Job ID = 9370017 sra ファイルのダウンロード中... Completed: 932654K bytes transferred in 19 seconds (400507K 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: PAIRED fastq に変換中... Written 7076912 spots for /home/okishinya/chipatlas/results/ce10/SRX2035133/SRR4044257.sra Written 7076912 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: 00:23:54 7076912 reads; of these: 7076912 (100.00%) were paired; of these: 1059124 (14.97%) aligned concordantly 0 times 5482438 (77.47%) aligned concordantly exactly 1 time 535350 (7.56%) aligned concordantly >1 times ---- 1059124 pairs aligned concordantly 0 times; of these: 485273 (45.82%) aligned discordantly 1 time ---- 573851 pairs aligned 0 times concordantly or discordantly; of these: 1147702 mates make up the pairs; of these: 980086 (85.40%) aligned 0 times 76774 (6.69%) aligned exactly 1 time 90842 (7.92%) aligned >1 times 93.08% overall alignment rate Time searching: 00:23:54 Overall time: 00:23:54 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 208537 / 6490648 = 0.0321 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 Aug 2017 12:26:47: # Command line: callpeak -t SRX2035133.bam -f BAM -g ce -n SRX2035133.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2035133.20 # format = BAM # ChIP-seq file = ['SRX2035133.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 Aug 2017 12:26:47: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:26:47: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:26:47: # Command line: callpeak -t SRX2035133.bam -f BAM -g ce -n SRX2035133.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2035133.10 # format = BAM # ChIP-seq file = ['SRX2035133.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 Aug 2017 12:26:47: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:26:47: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:26:47: # Command line: callpeak -t SRX2035133.bam -f BAM -g ce -n SRX2035133.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2035133.05 # format = BAM # ChIP-seq file = ['SRX2035133.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 Aug 2017 12:26:47: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:26:47: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:27:04: 1000000 INFO @ Fri, 04 Aug 2017 12:27:04: 1000000 INFO @ Fri, 04 Aug 2017 12:27:06: 1000000 INFO @ Fri, 04 Aug 2017 12:27:22: 2000000 INFO @ Fri, 04 Aug 2017 12:27:24: 2000000 INFO @ Fri, 04 Aug 2017 12:27:27: 2000000 INFO @ Fri, 04 Aug 2017 12:27:44: 3000000 INFO @ Fri, 04 Aug 2017 12:28:04: 3000000 INFO @ Fri, 04 Aug 2017 12:28:05: 3000000 INFO @ Fri, 04 Aug 2017 12:28:18: 4000000 INFO @ Fri, 04 Aug 2017 12:28:37: 4000000 INFO @ Fri, 04 Aug 2017 12:28:40: 4000000 INFO @ Fri, 04 Aug 2017 12:28:52: 5000000 INFO @ Fri, 04 Aug 2017 12:29:09: 5000000 INFO @ Fri, 04 Aug 2017 12:29:11: 5000000 INFO @ Fri, 04 Aug 2017 12:29:22: 6000000 INFO @ Fri, 04 Aug 2017 12:29:42: 6000000 INFO @ Fri, 04 Aug 2017 12:29:46: 6000000 INFO @ Fri, 04 Aug 2017 12:29:48: 7000000 INFO @ Fri, 04 Aug 2017 12:30:16: 7000000 INFO @ Fri, 04 Aug 2017 12:30:22: 8000000 INFO @ Fri, 04 Aug 2017 12:30:23: 7000000 INFO @ Fri, 04 Aug 2017 12:30:41: 8000000 INFO @ Fri, 04 Aug 2017 12:30:49: 9000000 INFO @ Fri, 04 Aug 2017 12:30:55: 8000000 INFO @ Fri, 04 Aug 2017 12:31:07: 9000000 INFO @ Fri, 04 Aug 2017 12:31:21: 10000000 INFO @ Fri, 04 Aug 2017 12:31:24: 9000000 INFO @ Fri, 04 Aug 2017 12:31:32: 10000000 INFO @ Fri, 04 Aug 2017 12:31:53: 10000000 INFO @ Fri, 04 Aug 2017 12:31:57: 11000000 INFO @ Fri, 04 Aug 2017 12:31:57: 11000000 INFO @ Fri, 04 Aug 2017 12:32:20: 11000000 INFO @ Fri, 04 Aug 2017 12:32:20: 12000000 INFO @ Fri, 04 Aug 2017 12:32:29: 12000000 INFO @ Fri, 04 Aug 2017 12:32:45: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 12:32:45: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 12:32:45: #1 total tags in treatment: 5813931 INFO @ Fri, 04 Aug 2017 12:32:45: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:32:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 12:32:45: #1 tags after filtering in treatment: 5187024 INFO @ Fri, 04 Aug 2017 12:32:45: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 04 Aug 2017 12:32:45: #1 finished! INFO @ Fri, 04 Aug 2017 12:32:45: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:32:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:32:47: #2 number of paired peaks: 4875 INFO @ Fri, 04 Aug 2017 12:32:47: start model_add_line... INFO @ Fri, 04 Aug 2017 12:32:47: start X-correlation... INFO @ Fri, 04 Aug 2017 12:32:47: end of X-cor