Job ID = 11388787 sra ファイルのダウンロード中... Completed: 1052879K bytes transferred in 16 seconds (533276K 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 34889222 spots for /home/okishinya/chipatlas/results/rn6/SRX1453551/SRR2962627.sra Written 34889222 spots for /home/okishinya/chipatlas/results/rn6/SRX1453551/SRR2962627.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: 00:00:02 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:10:44 34889222 reads; of these: 34889222 (100.00%) were unpaired; of these: 5669858 (16.25%) aligned 0 times 20007640 (57.35%) aligned exactly 1 time 9211724 (26.40%) aligned >1 times 83.75% overall alignment rate Time searching: 01:10:49 Overall time: 01:10:49 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] 19986853 / 29219364 = 0.6840 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 @ Wed, 12 Dec 2018 23:43:59: # Command line: callpeak -t SRX1453551.bam -f BAM -g 2.15e9 -n SRX1453551.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1453551.05 # format = BAM # ChIP-seq file = ['SRX1453551.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 @ Wed, 12 Dec 2018 23:43:59: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:43:59: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:43:59: # Command line: callpeak -t SRX1453551.bam -f BAM -g 2.15e9 -n SRX1453551.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1453551.20 # format = BAM # ChIP-seq file = ['SRX1453551.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 @ Wed, 12 Dec 2018 23:43:59: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:43:59: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:43:59: # Command line: callpeak -t SRX1453551.bam -f BAM -g 2.15e9 -n SRX1453551.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1453551.10 # format = BAM # ChIP-seq file = ['SRX1453551.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 @ Wed, 12 Dec 2018 23:43:59: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:43:59: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:44:12: 1000000 INFO @ Wed, 12 Dec 2018 23:44:15: 1000000 INFO @ Wed, 12 Dec 2018 23:44:20: 1000000 INFO @ Wed, 12 Dec 2018 23:44:27: 2000000 INFO @ Wed, 12 Dec 2018 23:44:31: 2000000 INFO @ Wed, 12 Dec 2018 23:44:41: 2000000 INFO @ Wed, 12 Dec 2018 23:44:42: 3000000 INFO @ Wed, 12 Dec 2018 23:44:51: 3000000 INFO @ Wed, 12 Dec 2018 23:45:01: 3000000 INFO @ Wed, 12 Dec 2018 23:45:02: 4000000 INFO @ Wed, 12 Dec 2018 23:45:13: 4000000 INFO @ Wed, 12 Dec 2018 23:45:20: 4000000 INFO @ Wed, 12 Dec 2018 23:45:21: 5000000 INFO @ Wed, 12 Dec 2018 23:45:28: 5000000 INFO @ Wed, 12 Dec 2018 23:45:37: 5000000 INFO @ Wed, 12 Dec 2018 23:45:41: 6000000 INFO @ Wed, 12 Dec 2018 23:45:44: 6000000 INFO @ Wed, 12 Dec 2018 23:45:52: 6000000 INFO @ Wed, 12 Dec 2018 23:46:01: 7000000 INFO @ Wed, 12 Dec 2018 23:46:04: 7000000 INFO @ Wed, 12 Dec 2018 23:46:06: 7000000 INFO @ Wed, 12 Dec 2018 23:46:17: 8000000 INFO @ Wed, 12 Dec 2018 23:46:22: 8000000 INFO @ Wed, 12 Dec 2018 23:46:25: 8000000 INFO @ Wed, 12 Dec 2018 23:46:35: 9000000 INFO @ Wed, 12 Dec 2018 23:46:37: 9000000 INFO @ Wed, 12 Dec 2018 23:46:40: #1 tag size is determined as 51 bps INFO @ Wed, 12 Dec 2018 23:46:40: #1 tag size = 51 INFO @ Wed, 12 Dec 2018 23:46:40: #1 total tags in treatment: 9232511 INFO @ Wed, 12 Dec 2018 23:46:40: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:46:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:46:40: #1 tag size is determined as 51 bps INFO @ Wed, 12 Dec 2018 23:46:40: #1 tag size = 51 INFO @ Wed, 12 Dec 2018 23:46:40: #1 total tags in treatment: 9232511 INFO @ Wed, 12 Dec 2018 23:46:40: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:46:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:46:40: #1 tags after filtering in treatment: 9232361 INFO @ Wed, 12 Dec 2018 23:46:40: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:46:40: #1 finished! INFO @ Wed, 12 Dec 2018 23:46:40: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:46:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:46:40: #1 tags after filtering in treatment: 9232361 INFO @ Wed, 12 Dec 2018 23:46:40: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:46:40: #1 finished! INFO @ Wed, 12 Dec 2018 