Job ID = 10608880 sra ファイルのダウンロード中... Completed: 599610K bytes transferred in 23 seconds (208265K 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... Written 21754381 spots for /home/okishinya/chipatlas/results/rn6/SRX3145018/SRR5989261.sra Written 21754381 spots total 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:14:22 21754381 reads; of these: 21754381 (100.00%) were unpaired; of these: 496247 (2.28%) aligned 0 times 17308480 (79.56%) aligned exactly 1 time 3949654 (18.16%) aligned >1 times 97.72% overall alignment rate Time searching: 00:14:25 Overall time: 00:14:25 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 983953 / 21258134 = 0.0463 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 @ Thu, 03 May 2018 22:40:38: # Command line: callpeak -t SRX3145018.bam -f BAM -g 2.15e9 -n SRX3145018.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3145018.05 # format = BAM # ChIP-seq file = ['SRX3145018.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Thu, 03 May 2018 22:40:38: #1 read tag files... INFO @ Thu, 03 May 2018 22:40:38: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:40:38: # Command line: callpeak -t SRX3145018.bam -f BAM -g 2.15e9 -n SRX3145018.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3145018.10 # format = BAM # ChIP-seq file = ['SRX3145018.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Thu, 03 May 2018 22:40:38: #1 read tag files... INFO @ Thu, 03 May 2018 22:40:38: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:40:38: # Command line: callpeak -t SRX3145018.bam -f BAM -g 2.15e9 -n SRX3145018.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3145018.20 # format = BAM # ChIP-seq file = ['SRX3145018.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Thu, 03 May 2018 22:40:38: #1 read tag files... INFO @ Thu, 03 May 2018 22:40:38: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:40:45: 1000000 INFO @ Thu, 03 May 2018 22:40:45: 1000000 INFO @ Thu, 03 May 2018 22:40:46: 1000000 INFO @ Thu, 03 May 2018 22:40:52: 2000000 INFO @ Thu, 03 May 2018 22:40:52: 2000000 INFO @ Thu, 03 May 2018 22:40:53: 2000000 INFO @ Thu, 03 May 2018 22:40:59: 3000000 INFO @ Thu, 03 May 2018 22:40:59: 3000000 INFO @ Thu, 03 May 2018 22:41:00: 3000000 INFO @ Thu, 03 May 2018 22:41:06: 4000000 INFO @ Thu, 03 May 2018 22:41:06: 4000000 INFO @ Thu, 03 May 2018 22:41:07: 4000000 INFO @ Thu, 03 May 2018 22:41:13: 5000000 INFO @ Thu, 03 May 2018 22:41:13: 5000000 INFO @ Thu, 03 May 2018 22:41:14: 5000000 INFO @ Thu, 03 May 2018 22:41:20: 6000000 INFO @ Thu, 03 May 2018 22:41:20: 6000000 INFO @ Thu, 03 May 2018 22:41:21: 6000000 INFO @ Thu, 03 May 2018 22:41:27: 7000000 INFO @ Thu, 03 May 2018 22:41:27: 7000000 INFO @ Thu, 03 May 2018 22:41:28: 7000000 INFO @ Thu, 03 May 2018 22:41:34: 8000000 INFO @ Thu, 03 May 2018 22:41:34: 8000000 INFO @ Thu, 03 May 2018 22:41:35: 8000000 INFO @ Thu, 03 May 2018 22:41:41: 9000000 INFO @ Thu, 03 May 2018 22:41:41: 9000000 INFO @ Thu, 03 May 2018 22:41:42: 9000000 INFO @ Thu, 03 May 2018 22:41:48: 10000000 INFO @ Thu, 03 May 2018 22:41:48: 10000000 INFO @ Thu, 03 May 2018 22:41:49: 10000000 INFO @ Thu, 03 May 2018 22:41:55: 11000000 INFO @ Thu, 03 May 2018 22:41:55: 11000000 INFO @ Thu, 03 May 2018 22:41:56: 11000000 INFO @ Thu, 03 May 2018 22:42:02: 12000000 INFO @ Thu, 03 May 2018 22:42:02: 12000000 INFO @ Thu, 03 May 2018 22:42:03: 12000000 INFO @ Thu, 03 May 2018 22:42:09: 13000000 INFO @ Thu, 03 May 2018 22:42:09: 13000000 INFO @ Thu, 03 May 2018 22:42:10: 13000000 INFO @ Thu, 03 May 2018 22:42:16: 14000000 INFO @ Thu, 03 May 2018 22:42:16: 14000000 INFO @ Thu, 03 May 2018 22:42:16: 14000000 INFO @ Thu, 03 May 2018 22:42:23: 15000000 INFO @ Thu, 03 May 2018 22:42:23: 15000000 INFO @ Thu, 03 May 2018 22:42:24: 15000000 INFO @ Thu, 03 May 2018 22:42:30: 16000000 INFO @ Thu, 03 May 2018 22:42:31: 16000000 INFO @ Thu, 03 May 2018 22:42:31: 16000000 INFO @ Thu, 03 May 2018 22:42:38: 17000000 INFO @ Thu, 03 May 2018 22:42:38: 17000000 INFO @ Thu, 03 May 2018 22:42:38: 17000000 INFO @ Thu, 03 May 2018 22:42:45: 18000000 INFO @ Thu, 03 May 2018 22:42:45: 18000000 INFO @ Thu, 03 May 2018 22:42:45: 18000000 INFO @ Thu, 03 May 2018 22:42:52: 19000000 INFO @ Thu, 03 May 2018 22:42:52: 19000000 INFO @ Thu, 03 May 2018 22:42:52: 19000000 INFO @ Thu, 03 May 2018 22:43:00: 20000000 INFO @ Thu, 03 May 2018 22:43:00: 20000000 INFO @ Thu, 03 May 2018 22:43:00: 20000000 INFO @ Thu, 03 May 2018 22:43:02: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:43:02: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:43:02: #1 total tags in treatment: 20274181 INFO @ Thu, 03 May 2018 22:43:02: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:43:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:43:02: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:43:02: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:43:02: #1 total tags in treatment: 20274181 INFO @ Thu, 03 May 2018 22:43:02: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:43:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:43:02: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:43:02: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:43:02: #1 total tags in treatment: 20274181 INFO @ Thu, 03 May 2018 22:43:02: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:43:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:43:02: #1 tags after filtering in treatment: 20273981 INFO @ Thu, 03 May 2018 22:43:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:43:02: #1 finished! INFO @ Thu, 03 May 2018 22:43:02: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:43:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:43:02: #1 tags after filtering in treatment: 20273981 INFO @ Thu, 03 May 2018 22:43:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:43:02: #1 finished! INFO @ Thu, 03 May 2018 22:43:02: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:43:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:43:03: #1 tags after filtering in treatment: 20273981 INFO @ Thu, 03 May 2018 22:43:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:43:03: #1 finished! INFO @ Thu, 03 May 2018 22:43:03: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:43:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:43:06: #2 number of paired peaks: 60579 INFO @ Thu, 03 May 2018 22:43:06: start model_add_line... INFO @ Thu, 03 May 2018 22:43:07: #2 number of paired peaks: 60579 INFO @ Thu, 03 May 2018 22:43:07: start model_add_line... INFO @ Thu, 03 May 2018 22:43:07: #2 number of paired peaks: 60579 INFO @ Thu, 03 May 2018 22:43:07: start model_add_line... INFO @ Thu, 03 May 2018 22:43:07: start X-correlation... INFO @ Thu, 03 May 2018 22:43:07: end of X-cor INFO @ Thu, 03 May 2018 22:43:07: #2 finished! INFO @ Thu, 03 May 2018 22:43:07: #2 predicted fragment length is 267 bps INFO @ Thu, 03 May 2018 22:43:07: #2 alternative fragment length(s) may be 267 bps INFO @ Thu, 03 May 2018 22:43:07: #2.2 Generate R script for model : SRX3145018.05_model.r INFO @ Thu, 03 May 2018 22:43:07: #3 Call peaks... INFO @ Thu, 03 May 2018 22:43:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:43:07: start X-correlation... INFO @ Thu, 03 May 2018 22:43:07: end of X-cor INFO @ Thu, 03 May 2018 22:43:07: #2 finished! INFO @ Thu, 03 May 2018 22:43:07: #2 predicted fragment length is 267 bps INFO @ Thu, 03 May 2018 22:43:07: #2 alternative fragment length(s) may be 267 bps INFO @ Thu, 03 May 2018 22:43:07: #2.2 Generate R script for model : SRX3145018.10_model.r INFO @ Thu, 03 May 2018 22:43:07: #3 Call peaks... INFO @ Thu, 03 May 2018 22:43:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:43:07: start X-correlation... INFO @ Thu, 03 May 2018 22:43:07: end of X-cor INFO @ Thu, 03 May 2018 22:43:07: #2 finished! INFO @ Thu, 03 May 2018 22:43:07: #2 predicted fragment length is 267 bps INFO @ Thu, 03 May 2018 22:43:07: #2 alternative fragment length(s) may be 267 bps INFO @ Thu, 03 May 2018 22:43:07: #2.2 Generate R script for model : SRX3145018.20_model.r INFO @ Thu, 03 May 2018 22:43:07: #3 Call peaks... INFO @ Thu, 03 May 2018 22:43:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:43:59: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:43:59: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:44:02: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:44:30: #4 Write output xls file... SRX3145018.20_peaks.xls INFO @ Thu, 03 May 2018 22:44:30: #4 Write peak in narrowPeak format file... SRX3145018.20_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:44:31: #4 Write summits bed file... SRX3145018.20_summits.bed INFO @ Thu, 03 May 2018 22:44:31: Done! pass1 - making usageList (47 chroms): 2 millis pass2 - checking and writing primary data (5568 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:44:33: #4 Write output xls file... SRX3145018.05_peaks.xls INFO @ Thu, 03 May 2018 22:44:33: #4 Write peak in narrowPeak format file... SRX3145018.05_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:44:34: #4 Write summits bed file... SRX3145018.05_summits.bed INFO @ Thu, 03 May 2018 22:44:34: Done! pass1 - making usageList (89 chroms): 4 millis pass2 - checking and writing primary data (18281 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:44:35: #4 Write output xls file... SRX3145018.10_peaks.xls INFO @ Thu, 03 May 2018 22:44:35: #4 Write peak in narrowPeak format file... SRX3145018.10_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:44:35: #4 Write summits bed file... SRX3145018.10_summits.bed INFO @ Thu, 03 May 2018 22:44:35: Done! pass1 - making usageList (68 chroms): 3 millis pass2 - checking and writing primary data (11250 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。