Job ID = 10194870 sra ファイルのダウンロード中... Completed: 206549K bytes transferred in 8 seconds (189956K bits/sec), in 1 file. Completed: 207199K bytes transferred in 8 seconds (192614K bits/sec), in 1 file. Completed: 197286K bytes transferred in 8 seconds (199230K bits/sec), in 1 file. Completed: 194694K bytes transferred in 5 seconds (276967K bits/sec), in 1 file. Completed: 222512K bytes transferred in 7 seconds (248139K bits/sec), in 1 file. Completed: 224618K bytes transferred in 8 seconds (207513K 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 4392909 spots for /home/okishinya/chipatlas/results/rn6/SRX2202866/SRR4319743.sra Written 4392909 spots total Written 4440650 spots for /home/okishinya/chipatlas/results/rn6/SRX2202866/SRR4319742.sra Written 4440650 spots total Written 4632552 spots for /home/okishinya/chipatlas/results/rn6/SRX2202866/SRR4319740.sra Written 4632552 spots total Written 4632049 spots for /home/okishinya/chipatlas/results/rn6/SRX2202866/SRR4319741.sra Written 4632049 spots total Written 4878853 spots for /home/okishinya/chipatlas/results/rn6/SRX2202866/SRR4319744.sra Written 4878853 spots total Written 4907318 spots for /home/okishinya/chipatlas/results/rn6/SRX2202866/SRR4319745.sra Written 4907318 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 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: 00:19:19 27884331 reads; of these: 27884331 (100.00%) were unpaired; of these: 2328512 (8.35%) aligned 0 times 19650186 (70.47%) aligned exactly 1 time 5905633 (21.18%) aligned >1 times 91.65% overall alignment rate Time searching: 00:19:22 Overall time: 00:19:22 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] 4036068 / 25555819 = 0.1579 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, 10 Nov 2017 17:46:19: # Command line: callpeak -t SRX2202866.bam -f BAM -g 2.15e9 -n SRX2202866.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202866.10 # format = BAM # ChIP-seq file = ['SRX2202866.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 @ Fri, 10 Nov 2017 17:46:19: # Command line: callpeak -t SRX2202866.bam -f BAM -g 2.15e9 -n SRX2202866.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202866.05 # format = BAM # ChIP-seq file = ['SRX2202866.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 @ Fri, 10 Nov 2017 17:46:19: # Command line: callpeak -t SRX2202866.bam -f BAM -g 2.15e9 -n SRX2202866.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202866.20 # format = BAM # ChIP-seq file = ['SRX2202866.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 @ Fri, 10 Nov 2017 17:46:19: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:46:19: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:46:19: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:46:19: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:46:19: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:46:19: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:46:26: 1000000 INFO @ Fri, 10 Nov 2017 17:46:26: 1000000 INFO @ Fri, 10 Nov 2017 17:46:26: 1000000 INFO @ Fri, 10 Nov 2017 17:46:33: 2000000 INFO @ Fri, 10 Nov 2017 17:46:33: 2000000 INFO @ Fri, 10 Nov 2017 17:46:33: 2000000 INFO @ Fri, 10 Nov 2017 17:46:40: 3000000 INFO @ Fri, 10 Nov 2017 17:46:40: 3000000 INFO @ Fri, 10 Nov 2017 17:46:40: 3000000 INFO @ Fri, 10 Nov 2017 17:46:48: 4000000 INFO @ Fri, 10 Nov 2017 17:46:48: 4000000 INFO @ Fri, 10 Nov 2017 17:46:48: 4000000 INFO @ Fri, 10 Nov 2017 17:46:56: 5000000 INFO @ Fri, 10 Nov 2017 17:46:57: 5000000 INFO @ Fri, 10 Nov 2017 17:46:57: 5000000 INFO @ Fri, 10 Nov 2017 17:47:04: 6000000 INFO @ Fri, 10 Nov 2017 17:47:05: 6000000 INFO @ Fri, 10 Nov 2017 