Job ID = 11388781 sra ファイルのダウンロード中... Completed: 240051K bytes transferred in 6 seconds (293563K 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 9188436 spots for /home/okishinya/chipatlas/results/rn6/SRX1453547/SRR2962623.sra Written 9188436 spots for /home/okishinya/chipatlas/results/rn6/SRX1453547/SRR2962623.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: 00:00:01 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:49:07 9188436 reads; of these: 9188436 (100.00%) were unpaired; of these: 1421276 (15.47%) aligned 0 times 2616774 (28.48%) aligned exactly 1 time 5150386 (56.05%) aligned >1 times 84.53% overall alignment rate Time searching: 00:49:14 Overall time: 00:49:14 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] 1230729 / 7767160 = 0.1585 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 23:04:18: # Command line: callpeak -t SRX1453547.bam -f BAM -g 2.15e9 -n SRX1453547.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1453547.20 # format = BAM # ChIP-seq file = ['SRX1453547.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 23:04:18: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:04:18: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:04:18: # Command line: callpeak -t SRX1453547.bam -f BAM -g 2.15e9 -n SRX1453547.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1453547.10 # format = BAM # ChIP-seq file = ['SRX1453547.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 23:04:18: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:04:18: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:04:18: # Command line: callpeak -t SRX1453547.bam -f BAM -g 2.15e9 -n SRX1453547.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1453547.05 # format = BAM # ChIP-seq file = ['SRX1453547.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 23:04:18: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:04:18: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:04:29: 1000000 INFO @ Wed, 12 Dec 2018 23:04:37: 1000000 INFO @ Wed, 12 Dec 2018 23:04:38: 2000000 INFO @ Wed, 12 Dec 2018 23:04:38: 1000000 INFO @ Wed, 12 Dec 2018 23:04:47: 3000000 INFO @ Wed, 12 Dec 2018 23:04:56: 2000000 INFO @ Wed, 12 Dec 2018 23:04:56: 4000000 INFO @ Wed, 12 Dec 2018 23:04:58: 2000000 INFO @ Wed, 12 Dec 2018 23:05:05: 5000000 INFO @ Wed, 12 Dec 2018 23:05:15: 6000000 INFO @ Wed, 12 Dec 2018 23:05:16: 3000000 INFO @ Wed, 12 Dec 2018 23:05:17: 3000000 INFO @ Wed, 12 Dec 2018 23:05:20: #1 tag size is determined as 51 bps INFO @ Wed, 12 Dec 2018 23:05:20: #1 tag size = 51 INFO @ Wed, 12 Dec 2018 23:05:20: #1 total tags in treatment: 6536431 INFO @ Wed, 12 Dec 2018 23:05:20: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:05:20: #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 23:05:20: #1 tags after filtering in treatment: 6536194 INFO @ Wed, 12 Dec 2018 23:05:20: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:05:20: #1 finished! INFO @ Wed, 12 Dec 2018 23:05:20: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:05:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:05:25: #2 number of paired peaks: 95609 INFO @ Wed, 12 Dec 2018 23:05:25: start model_add_line... INFO @ Wed, 12 Dec 2018 23:05:25: start X-correlation... INFO @ Wed, 12 Dec 2018 23:05:25: end of X-cor INFO @ Wed, 12 Dec 2018 23:05:25: #2 finished! INFO @ Wed, 12 Dec 2018 23:05:25: #2 predicted fragment length is 136 bps INFO @ Wed, 12 Dec 2018 23:05:25: #2 alternative fragment length(s) may be 136 bps INFO @ Wed, 12 Dec 2018 23:05:25: #2.2 Generate R script for model : SRX1453547.05_model.r INFO @ Wed, 12 Dec 2018 23:05:25: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:05:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:05:36: 4000000 INFO @ Wed, 12 Dec 2018 23:05:38: 4000000 INFO @ Wed, 12 Dec 2018 23:05:47: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:05:54: 5000000 INFO @ Wed, 12 Dec 2018 23:05:57: 5000000 INFO @ Wed, 12 Dec 2018 23:05:59: #4 Write output xls file... SRX1453547.05_peaks.xls INFO @ Wed, 12 