Job ID = 10609092 sra ファイルのダウンロード中... Completed: 446742K bytes transferred in 58 seconds (63009K 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 21893597 spots for /home/okishinya/chipatlas/results/dm3/SRX3011230/SRR5834707.sra Written 21893597 spots for /home/okishinya/chipatlas/results/dm3/SRX3011230/SRR5834707.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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:48 21893597 reads; of these: 21893597 (100.00%) were unpaired; of these: 195316 (0.89%) aligned 0 times 21419483 (97.83%) aligned exactly 1 time 278798 (1.27%) aligned >1 times 99.11% overall alignment rate Time searching: 00:03:48 Overall time: 00:03:48 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 9512006 / 21698281 = 0.4384 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, 04 May 2018 07:11:54: # Command line: callpeak -t SRX3011230.bam -f BAM -g dm -n SRX3011230.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3011230.20 # format = BAM # ChIP-seq file = ['SRX3011230.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 04 May 2018 07:11:54: #1 read tag files... INFO @ Fri, 04 May 2018 07:11:54: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:11:54: # Command line: callpeak -t SRX3011230.bam -f BAM -g dm -n SRX3011230.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3011230.05 # format = BAM # ChIP-seq file = ['SRX3011230.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 04 May 2018 07:11:54: #1 read tag files... INFO @ Fri, 04 May 2018 07:11:54: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:11:54: # Command line: callpeak -t SRX3011230.bam -f BAM -g dm -n SRX3011230.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3011230.10 # format = BAM # ChIP-seq file = ['SRX3011230.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 04 May 2018 07:11:54: #1 read tag files... INFO @ Fri, 04 May 2018 07:11:54: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:12:00: 1000000 INFO @ Fri, 04 May 2018 07:12:02: 1000000 INFO @ Fri, 04 May 2018 07:12:02: 1000000 INFO @ Fri, 04 May 2018 07:12:07: 2000000 INFO @ Fri, 04 May 2018 07:12:09: 2000000 INFO @ Fri, 04 May 2018 07:12:09: 2000000 INFO @ Fri, 04 May 2018 07:12:13: 3000000 INFO @ Fri, 04 May 2018 07:12:17: 3000000 INFO @ Fri, 04 May 2018 07:12:17: 3000000 INFO @ Fri, 04 May 2018 07:12:19: 4000000 INFO @ Fri, 04 May 2018 07:12:24: 4000000 INFO @ Fri, 04 May 2018 07:12:24: 4000000 INFO @ Fri, 04 May 2018 07:12:26: 5000000 INFO @ Fri, 04 May 2018 07:12:32: 5000000 INFO @ Fri, 04 May 2018 07:12:32: 5000000 INFO @ Fri, 04 May 2018 07:12:32: 6000000 INFO @ Fri, 04 May 2018 07:12:38: 7000000 INFO @ Fri, 04 May 2018 07:12:39: 6000000 INFO @ Fri, 04 May 2018 07:12:39: 6000000 INFO @ Fri, 04 May 2018 07:12:44: 8000000 INFO @ Fri, 04 May 2018 07:12:46: 7000000 INFO @ Fri, 04 May 2018 07:12:46: 7000000 INFO @ Fri, 04 May 2018 07:12:50: 9000000 INFO @ Fri, 04 May 2018 07:12:54: 8000000 INFO @ Fri, 04 May 2018 07:12:54: 8000000 INFO @ Fri, 04 May 2018 07:12:56: 10000000 INFO @ Fri, 04 May 2018 07:13:01: 9000000 INFO @ Fri, 04 May 2018 07:13:01: 9000000 INFO @ Fri, 04 May 2018 07:13:02: 11000000 INFO @ Fri, 04 May 2018 07:13:08: 12000000 INFO @ Fri, 04 May 2018 07:13:09: 10000000 INFO @ Fri, 04 May 2018 07:13:09: 10000000 INFO @ Fri, 04 May 2018 07:13:09: #1 tag size is determined as 50 bps INFO @ Fri, 04 May 2018 07:13:09: #1 tag size = 50 INFO @ Fri, 04 May 2018 07:13:09: #1 total tags in treatment: 12186275 INFO @ Fri, 04 May 2018 07:13:09: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:13:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:13:10: #1 tags after filtering in treatment: 12186275 INFO @ Fri, 04 May 2018 07:13:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:13:10: #1 finished! INFO @ Fri, 04 May 2018 07:13:10: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:13:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:13:11: #2 number of paired peaks: 8340 INFO @ Fri, 04 May 2018 07:13:11: start model_add_line... INFO @ Fri, 04 May 2018 07:13:12: start X-correlation... INFO @ Fri, 04 May 2018 07:13:12: end of X-cor INFO @ Fri, 04 May 2018 07:13:12: #2 finished! INFO @ Fri, 04 May 2018 07:13:12: #2 predicted fragment length is 210 bps INFO @ Fri, 04 May 2018 07:13:12: #2 alternative