23:46:40: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:46:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:46:44: #2 number of paired peaks: 68125 INFO @ Wed, 12 Dec 2018 23:46:44: start model_add_line... INFO @ Wed, 12 Dec 2018 23:46:44: #2 number of paired peaks: 68125 INFO @ Wed, 12 Dec 2018 23:46:44: start model_add_line... INFO @ Wed, 12 Dec 2018 23:46:45: start X-correlation... INFO @ Wed, 12 Dec 2018 23:46:45: end of X-cor INFO @ Wed, 12 Dec 2018 23:46:45: #2 finished! INFO @ Wed, 12 Dec 2018 23:46:45: #2 predicted fragment length is 222 bps INFO @ Wed, 12 Dec 2018 23:46:45: #2 alternative fragment length(s) may be 184,222 bps INFO @ Wed, 12 Dec 2018 23:46:45: #2.2 Generate R script for model : SRX1453551.10_model.r INFO @ Wed, 12 Dec 2018 23:46:45: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:46:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:46:45: start X-correlation... INFO @ Wed, 12 Dec 2018 23:46:45: end of X-cor INFO @ Wed, 12 Dec 2018 23:46:45: #2 finished! INFO @ Wed, 12 Dec 2018 23:46:45: #2 predicted fragment length is 222 bps INFO @ Wed, 12 Dec 2018 23:46:45: #2 alternative fragment length(s) may be 184,222 bps INFO @ Wed, 12 Dec 2018 23:46:45: #2.2 Generate R script for model : SRX1453551.20_model.r INFO @ Wed, 12 Dec 2018 23:46:45: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:46:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:46:48: 9000000 INFO @ Wed, 12 Dec 2018 23:46:52: #1 tag size is determined as 51 bps INFO @ Wed, 12 Dec 2018 23:46:52: #1 tag size = 51 INFO @ Wed, 12 Dec 2018 23:46:52: #1 total tags in treatment: 9232511 INFO @ Wed, 12 Dec 2018 23:46:52: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:46:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:46:53: #1 tags after filtering in treatment: 9232361 INFO @ Wed, 12 Dec 2018 23:46:53: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:46:53: #1 finished! INFO @ Wed, 12 Dec 2018 23:46:53: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:46:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:46:57: #2 number of paired peaks: 68125 INFO @ Wed, 12 Dec 2018 23:46:57: start model_add_line... INFO @ Wed, 12 Dec 2018 23:46:57: start X-correlation... INFO @ Wed, 12 Dec 2018 23:46:57: end of X-cor INFO @ Wed, 12 Dec 2018 23:46:57: #2 finished! INFO @ Wed, 12 Dec 2018 23:46:57: #2 predicted fragment length is 222 bps INFO @ Wed, 12 Dec 2018 23:46:57: #2 alternative fragment length(s) may be 184,222 bps INFO @ Wed, 12 Dec 2018 23:46:57: #2.2 Generate R script for model : SRX1453551.05_model.r INFO @ Wed, 12 Dec 2018 23:46:57: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:46:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:47:14: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:47:14: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:47:27: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:47:32: #4 Write output xls file... SRX1453551.20_peaks.xls INFO @ Wed, 12 Dec 2018 23:47:32: #4 Write peak in narrowPeak format file... SRX1453551.20_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:47:32: #4 Write summits bed file... SRX1453551.20_summits.bed INFO @ Wed, 12 Dec 2018 23:47:32: Done! pass1 - making usageList (35 chroms): 2 millis pass2 - checking and writing primary data (289 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:47:32: #4 Write output xls file... SRX1453551.10_peaks.xls INFO @ Wed, 12 Dec 2018 23:47:32: #4 Write peak in narrowPeak format file... SRX1453551.10_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:47:32: #4 Write summits bed file... SRX1453551.10_summits.bed INFO @ Wed, 12 Dec 2018 23:47:32: Done! pass1 - making usageList (43 chroms): 2 millis pass2 - checking and writing primary data (525 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:47:47: #4 Write output xls file... SRX1453551.05_peaks.xls INFO @ Wed, 12 Dec 2018 23:47:47: #4 Write peak in narrowPeak format file... SRX1453551.05_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:47:47: #4 Write summits bed file... SRX1453551.05_summits.bed INFO @ Wed, 12 Dec 2018 23:47:47: Done! pass1 - making usageList (53 chroms): 2 millis pass2 - checking and writing primary data (982 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。