Job ID = 10714403 sra ファイルのダウンロード中... Completed: 407451K bytes transferred in 10 seconds (306623K 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 18559199 spots for /home/okishinya/chipatlas/results/ce10/SRX4082363/SRR7164181.sra Written 18559199 spots for /home/okishinya/chipatlas/results/ce10/SRX4082363/SRR7164181.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: 00:04:37 18559199 reads; of these: 18559199 (100.00%) were unpaired; of these: 249194 (1.34%) aligned 0 times 16386751 (88.29%) aligned exactly 1 time 1923254 (10.36%) aligned >1 times 98.66% overall alignment rate Time searching: 00:04:37 Overall time: 00:04:37 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] 3475174 / 18310005 = 0.1898 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 @ Sun, 03 Jun 2018 12:39:08: # Command line: callpeak -t SRX4082363.bam -f BAM -g ce -n SRX4082363.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082363.05 # format = BAM # ChIP-seq file = ['SRX4082363.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 @ Sun, 03 Jun 2018 12:39:08: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:39:08: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:39:08: # Command line: callpeak -t SRX4082363.bam -f BAM -g ce -n SRX4082363.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082363.20 # format = BAM # ChIP-seq file = ['SRX4082363.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 @ Sun, 03 Jun 2018 12:39:08: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:39:08: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:39:08: # Command line: callpeak -t SRX4082363.bam -f BAM -g ce -n SRX4082363.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082363.10 # format = BAM # ChIP-seq file = ['SRX4082363.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 @ Sun, 03 Jun 2018 12:39:08: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:39:08: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:39:15: 1000000 INFO @ Sun, 03 Jun 2018 12:39:15: 1000000 INFO @ Sun, 03 Jun 2018 12:39:16: 1000000 INFO @ Sun, 03 Jun 2018 12:39:21: 2000000 INFO @ Sun, 03 Jun 2018 12:39:21: 2000000 INFO @ Sun, 03 Jun 2018 12:39:23: 2000000 INFO @ Sun, 03 Jun 2018 12:39:28: 3000000 INFO @ Sun, 03 Jun 2018 12:39:28: 3000000 INFO @ Sun, 03 Jun 2018 12:39:30: 3000000 INFO @ Sun, 03 Jun 2018 12:39:34: 4000000 INFO @ Sun, 03 Jun 2018 12:39:34: 4000000 INFO @ Sun, 03 Jun 2018 12:39:37: 4000000 INFO @ Sun, 03 Jun 2018 12:39:41: 5000000 INFO @ Sun, 03 Jun 2018 12:39:41: 5000000 INFO @ Sun, 03 Jun 2018 12:39:45: 5000000 INFO @ Sun, 03 Jun 2018 12:39:47: 6000000 INFO @ Sun, 03 Jun 2018 12:39:47: 6000000 INFO @ Sun, 03 Jun 2018 12:39:52: 6000000 INFO @ Sun, 03 Jun 2018 12:39:54: 7000000 INFO @ Sun, 03 Jun 2018 12:39:54: 7000000 INFO @ Sun, 03 Jun 2018 12:40:00: 7000000 INFO @ Sun, 03 Jun 2018 12:40:00: 8000000 INFO @ Sun, 03 Jun 2018 12:40:00: 8000000 INFO @ Sun, 03 Jun 2018 12:40:07: 9000000 INFO @ Sun, 03 Jun 2018 12:40:07: 8000000 INFO @ Sun, 03 Jun 2018 12:40:07: 9000000 INFO @ Sun, 03 Jun 2018 12:40:13: 10000000 INFO @ Sun, 03 Jun 2018 12:40:13: 10000000 INFO @ Sun, 03 Jun 2018 12:40:14: 9000000 INFO @ Sun, 03 Jun 2018 12:40:20: 11000000 INFO @ Sun, 03 Jun 2018 12:40:20: 11000000 INFO @ Sun, 03 Jun 2018 12:40:21: 10000000 INFO @ Sun, 03 Jun 2018 12:40:26: 12000000 INFO @ Sun, 03 Jun 2018 12:40:27: 12000000 INFO @ Sun, 03 Jun 2018 12:40:28: 11000000 INFO @ Sun, 03 Jun 2018 12:40:33: 13000000 INFO @ Sun, 03 Jun 2018 12:40:33: 13000000 INFO @ Sun, 03 Jun 2018 12:40:35: 12000000 INFO @ Sun, 03 Jun 2018 12:40:40: 14000000 INFO @ Sun, 03 Jun 2018 12:40:40: 14000000 INFO @ Sun, 03 Jun 2018 12:40:42: 13000000 INFO @ Sun, 03 Jun 2018 12:40:46: #1 tag size is determined as 49 bps INFO @ Sun, 03 Jun 2018 12:40:46: #1 tag size = 49 INFO @ Sun, 03 Jun 2018 12:40:46: #1 total tags in treatment: 14834831 INFO @ Sun, 03 Jun 2018 12:40:46: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:40:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:40:46: #1 tag size is determined as 49 bps INFO @ Sun, 03 Jun 2018 12:40:46: #1 tag size = 49 INFO @ Sun, 03 Jun 2018 12:40:46: #1 total tags in treatment: 14834831 INFO @ Sun, 03 Jun 2018 12:40:46: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:40:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:40:46: #1 tags after filtering in treatment: 14834831 INFO @ Sun, 03 Jun 2018 12:40:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:40:46: #1 finished! INFO @ Sun, 03 Jun 2018 12:40:46: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:40:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:40:46: #1 tags after filtering in treatment: 14834831 INFO @ Sun, 03 Jun 2018 12:40:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:40:46: #1 finished! INFO @ Sun, 03 Jun 2018 12:40:46: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:40:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:40:47: #2 number of paired peaks: 2539 INFO @ Sun, 03 Jun 2018 12:40:47: start model_add_line... INFO @ Sun, 03 Jun 2018 12:40:47: #2 number of paired peaks: 2539 INFO @ Sun, 03 Jun 2018 12:40:47: start model_add_line... INFO @ Sun, 03 Jun 2018 12:40:47: start X-correlation... INFO @ Sun, 03 Jun 2018 12:40:47: end of X-cor INFO @ Sun, 03 Jun 2018 12:40:47: #2 finished! INFO @ Sun, 03 Jun 2018 12:40:47: #2 predicted fragment length is 156 bps INFO @ Sun, 03 Jun 2018 12:40:47: #2 alternative fragment length(s) may be 3,156 bps INFO @ Sun, 03 Jun 2018 12:40:47: #2.2 Generate R script for model : SRX4082363.20_model.r INFO @ Sun, 03 Jun 2018 12:40:47: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:40:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:40:47: start X-correlation... INFO @ Sun, 03 Jun 2018 12:40:47: end of X-cor INFO @ Sun, 03 Jun 2018 12:40:47: #2 finished! INFO @ Sun, 03 Jun 2018 12:40:47: #2 predicted fragment length is 156 bps INFO @ Sun, 03 Jun 2018 12:40:47: #2 alternative fragment length(s) may be 3,156 bps INFO @ Sun, 03 Jun 2018 12:40:47: #2.2 Generate R script for model : SRX4082363.05_model.r INFO @ Sun, 03 Jun 2018 12:40:47: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:40:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:40:49: 14000000 INFO @ Sun, 03 Jun 2018 12:40:55: #1 tag size is determined as 49 bps INFO @ Sun, 03 Jun 2018 12:40:55: #1 tag size = 49 INFO @ Sun, 03 Jun 2018 12:40:55: #1 total tags in treatment: 14834831 INFO @ Sun, 03 Jun 2018 12:40:55: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:40:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:40:55: #1 tags after filtering in treatment: 14834831 INFO @ Sun, 03 Jun 2018 12:40:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:40:55: #1 finished! INFO @ Sun, 03 Jun 2018 12:40:55: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:40:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:40:56: #2 number of paired peaks: 2539 INFO @ Sun, 03 Jun 2018 12:40:56: start model_add_line... INFO @ Sun, 03 Jun 2018 12:40:56: start X-correlation... INFO @ Sun, 03 Jun 2018 12:40:56: end of X-cor INFO @ Sun, 03 Jun 2018 12:40:56: #2 finished! INFO @ Sun, 03 Jun 2018 12:40:56: #2 predicted fragment length is 156 bps INFO @ Sun, 03 Jun 2018 12:40:56: #2 alternative fragment length(s) may be 3,156 bps INFO @ Sun, 03 Jun 2018 12:40:56: #2.2 Generate R script for model : SRX4082363.10_model.r INFO @ Sun, 03 Jun 2018 12:40:56: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:40:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:41:27: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:41:27: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:41:35: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:41:45: #4 Write output xls file... SRX4082363.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:41:45: #4 Write peak in narrowPeak format file... SRX4082363.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:41:45: #4 Write summits bed file... SRX4082363.20_summits.bed INFO @ Sun, 03 Jun 2018 12:41:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2785 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:41:47: #4 Write output xls file... SRX4082363.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:41:47: #4 Write peak in narrowPeak format file... SRX4082363.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:41:47: #4 Write summits bed file... SRX4082363.05_summits.bed INFO @ Sun, 03 Jun 2018 12:41:47: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (10552 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:41:54: #4 Write output xls file... SRX4082363.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:41:54: #4 Write peak in narrowPeak format file... SRX4082363.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:41:54: #4 Write summits bed file... SRX4082363.10_summits.bed INFO @ Sun, 03 Jun 2018 12:41:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6934 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。