1 tags after filtering in treatment: 5476971 INFO @ Tue, 27 Jun 2017 10:46:04: #1 tags after filtering in treatment: 5476971 INFO @ Tue, 27 Jun 2017 10:46:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:46:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:46:04: #1 finished! INFO @ Tue, 27 Jun 2017 10:46:04: #1 finished! INFO @ Tue, 27 Jun 2017 10:46:04: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:46:04: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:46:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:46:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:46:04: #2 number of paired peaks: 1307 INFO @ Tue, 27 Jun 2017 10:46:04: start model_add_line... INFO @ Tue, 27 Jun 2017 10:46:04: #2 number of paired peaks: 1307 INFO @ Tue, 27 Jun 2017 10:46:04: start model_add_line... INFO @ Tue, 27 Jun 2017 10:46:05: start X-correlation... INFO @ Tue, 27 Jun 2017 10:46:05: start X-correlation... INFO @ Tue, 27 Jun 2017 10:46:05: end of X-cor INFO @ Tue, 27 Jun 2017 10:46:05: #2 finished! INFO @ Tue, 27 Jun 2017 10:46:05: #2 predicted fragment length is 113 bps INFO @ Tue, 27 Jun 2017 10:46:05: #2 alternative fragment length(s) may be 4,113 bps INFO @ Tue, 27 Jun 2017 10:46:05: #2.2 Generate R script for model : SRX2228862.05_model.r INFO @ Tue, 27 Jun 2017 10:46:05: end of X-cor INFO @ Tue, 27 Jun 2017 10:46:05: #2 finished! INFO @ Tue, 27 Jun 2017 10:46:05: #2 predicted fragment length is 113 bps INFO @ Tue, 27 Jun 2017 10:46:05: #2 alternative fragment length(s) may be 4,113 bps INFO @ Tue, 27 Jun 2017 10:46:05: #2.2 Generate R script for model : SRX2228862.10_model.r INFO @ Tue, 27 Jun 2017 10:46:05: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:46:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:46:05: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:46:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:46:06: #1 tag size is determined as 35 bps INFO @ Tue, 27 Jun 2017 10:46:06: #1 tag size = 35 INFO @ Tue, 27 Jun 2017 10:46:06: #1 total tags in treatment: 5476971 INFO @ Tue, 27 Jun 2017 10:46:06: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:46:06: #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 10:46:06: #1 tags after filtering in treatment: 5476971 INFO @ Tue, 27 Jun 2017 10:46:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:46:06: #1 finished! INFO @ Tue, 27 Jun 2017 10:46:06: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:46:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:46:06: #2 number of paired peaks: 1307 INFO @ Tue, 27 Jun 2017 10:46:06: start model_add_line... INFO @ Tue, 27 Jun 2017 10:46:07: start X-correlation... INFO @ Tue, 27 Jun 2017 10:46:07: end of X-cor INFO @ Tue, 27 Jun 2017 10:46:07: #2 finished! INFO @ Tue, 27 Jun 2017 10:46:07: #2 predicted fragment length is 113 bps INFO @ Tue, 27 Jun 2017 10:46:07: #2 alternative fragment length(s) may be 4,113 bps INFO @ Tue, 27 Jun 2017 10:46:07: #2.2 Generate R script for model : SRX2228862.20_model.r INFO @ Tue, 27 Jun 2017 10:46:07: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:46:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:46:19: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:46:21: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:46:21: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:46:27: #4 Write output xls file... SRX2228862.05_peaks.xls INFO @ Tue, 27 Jun 2017 10:46:27: #4 Write peak in narrowPeak format file... SRX2228862.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:46:27: #4 Write summits bed file... SRX2228862.05_summits.bed INFO @ Tue, 27 Jun 2017 10:46:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2119 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:46:28: #4 Write output xls file... SRX2228862.20_peaks.xls INFO @ Tue, 27 Jun 2017 10:46:29: #4 Write peak in narrowPeak format file... SRX2228862.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:46:29: #4 Write summits bed file... SRX2228862.20_summits.bed INFO @ Tue, 27 Jun 2017 10:46:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (592 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:46:29: #4 Write output xls file... SRX2228862.10_peaks.xls INFO @ Tue, 27 Jun 2017 10:46:29: #4 Write peak in narrowPeak format file... SRX2228862.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:46:29: #4 Write summits bed file... SRX2228862.10_summits.bed INFO @ Tue, 27 Jun 2017 10:46:29: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1093 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。