Job ID = 10609055 sra ファイルのダウンロード中... Completed: 235746K bytes transferred in 6 seconds (288410K 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... Read 23888948 spots for /home/okishinya/chipatlas/results/ce10/SRX2202782/SRR4319288.sra Written 23888948 spots for /home/okishinya/chipatlas/results/ce10/SRX2202782/SRR4319288.sra 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: 00:05:07 23888948 reads; of these: 23888948 (100.00%) were unpaired; of these: 1448277 (6.06%) aligned 0 times 17464316 (73.11%) aligned exactly 1 time 4976355 (20.83%) aligned >1 times 93.94% overall alignment rate Time searching: 00:05:07 Overall time: 00:05:07 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 12 files... [bam_rmdupse_core] 4897030 / 22440671 = 0.2182 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, 04 May 2018 07:13:28: # Command line: callpeak -t SRX2202782.bam -f BAM -g ce -n SRX2202782.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202782.05 # format = BAM # ChIP-seq file = ['SRX2202782.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 @ Fri, 04 May 2018 07:13:28: #1 read tag files... INFO @ Fri, 04 May 2018 07:13:28: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:13:28: # Command line: callpeak -t SRX2202782.bam -f BAM -g ce -n SRX2202782.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202782.20 # format = BAM # ChIP-seq file = ['SRX2202782.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 @ Fri, 04 May 2018 07:13:28: #1 read tag files... INFO @ Fri, 04 May 2018 07:13:28: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:13:28: # Command line: callpeak -t SRX2202782.bam -f BAM -g ce -n SRX2202782.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202782.10 # format = BAM # ChIP-seq file = ['SRX2202782.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 @ Fri, 04 May 2018 07:13:28: #1 read tag files... INFO @ Fri, 04 May 2018 07:13:28: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:13:34: 1000000 INFO @ Fri, 04 May 2018 07:13:34: 1000000 INFO @ Fri, 04 May 2018 07:13:34: 1000000 INFO @ Fri, 04 May 2018 07:13:41: 2000000 INFO @ Fri, 04 May 2018 07:13:41: 2000000 INFO @ Fri, 04 May 2018 07:13:41: 2000000 INFO @ Fri, 04 May 2018 07:13:47: 3000000 INFO @ Fri, 04 May 2018 07:13:47: 3000000 INFO @ Fri, 04 May 2018 07:13:47: 3000000 INFO @ Fri, 04 May 2018 07:13:53: 4000000 INFO @ Fri, 04 May 2018 07:13:54: 4000000 INFO @ Fri, 04 May 2018 07:13:54: 4000000 INFO @ Fri, 04 May 2018 07:13:59: 5000000 INFO @ Fri, 04 May 2018 07:14:00: 5000000 INFO @ Fri, 04 May 2018 07:14:00: 5000000 INFO @ Fri, 04 May 2018 07:14:06: 6000000 INFO @ Fri, 04 May 2018 07:14:07: 6000000 INFO @ Fri, 04 May 2018 07:14:07: 6000000 INFO @ Fri, 04 May 2018 07:14:12: 7000000 INFO @ Fri, 04 May 2018 07:14:13: 7000000 INFO @ Fri, 04 May 2018 07:14:13: 7000000 INFO @ Fri, 04 May 2018 07:14:18: 8000000 INFO @ Fri, 04 May 2018 07:14:20: 8000000 INFO @ Fri, 04 May 2018 07:14:20: 8000000 INFO @ Fri, 04 May 2018 07:14:25: 9000000 INFO @ Fri, 04 May 2018 07:14:26: 9000000 INFO @ Fri, 04 May 2018 07:14:27: 9000000 INFO @ Fri, 04 May 2018 07:14:31: 10000000 INFO @ Fri, 04 May 2018 07:14:32: 10000000 INFO @ Fri, 04 May 2018 07:14:34: 10000000 INFO @ Fri, 04 May 2018 07:14:38: 11000000 INFO @ Fri, 04 May 2018 07:14:39: 11000000 INFO @ Fri, 04 May 2018 07:14:40: 11000000 INFO @ Fri, 04 May 2018 07:14:45: 12000000 INFO @ Fri, 04 May 2018 07:14:46: 12000000 INFO @ Fri, 04 May 2018 07:14:46: 12000000 INFO @ Fri, 04 May 2018 07:14:52: 13000000 INFO @ Fri, 04 May 2018 07:14:52: 13000000 INFO @ Fri, 04 May 2018 07:14:53: 13000000 INFO @ Fri, 04 May 2018 07:14:58: 14000000 INFO @ Fri, 04 May 2018 07:14:59: 14000000 INFO @ Fri, 04 May 2018 07:14:59: 14000000 INFO @ Fri, 04 May 2018 07:15:05: 15000000 INFO @ Fri, 04 May 2018 07:15:05: 15000000 INFO @ Fri, 04 May 2018 07:15:05: 15000000 INFO @ Fri, 04 May 2018 07:15:12: 16000000 INFO @ Fri, 04 May 2018 07:15:12: 16000000 INFO @ Fri, 04 May 2018 07:15:12: 16000000 INFO @ Fri, 04 May 2018 07:15:18: 17000000 INFO @ Fri, 04 May 2018 07:15:18: 17000000 INFO @ Fri, 04 May 2018 07:15:18: 17000000 INFO @ Fri, 04 May 2018 07:15:22: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:15:22: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:15:22: #1 total tags in treatment: 17543641 INFO @ Fri, 04 May 2018 07:15:22: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:15:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:15:22: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:15:22: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:15:22: #1 total tags in treatment: 17543641 INFO @ Fri, 04 May 2018 07:15:22: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:15:22: #1 tag size is determined as 51 bps INFO @ Fri, 04 May 2018 07:15:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:15:22: #1 tag size = 