INFO @ Fri, 04 Aug 2017 12:32:47: #2 finished! INFO @ Fri, 04 Aug 2017 12:32:47: #2 predicted fragment length is 269 bps INFO @ Fri, 04 Aug 2017 12:32:47: #2 alternative fragment length(s) may be 269 bps INFO @ Fri, 04 Aug 2017 12:32:47: #2.2 Generate R script for model : SRX2035133.10_model.r INFO @ Fri, 04 Aug 2017 12:32:48: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:32:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:32:48: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 12:32:48: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 12:32:48: #1 total tags in treatment: 5813931 INFO @ Fri, 04 Aug 2017 12:32:48: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:32:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 12:32:48: #1 tags after filtering in treatment: 5187024 INFO @ Fri, 04 Aug 2017 12:32:48: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 04 Aug 2017 12:32:48: #1 finished! INFO @ Fri, 04 Aug 2017 12:32:48: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:32:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:32:50: 12000000 INFO @ Fri, 04 Aug 2017 12:32:51: #2 number of paired peaks: 4875 INFO @ Fri, 04 Aug 2017 12:32:51: start model_add_line... INFO @ Fri, 04 Aug 2017 12:32:51: start X-correlation... INFO @ Fri, 04 Aug 2017 12:32:51: end of X-cor INFO @ Fri, 04 Aug 2017 12:32:51: #2 finished! INFO @ Fri, 04 Aug 2017 12:32:51: #2 predicted fragment length is 269 bps INFO @ Fri, 04 Aug 2017 12:32:51: #2 alternative fragment length(s) may be 269 bps INFO @ Fri, 04 Aug 2017 12:32:51: #2.2 Generate R script for model : SRX2035133.20_model.r INFO @ Fri, 04 Aug 2017 12:32:51: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:32:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:33:13: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 12:33:13: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 12:33:13: #1 total tags in treatment: 5813931 INFO @ Fri, 04 Aug 2017 12:33:13: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:33:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 12:33:13: #1 tags after filtering in treatment: 5187024 INFO @ Fri, 04 Aug 2017 12:33:13: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 04 Aug 2017 12:33:13: #1 finished! INFO @ Fri, 04 Aug 2017 12:33:13: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:33:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:33:15: #2 number of paired peaks: 4875 INFO @ Fri, 04 Aug 2017 12:33:15: start model_add_line... INFO @ Fri, 04 Aug 2017 12:33:15: start X-correlation... INFO @ Fri, 04 Aug 2017 12:33:15: end of X-cor INFO @ Fri, 04 Aug 2017 12:33:15: #2 finished! INFO @ Fri, 04 Aug 2017 12:33:15: #2 predicted fragment length is 269 bps INFO @ Fri, 04 Aug 2017 12:33:15: #2 alternative fragment length(s) may be 269 bps INFO @ Fri, 04 Aug 2017 12:33:15: #2.2 Generate R script for model : SRX2035133.05_model.r INFO @ Fri, 04 Aug 2017 12:33:15: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:33:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:33:31: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:33:32: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:33:46: #4 Write output xls file... SRX2035133.20_peaks.xls INFO @ Fri, 04 Aug 2017 12:33:46: #4 Write peak in narrowPeak format file... SRX2035133.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:33:46: #4 Write summits bed file... SRX2035133.20_summits.bed INFO @ Fri, 04 Aug 2017 12:33:46: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2699 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 12:33:48: #4 Write output xls file... SRX2035133.10_peaks.xls INFO @ Fri, 04 Aug 2017 12:33:48: #4 Write peak in narrowPeak format file... SRX2035133.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:33:48: #4 Write summits bed file... SRX2035133.10_summits.bed INFO @ Fri, 04 Aug 2017 12:33:48: Done! pass1 - making usageList (6 chroms): 14 millis pass2 - checking and writing primary data (3483 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 12:33:58: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:34:14: #4 Write output xls file... SRX2035133.05_peaks.xls INFO @ Fri, 04 Aug 2017 12:34:14: #4 Write peak in narrowPeak format file... SRX2035133.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:34:14: #4 Write summits bed file... SRX2035133.05_summits.bed INFO @ Fri, 04 Aug 2017 12:34:14: Done! pass1 - making usageList (6 chroms): 8 millis pass2 - checking and writing primary data (4389 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。