Job ID = 11388780 sra ファイルのダウンロード中... Completed: 231187K bytes transferred in 7 seconds (250685K 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 8677125 spots for /home/okishinya/chipatlas/results/rn6/SRX1453546/SRR2962622.sra Written 8677125 spots for /home/okishinya/chipatlas/results/rn6/SRX1453546/SRR2962622.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: 00:00:04 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:59:55 8677125 reads; of these: 8677125 (100.00%) were unpaired; of these: 670100 (7.72%) aligned 0 times 3282023 (37.82%) aligned exactly 1 time 4725002 (54.45%) aligned >1 times 92.28% overall alignment rate Time searching: 01:00:03 Overall time: 01:00:04 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_rmdupse_core] 952506 / 8007025 = 0.1190 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 23:15:26: # Command line: callpeak -t SRX1453546.bam -f BAM -g 2.15e9 -n SRX1453546.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1453546.05 # format = BAM # ChIP-seq file = ['SRX1453546.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 23:15:26: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:15:26: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:15:26: # Command line: callpeak -t SRX1453546.bam -f BAM -g 2.15e9 -n SRX1453546.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1453546.20 # format = BAM # ChIP-seq file = ['SRX1453546.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 23:15:26: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:15:26: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:15:26: # Command line: callpeak -t SRX1453546.bam -f BAM -g 2.15e9 -n SRX1453546.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1453546.10 # format = BAM # ChIP-seq file = ['SRX1453546.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 23:15:26: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:15:26: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:15:36: 1000000 INFO @ Wed, 12 Dec 2018 23:15:39: 1000000 INFO @ Wed, 12 Dec 2018 23:15:41: 1000000 INFO @ Wed, 12 Dec 2018 23:15:45: 2000000 INFO @ Wed, 12 Dec 2018 23:15:53: 2000000 INFO @ Wed, 12 Dec 2018 23:15:56: 2000000 INFO @ Wed, 12 Dec 2018 23:15:57: 3000000 INFO @ Wed, 12 Dec 2018 23:16:03: 3000000 INFO @ Wed, 12 Dec 2018 23:16:09: 4000000 INFO @ Wed, 12 Dec 2018 23:16:11: 4000000 INFO @ Wed, 12 Dec 2018 23:16:13: 3000000 INFO @ Wed, 12 Dec 2018 23:16:20: 5000000 INFO @ Wed, 12 Dec 2018 23:16:22: 5000000 INFO @ Wed, 12 Dec 2018 23:16:28: 6000000 INFO @ Wed, 12 Dec 2018 23:16:28: 4000000 INFO @ Wed, 12 Dec 2018 23:16:34: 6000000 INFO @ Wed, 12 Dec 2018 23:16:37: 7000000 INFO @ Wed, 12 Dec 2018 23:16:37: #1 tag size is determined as 51 bps INFO @ Wed, 12 Dec 2018 23:16:37: #1 tag size = 51 INFO @ Wed, 12 Dec 2018 23:16:37: #1 total tags in treatment: 7054519 INFO @ Wed, 12 Dec 2018 23:16:37: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:16:37: #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 23:16:38: #1 tags after filtering in treatment: 7054334 INFO @ Wed, 12 Dec 2018 23:16:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:16:38: #1 finished! INFO @ Wed, 12 Dec 2018 23:16:38: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:16:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:16:40: 5000000 INFO @ Wed, 12 Dec 2018 23:16:43: #2 number of paired peaks: 77915 INFO @ Wed, 12 Dec 2018 23:16:43: start model_add_line... INFO @ Wed, 12 Dec 2018 23:16:43: start X-correlation... INFO @ Wed, 12 Dec 2018 23:16:43: end of X-cor INFO @ Wed, 12 Dec 2018 23:16:43: #2 finished! INFO @ Wed, 12 Dec 2018 23:16:43: #2 predicted fragment length is 128 bps INFO @ Wed, 12 Dec 2018 23:16:43: #2 alternative fragment length(s) may be 128 bps INFO @ Wed, 12 Dec 2018 23:16:43: #2.2 Generate R script for model : SRX1453546.10_model.r INFO @ Wed, 12 Dec 2018 23:16:43: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:16:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:16:48: 7000000 INFO @ Wed, 12 Dec 2018 23:16:48: #1 tag size is determined as 51 bps INFO @ Wed, 12 Dec 2018 23:16:48: #1 tag size = 51 INFO @ Wed, 12 Dec 2018 23:16:48: #1 total tags in treatment: 7054519 INFO @ Wed, 12 Dec 2018 23:16:48: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:16:48: #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 23:16:49: #1 tags after filtering in treatment: 7054334 INFO @ Wed, 12 Dec 2018 23:16:49: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:16:49: #1 finished! INFO @ Wed, 12 Dec 2018 23:16:49: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:16:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:16:52: 6000000 INFO @ Wed, 12 Dec 2018 23:16:54: #2 number of paired peaks: 77915 INFO @ Wed, 12 Dec 2018 23:16:54: start model_add_line... INFO @ Wed, 12 Dec 2018 23:16:54: start X-correlation... INFO @ Wed, 12 Dec 2018 23:16:54: end of X-cor INFO @ Wed, 12 Dec 2018 23:16:54: #2 finished! INFO @ Wed, 12 Dec 2018 23:16:54: #2 predicted fragment length is 128 bps INFO @ Wed, 12 Dec 2018 23:16:54: #2 alternative fragment length(s) may be 128 bps INFO @ Wed, 12 Dec 2018 23:16:54: #2.2 Generate R script for model : SRX1453546.05_model.r INFO @ Wed, 12 Dec 2018 23:16:54: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:16:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:17:05: 7000000 INFO @ Wed, 12 Dec 2018 23:17:05: #1 tag size is determined as 51 bps INFO @ Wed, 12 Dec 2018 23:17:05: #1 tag size = 51 INFO @ Wed, 12 Dec 2018 23:17:05: #1 total tags in treatment: 7054519 INFO @ Wed, 12 Dec 2018 23:17:05: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:17:05: #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 23:17:06: #1 tags after filtering in treatment: 7054334 INFO @ Wed, 12 Dec 2018 23:17:06: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:17:06: #1 finished! INFO @ Wed, 12 Dec 2018 23:17:06: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:17:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:17:06: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:17:11: #2 number of paired peaks: 77915 INFO @ Wed, 12 Dec 2018 23:17:11: start model_add_line... INFO @ Wed, 12 Dec 2018 23:17:11: start X-correlation... INFO @ Wed, 12 Dec 2018 23:17:11: end of X-cor INFO @ Wed, 12 Dec 2018 23:17:11: #2 finished! INFO @ Wed, 12 Dec 2018 23:17:11: #2 predicted fragment length is 128 bps INFO @ Wed, 12 Dec 2018 23:17:11: #2 alternative fragment length(s) may be 128 bps INFO @ Wed, 12 Dec 2018 23:17:11: #2.2 Generate R script for model : SRX1453546.20_model.r INFO @ Wed, 12 Dec 2018 23:17:11: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:17:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:17:17: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:17:20: #4 Write output xls file... SRX1453546.10_peaks.xls INFO @ Wed, 12 Dec 2018 23:17:20: #4 Write peak in narrowPeak format file... SRX1453546.10_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:17:20: #4 Write summits bed file... SRX1453546.10_summits.bed INFO @ Wed, 12 Dec 2018 23:17:20: Done! pass1 - making usageList (54 chroms): 3 millis pass2 - checking and writing primary data (1303 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:17:31: #4 Write output xls file... SRX1453546.05_peaks.xls INFO @ Wed, 12 Dec 2018 23:17:31: #4 Write peak in narrowPeak format file... SRX1453546.05_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:17:31: #4 Write summits bed file... SRX1453546.05_summits.bed INFO @ Wed, 12 Dec 2018 23:17:31: Done! pass1 - making usageList (83 chroms): 3 millis pass2 - checking and writing primary data (5396 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:17:34: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:17:48: #4 Write output xls file... SRX1453546.20_peaks.xls INFO @ Wed, 12 Dec 2018 23:17:48: #4 Write peak in narrowPeak format file... SRX1453546.20_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:17:48: #4 Write summits bed file... SRX1453546.20_summits.bed INFO @ Wed, 12 Dec 2018 23:17:48: Done! pass1 - making usageList (39 chroms): 3 millis pass2 - checking and writing primary data (487 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。