Job ID = 10608872 sra ファイルのダウンロード中... Completed: 505220K bytes transferred in 21 seconds (196982K 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 10816516 spots for /home/okishinya/chipatlas/results/rn6/SRX2727607/SRR5437670.sra Written 10816516 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: 00:00:00 Multiseed full-index search: 00:18:40 10816516 reads; of these: 10816516 (100.00%) were unpaired; of these: 332877 (3.08%) aligned 0 times 9152406 (84.62%) aligned exactly 1 time 1331233 (12.31%) aligned >1 times 96.92% overall alignment rate Time searching: 00:18:42 Overall time: 00:18:42 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 8 files... [bam_rmdupse_core] 429131 / 10483639 = 0.0409 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 22:39:27: # Command line: callpeak -t SRX2727607.bam -f BAM -g 2.15e9 -n SRX2727607.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2727607.10 # format = BAM # ChIP-seq file = ['SRX2727607.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 22:39:27: #1 read tag files... INFO @ Thu, 03 May 2018 22:39:27: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:39:27: # Command line: callpeak -t SRX2727607.bam -f BAM -g 2.15e9 -n SRX2727607.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2727607.20 # format = BAM # ChIP-seq file = ['SRX2727607.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 22:39:27: #1 read tag files... INFO @ Thu, 03 May 2018 22:39:27: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:39:27: # Command line: callpeak -t SRX2727607.bam -f BAM -g 2.15e9 -n SRX2727607.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2727607.05 # format = BAM # ChIP-seq file = ['SRX2727607.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 22:39:27: #1 read tag files... INFO @ Thu, 03 May 2018 22:39:27: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:39:37: 1000000 INFO @ Thu, 03 May 2018 22:39:39: 1000000 INFO @ Thu, 03 May 2018 22:39:39: 1000000 INFO @ Thu, 03 May 2018 22:39:47: 2000000 INFO @ Thu, 03 May 2018 22:39:51: 2000000 INFO @ Thu, 03 May 2018 22:39:51: 2000000 INFO @ Thu, 03 May 2018 22:39:56: 3000000 INFO @ Thu, 03 May 2018 22:40:03: 3000000 INFO @ Thu, 03 May 2018 22:40:03: 3000000 INFO @ Thu, 03 May 2018 22:40:06: 4000000 INFO @ Thu, 03 May 2018 22:40:14: 4000000 INFO @ Thu, 03 May 2018 22:40:14: 4000000 INFO @ Thu, 03 May 2018 22:40:16: 5000000 INFO @ Thu, 03 May 2018 22:40:25: 5000000 INFO @ Thu, 03 May 2018 22:40:25: 5000000 INFO @ Thu, 03 May 2018 22:40:25: 6000000 INFO @ Thu, 03 May 2018 22:40:35: 7000000 INFO @ Thu, 03 May 2018 22:40:35: 6000000 INFO @ Thu, 03 May 2018 22:40:35: 6000000 INFO @ Thu, 03 May 2018 22:40:44: 8000000 INFO @ Thu, 03 May 2018 22:40:46: 7000000 INFO @ Thu, 03 May 2018 22:40:46: 7000000 INFO @ Thu, 03 May 2018 22:40:53: 9000000 INFO @ Thu, 03 May 2018 22:40:56: 8000000 INFO @ Thu, 03 May 2018 22:40:56: 8000000 INFO @ Thu, 03 May 2018 22:41:02: 10000000 INFO @ Thu, 03 May 2018 22:41:03: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:41:03: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:41:03: #1 total tags in treatment: 10054508 INFO @ Thu, 03 May 2018 22:41:03: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:41:03: #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 22:41:03: #1 tags after filtering in treatment: 10054233 INFO @ Thu, 03 May 2018 22:41:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:41:03: #1 finished! INFO @ Thu, 03 May 2018 22:41:03: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:41:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:41:06: 9000000 INFO @ Thu, 03 May 2018 22:41:06: 9000000 INFO @ Thu, 03 May 2018 22:41:07: #2 number of paired peaks: 96351 INFO @ Thu, 03 May 2018 22:41:07: start model_add_line... INFO @ Thu, 03 May 2018 22:41:08: start X-correlation... INFO @ Thu, 03 May 2018 22:41:08: end of X-cor INFO @ Thu, 03 May 2018 22:41:08: #2 finished! INFO @ Thu, 03 May 2018 22:41:08: #2 predicted fragment length is 259 bps INFO @ Thu, 03 May 2018 22:41:08: #2 alternative fragment length(s) may be 259 bps INFO @ Thu, 03 May 2018 22:41:08: #2.2 Generate R script for model : SRX2727607.05_model.r INFO @ Thu, 03 May 2018 22:41:08: #3 Call peaks... INFO @ Thu, 03 May 2018 22:41:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:41:17: 10000000 INFO @ Thu, 03 May 2018 22:41:17: 10000000 INFO @ Thu, 03 May 2018 22:41:17: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:41:17: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:41:17: #1 total tags in treatment: 10054508 INFO @ Thu, 03 May 2018 22:41:17: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:41:17: #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 22:41:17: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 22:41:17: #1 tag size = 100 INFO @ Thu, 03 May 2018 22:41:17: #1 total tags in treatment: 10054508 INFO @ Thu, 03 May 2018 22:41:17: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:41:17: #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 22:41:18: #1 tags after filtering in treatment: 10054233 INFO @ Thu, 03 May 2018 22:41:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:41:18: #1 finished! INFO @ Thu, 03 May 2018 22:41:18: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:41:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:41:18: #1 tags after filtering in treatment: 10054233 INFO @ Thu, 03 May 2018 22:41:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:41:18: #1 finished! INFO @ Thu, 03 May 2018 22:41:18: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:41:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:41:22: #2 number of paired peaks: 96351 INFO @ Thu, 03 May 2018 22:41:22: start model_add_line... INFO @ Thu, 03 May 2018 22:41:22: #2 number of paired peaks: 96351 INFO @ Thu, 03 May 2018 22:41:22: start model_add_line... INFO @ Thu, 03 May 2018 22:41:22: start X-correlation... INFO @ Thu, 03 May 2018 22:41:22: end of X-cor INFO @ Thu, 03 May 2018 22:41:22: #2 finished! INFO @ Thu, 03 May 2018 22:41:22: #2 predicted fragment length is 259 bps INFO @ Thu, 03 May 2018 22:41:22: #2 alternative fragment length(s) may be 259 bps INFO @ Thu, 03 May 2018 22:41:22: #2.2 Generate R script for model : SRX2727607.10_model.r INFO @ Thu, 03 May 2018 22:41:22: #3 Call peaks... INFO @ Thu, 03 May 2018 22:41:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:41:22: start X-correlation... INFO @ Thu, 03 May 2018 22:41:22: end of X-cor INFO @ Thu, 03 May 2018 22:41:22: #2 finished! INFO @ Thu, 03 May 2018 22:41:22: #2 predicted fragment length is 259 bps INFO @ Thu, 03 May 2018 22:41:22: #2 alternative fragment length(s) may be 259 bps INFO @ Thu, 03 May 2018 22:41:22: #2.2 Generate R script for model : SRX2727607.20_model.r INFO @ Thu, 03 May 2018 22:41:22: #3 Call peaks... INFO @ Thu, 03 May 2018 22:41:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:41:35: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:41:49: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:41:49: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:41:53: #4 Write output xls file... SRX2727607.05_peaks.xls INFO @ Thu, 03 May 2018 22:41:53: #4 Write peak in narrowPeak format file... SRX2727607.05_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:41:54: #4 Write summits bed file... SRX2727607.05_summits.bed INFO @ Thu, 03 May 2018 22:41:54: Done! pass1 - making usageList (82 chroms): 5 millis pass2 - checking and writing primary data (23907 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:42:05: #4 Write output xls file... SRX2727607.10_peaks.xls INFO @ Thu, 03 May 2018 22:42:05: #4 Write peak in narrowPeak format file... SRX2727607.10_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:42:05: #4 Write summits bed file... SRX2727607.10_summits.bed INFO @ Thu, 03 May 2018 22:42:05: Done! pass1 - making usageList (55 chroms): 3 millis pass2 - checking and writing primary data (10817 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:42:06: #4 Write output xls file... SRX2727607.20_peaks.xls INFO @ Thu, 03 May 2018 22:42:06: #4 Write peak in narrowPeak format file... SRX2727607.20_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:42:06: #4 Write summits bed file... SRX2727607.20_summits.bed INFO @ Thu, 03 May 2018 22:42:06: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (2285 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。