Dec 2018 23:05:59: #4 Write peak in narrowPeak format file... SRX1453547.05_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:05:59: #4 Write summits bed file... SRX1453547.05_summits.bed INFO @ Wed, 12 Dec 2018 23:05:59: Done! pass1 - making usageList (82 chroms): 3 millis pass2 - checking and writing primary data (3209 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:06:13: 6000000 INFO @ Wed, 12 Dec 2018 23:06:16: 6000000 INFO @ Wed, 12 Dec 2018 23:06:22: #1 tag size is determined as 51 bps INFO @ Wed, 12 Dec 2018 23:06:22: #1 tag size = 51 INFO @ Wed, 12 Dec 2018 23:06:22: #1 total tags in treatment: 6536431 INFO @ Wed, 12 Dec 2018 23:06:22: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:06:22: #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 23:06:23: #1 tags after filtering in treatment: 6536194 INFO @ Wed, 12 Dec 2018 23:06:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:06:23: #1 finished! INFO @ Wed, 12 Dec 2018 23:06:23: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:06:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:06:25: #1 tag size is determined as 51 bps INFO @ Wed, 12 Dec 2018 23:06:25: #1 tag size = 51 INFO @ Wed, 12 Dec 2018 23:06:25: #1 total tags in treatment: 6536431 INFO @ Wed, 12 Dec 2018 23:06:25: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:06:25: #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 23:06:26: #1 tags after filtering in treatment: 6536194 INFO @ Wed, 12 Dec 2018 23:06:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:06:26: #1 finished! INFO @ Wed, 12 Dec 2018 23:06:26: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:06:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:06:27: #2 number of paired peaks: 95609 INFO @ Wed, 12 Dec 2018 23:06:27: start model_add_line... INFO @ Wed, 12 Dec 2018 23:06:27: start X-correlation... INFO @ Wed, 12 Dec 2018 23:06:27: end of X-cor INFO @ Wed, 12 Dec 2018 23:06:27: #2 finished! INFO @ Wed, 12 Dec 2018 23:06:27: #2 predicted fragment length is 136 bps INFO @ Wed, 12 Dec 2018 23:06:27: #2 alternative fragment length(s) may be 136 bps INFO @ Wed, 12 Dec 2018 23:06:27: #2.2 Generate R script for model : SRX1453547.20_model.r INFO @ Wed, 12 Dec 2018 23:06:27: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:06:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:06:30: #2 number of paired peaks: 95609 INFO @ Wed, 12 Dec 2018 23:06:30: start model_add_line... INFO @ Wed, 12 Dec 2018 23:06:30: start X-correlation... INFO @ Wed, 12 Dec 2018 23:06:30: end of X-cor INFO @ Wed, 12 Dec 2018 23:06:30: #2 finished! INFO @ Wed, 12 Dec 2018 23:06:30: #2 predicted fragment length is 136 bps INFO @ Wed, 12 Dec 2018 23:06:30: #2 alternative fragment length(s) may be 136 bps INFO @ Wed, 12 Dec 2018 23:06:30: #2.2 Generate R script for model : SRX1453547.10_model.r INFO @ Wed, 12 Dec 2018 23:06:30: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:06:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:06:49: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:06:52: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:07:01: #4 Write output xls file... SRX1453547.20_peaks.xls INFO @ Wed, 12 Dec 2018 23:07:01: #4 Write peak in narrowPeak format file... SRX1453547.20_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:07:01: #4 Write summits bed file... SRX1453547.20_summits.bed INFO @ Wed, 12 Dec 2018 23:07:01: Done! pass1 - making usageList (41 chroms): 3 millis pass2 - checking and writing primary data (418 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:07:04: #4 Write output xls file... SRX1453547.10_peaks.xls INFO @ Wed, 12 Dec 2018 23:07:04: #4 Write peak in narrowPeak format file... SRX1453547.10_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:07:04: #4 Write summits bed file... SRX1453547.10_summits.bed INFO @ Wed, 12 Dec 2018 23:07:04: Done! pass1 - making usageList (52 chroms): 3 millis pass2 - checking and writing primary data (773 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。