17:47:05: 6000000 INFO @ Fri, 10 Nov 2017 17:47:11: 7000000 INFO @ Fri, 10 Nov 2017 17:47:14: 7000000 INFO @ Fri, 10 Nov 2017 17:47:14: 7000000 INFO @ Fri, 10 Nov 2017 17:47:19: 8000000 INFO @ Fri, 10 Nov 2017 17:47:22: 8000000 INFO @ Fri, 10 Nov 2017 17:47:22: 8000000 INFO @ Fri, 10 Nov 2017 17:47:27: 9000000 INFO @ Fri, 10 Nov 2017 17:47:31: 9000000 INFO @ Fri, 10 Nov 2017 17:47:31: 9000000 INFO @ Fri, 10 Nov 2017 17:47:35: 10000000 INFO @ Fri, 10 Nov 2017 17:47:39: 10000000 INFO @ Fri, 10 Nov 2017 17:47:39: 10000000 INFO @ Fri, 10 Nov 2017 17:47:43: 11000000 INFO @ Fri, 10 Nov 2017 17:47:47: 11000000 INFO @ Fri, 10 Nov 2017 17:47:47: 11000000 INFO @ Fri, 10 Nov 2017 17:47:51: 12000000 INFO @ Fri, 10 Nov 2017 17:47:56: 12000000 INFO @ Fri, 10 Nov 2017 17:47:56: 12000000 INFO @ Fri, 10 Nov 2017 17:47:59: 13000000 INFO @ Fri, 10 Nov 2017 17:48:04: 13000000 INFO @ Fri, 10 Nov 2017 17:48:04: 13000000 INFO @ Fri, 10 Nov 2017 17:48:06: 14000000 INFO @ Fri, 10 Nov 2017 17:48:11: 14000000 INFO @ Fri, 10 Nov 2017 17:48:11: 14000000 INFO @ Fri, 10 Nov 2017 17:48:13: 15000000 INFO @ Fri, 10 Nov 2017 17:48:18: 15000000 INFO @ Fri, 10 Nov 2017 17:48:18: 15000000 INFO @ Fri, 10 Nov 2017 17:48:20: 16000000 INFO @ Fri, 10 Nov 2017 17:48:25: 16000000 INFO @ Fri, 10 Nov 2017 17:48:25: 16000000 INFO @ Fri, 10 Nov 2017 17:48:27: 17000000 INFO @ Fri, 10 Nov 2017 17:48:32: 17000000 INFO @ Fri, 10 Nov 2017 17:48:32: 17000000 INFO @ Fri, 10 Nov 2017 17:48:34: 18000000 INFO @ Fri, 10 Nov 2017 17:48:39: 18000000 INFO @ Fri, 10 Nov 2017 17:48:39: 18000000 INFO @ Fri, 10 Nov 2017 17:48:41: 19000000 INFO @ Fri, 10 Nov 2017 17:48:46: 19000000 INFO @ Fri, 10 Nov 2017 17:48:46: 19000000 INFO @ Fri, 10 Nov 2017 17:48:48: 20000000 INFO @ Fri, 10 Nov 2017 17:48:52: 20000000 INFO @ Fri, 10 Nov 2017 17:48:52: 20000000 INFO @ Fri, 10 Nov 2017 17:48:55: 21000000 INFO @ Fri, 10 Nov 2017 17:48:58: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:48:58: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:48:58: #1 total tags in treatment: 21519751 INFO @ Fri, 10 Nov 2017 17:48:58: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:48:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 17:48:59: #1 tags after filtering in treatment: 21519598 INFO @ Fri, 10 Nov 2017 17:48:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:48:59: #1 finished! INFO @ Fri, 10 Nov 2017 17:48:59: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:48:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:48:59: 21000000 INFO @ Fri, 10 Nov 2017 17:48:59: 21000000 INFO @ Fri, 10 Nov 2017 17:49:02: #2 number of paired peaks: 42164 INFO @ Fri, 10 Nov 2017 17:49:02: start model_add_line... INFO @ Fri, 10 Nov 2017 17:49:03: start X-correlation... INFO @ Fri, 10 Nov 2017 17:49:03: end of X-cor INFO @ Fri, 10 Nov 2017 17:49:03: #2 finished! INFO @ Fri, 10 Nov 2017 17:49:03: #2 predicted fragment length is 150 bps INFO @ Fri, 10 Nov 2017 17:49:03: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 10 Nov 2017 17:49:03: #2.2 Generate R script for model : SRX2202866.10_model.r INFO @ Fri, 10 Nov 2017 17:49:03: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:49:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:49:03: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:49:03: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:49:03: #1 total tags in treatment: 21519751 INFO @ Fri, 10 Nov 2017 17:49:03: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:49:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 17:49:03: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:49:03: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:49:03: #1 total tags in treatment: 21519751 INFO @ Fri, 10 Nov 2017 17:49:03: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:49:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 17:49:04: #1 tags after filtering in treatment: 21519598 INFO @ Fri, 10 Nov 2017 17:49:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:49:04: #1 finished! INFO @ Fri, 10 Nov 2017 17:49:04: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:49:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:49:04: #1 tags after filtering in treatment: 21519598 INFO @ Fri, 10 Nov 2017 17:49:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:49:04: #1 finished! INFO @ Fri, 10 Nov 2017 17:49:04: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:49:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:49:07: #2 number of paired peaks: 42164 INFO @ Fri, 10 Nov 2017 17:49:07: start model_add_line... INFO @ Fri, 10 Nov 2017 17:49:07: #2 number of paired peaks: 42164 INFO @ Fri, 10 Nov 2017 17:49:07: start model_add_line... INFO @ Fri, 10 Nov 2017 17:49:07: start X-correlation... INFO @ Fri, 10 Nov 2017 17:49:07: start X-correlation... INFO @ Fri, 10 Nov 2017 17:49:07: end of X-cor INFO @ Fri, 10 Nov 2017 17:49:07: #2 finished! INFO @ Fri, 10 Nov 2017 17:49:07: #2 predicted fragment length is 150 bps INFO @ Fri, 10 Nov 2017 17:49:07: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 10 Nov 2017 17:49:07: #2.2 Generate R script for model : SRX2202866.20_model.r INFO @ Fri, 10 Nov 2017 17:49:07: end of X-cor INFO @ Fri, 10 Nov 2017 17:49:07: #2 finished! INFO @ Fri, 10 Nov 2017 17:49:07: #2 predicted fragment length is 150 bps INFO @ Fri, 10 Nov 2017 17:49:07: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 10 Nov 2017 17:49:07: #2.2 Generate R script for model : SRX2202866.05_model.r INFO @ Fri, 10 Nov 2017 17:49:07: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:49:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:49:07: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:49:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:49:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:49:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:50:02: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:50:26: #4 Write output xls file... SRX2202866.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:50:26: #4 Write peak in narrowPeak format file... SRX2202866.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:50:26: #4 Write summits bed file... SRX2202866.10_summits.bed INFO @ Fri, 10 Nov 2017 17:50:26: Done! pass1 - making usageList (53 chroms): 2 millis pass2 - checking and writing primary data (6009 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:50:34: #4 Write output xls file... SRX2202866.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:50:34: #4 Write output xls file... SRX2202866.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:50:34: #4 Write peak in narrowPeak format file... SRX2202866.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:50:34: #4 Write summits bed file... SRX2202866.20_summits.bed INFO @ Fri, 10 Nov 2017 17:50:34: Done! pass1 - making usageList (34 chroms): 0 millis pass2 - checking and writing primary data (788 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:50:34: #4 Write peak in narrowPeak format file... SRX2202866.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:50:34: #4 Write summits bed file... SRX2202866.05_summits.bed INFO @ Fri, 10 Nov 2017 17:50:34: Done! pass1 - making usageList (79 chroms): 3 millis pass2 - checking and writing primary data (15385 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。