51 INFO @ Fri, 04 May 2018 07:15:22: #1 total tags in treatment: 17543641 INFO @ Fri, 04 May 2018 07:15:22: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:15:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:15:22: #1 tags after filtering in treatment: 17543641 INFO @ Fri, 04 May 2018 07:15:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:15:22: #1 finished! INFO @ Fri, 04 May 2018 07:15:22: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:15:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:15:22: #1 tags after filtering in treatment: 17543641 INFO @ Fri, 04 May 2018 07:15:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:15:22: #1 finished! INFO @ Fri, 04 May 2018 07:15:22: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:15:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:15:22: #1 tags after filtering in treatment: 17543641 INFO @ Fri, 04 May 2018 07:15:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:15:22: #1 finished! INFO @ Fri, 04 May 2018 07:15:22: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:15:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:15:24: #2 number of paired peaks: 913 WARNING @ Fri, 04 May 2018 07:15:24: Fewer paired peaks (913) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 913 pairs to build model! INFO @ Fri, 04 May 2018 07:15:24: start model_add_line... INFO @ Fri, 04 May 2018 07:15:24: #2 number of paired peaks: 913 WARNING @ Fri, 04 May 2018 07:15:24: Fewer paired peaks (913) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 913 pairs to build model! INFO @ Fri, 04 May 2018 07:15:24: start model_add_line... INFO @ Fri, 04 May 2018 07:15:24: #2 number of paired peaks: 913 WARNING @ Fri, 04 May 2018 07:15:24: Fewer paired peaks (913) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 913 pairs to build model! INFO @ Fri, 04 May 2018 07:15:24: start model_add_line... INFO @ Fri, 04 May 2018 07:15:24: start X-correlation... INFO @ Fri, 04 May 2018 07:15:24: end of X-cor INFO @ Fri, 04 May 2018 07:15:24: #2 finished! INFO @ Fri, 04 May 2018 07:15:24: #2 predicted fragment length is 108 bps INFO @ Fri, 04 May 2018 07:15:24: #2 alternative fragment length(s) may be 4,108 bps INFO @ Fri, 04 May 2018 07:15:24: #2.2 Generate R script for model : SRX2202782.20_model.r INFO @ Fri, 04 May 2018 07:15:24: #3 Call peaks... INFO @ Fri, 04 May 2018 07:15:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:15:24: start X-correlation... INFO @ Fri, 04 May 2018 07:15:24: end of X-cor INFO @ Fri, 04 May 2018 07:15:24: #2 finished! INFO @ Fri, 04 May 2018 07:15:24: #2 predicted fragment length is 108 bps INFO @ Fri, 04 May 2018 07:15:24: #2 alternative fragment length(s) may be 4,108 bps INFO @ Fri, 04 May 2018 07:15:24: #2.2 Generate R script for model : SRX2202782.05_model.r INFO @ Fri, 04 May 2018 07:15:24: #3 Call peaks... INFO @ Fri, 04 May 2018 07:15:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:15:24: start X-correlation... INFO @ Fri, 04 May 2018 07:15:24: end of X-cor INFO @ Fri, 04 May 2018 07:15:24: #2 finished! INFO @ Fri, 04 May 2018 07:15:24: #2 predicted fragment length is 108 bps INFO @ Fri, 04 May 2018 07:15:24: #2 alternative fragment length(s) may be 4,108 bps INFO @ Fri, 04 May 2018 07:15:24: #2.2 Generate R script for model : SRX2202782.10_model.r INFO @ Fri, 04 May 2018 07:15:24: #3 Call peaks... INFO @ Fri, 04 May 2018 07:15:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:16:03: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:16:04: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:16:05: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:16:24: #4 Write output xls file... SRX2202782.20_peaks.xls INFO @ Fri, 04 May 2018 07:16:24: #4 Write peak in narrowPeak format file... SRX2202782.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:16:24: #4 Write summits bed file... SRX2202782.20_summits.bed INFO @ Fri, 04 May 2018 07:16:24: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1837 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:16:24: #4 Write output xls file... SRX2202782.10_peaks.xls INFO @ Fri, 04 May 2018 07:16:24: #4 Write peak in narrowPeak format file... SRX2202782.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:16:24: #4 Write summits bed file... SRX2202782.10_summits.bed INFO @ Fri, 04 May 2018 07:16:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4790 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:16:27: #4 Write output xls file... SRX2202782.05_peaks.xls INFO @ Fri, 04 May 2018 07:16:28: #4 Write peak in narrowPeak format file... SRX2202782.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:16:28: #4 Write summits bed file... SRX2202782.05_summits.bed INFO @ Fri, 04 May 2018 07:16:28: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8968 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。