fragment length(s) may be 210 bps INFO @ Fri, 04 May 2018 07:13:12: #2.2 Generate R script for model : SRX3011230.20_model.r INFO @ Fri, 04 May 2018 07:13:12: #3 Call peaks... INFO @ Fri, 04 May 2018 07:13:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:13:16: 11000000 INFO @ Fri, 04 May 2018 07:13:16: 11000000 INFO @ Fri, 04 May 2018 07:13:24: 12000000 INFO @ Fri, 04 May 2018 07:13:24: 12000000 INFO @ Fri, 04 May 2018 07:13:25: #1 tag size is determined as 50 bps INFO @ Fri, 04 May 2018 07:13:25: #1 tag size = 50 INFO @ Fri, 04 May 2018 07:13:25: #1 total tags in treatment: 12186275 INFO @ Fri, 04 May 2018 07:13:25: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:13:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:13:25: #1 tag size is determined as 50 bps INFO @ Fri, 04 May 2018 07:13:25: #1 tag size = 50 INFO @ Fri, 04 May 2018 07:13:25: #1 total tags in treatment: 12186275 INFO @ Fri, 04 May 2018 07:13:25: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:13:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:13:26: #1 tags after filtering in treatment: 12186275 INFO @ Fri, 04 May 2018 07:13:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:13:26: #1 tags after filtering in treatment: 12186275 INFO @ Fri, 04 May 2018 07:13:26: #1 finished! INFO @ Fri, 04 May 2018 07:13:26: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:13:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:13:26: #1 finished! INFO @ Fri, 04 May 2018 07:13:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:13:26: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:13:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:13:27: #2 number of paired peaks: 8340 INFO @ Fri, 04 May 2018 07:13:27: start model_add_line... INFO @ Fri, 04 May 2018 07:13:27: #2 number of paired peaks: 8340 INFO @ Fri, 04 May 2018 07:13:27: start model_add_line... INFO @ Fri, 04 May 2018 07:13:28: start X-correlation... INFO @ Fri, 04 May 2018 07:13:28: start X-correlation... INFO @ Fri, 04 May 2018 07:13:28: end of X-cor INFO @ Fri, 04 May 2018 07:13:28: #2 finished! INFO @ Fri, 04 May 2018 07:13:28: #2 predicted fragment length is 210 bps INFO @ Fri, 04 May 2018 07:13:28: #2 alternative fragment length(s) may be 210 bps INFO @ Fri, 04 May 2018 07:13:28: #2.2 Generate R script for model : SRX3011230.10_model.r INFO @ Fri, 04 May 2018 07:13:28: end of X-cor INFO @ Fri, 04 May 2018 07:13:28: #2 finished! INFO @ Fri, 04 May 2018 07:13:28: #2 predicted fragment length is 210 bps INFO @ Fri, 04 May 2018 07:13:28: #2 alternative fragment length(s) may be 210 bps INFO @ Fri, 04 May 2018 07:13:28: #2.2 Generate R script for model : SRX3011230.05_model.r INFO @ Fri, 04 May 2018 07:13:28: #3 Call peaks... INFO @ Fri, 04 May 2018 07:13:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:13:28: #3 Call peaks... INFO @ Fri, 04 May 2018 07:13:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:13:58: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:14:16: #4 Write output xls file... SRX3011230.20_peaks.xls INFO @ Fri, 04 May 2018 07:14:16: #4 Write peak in narrowPeak format file... SRX3011230.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:14:16: #4 Write summits bed file... SRX3011230.20_summits.bed INFO @ Fri, 04 May 2018 07:14:16: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6504 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:14:17: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:14:17: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:14:36: #4 Write output xls file... SRX3011230.10_peaks.xls INFO @ Fri, 04 May 2018 07:14:36: #4 Write peak in narrowPeak format file... SRX3011230.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:14:36: #4 Write summits bed file... SRX3011230.10_summits.bed INFO @ Fri, 04 May 2018 07:14:36: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (8452 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:14:37: #4 Write output xls file... SRX3011230.05_peaks.xls INFO @ Fri, 04 May 2018 07:14:37: #4 Write peak in narrowPeak format file... SRX3011230.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:14:37: #4 Write summits bed file... SRX3011230.05_summits.bed INFO @ Fri, 04 May 2018 07:14:37: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (10395 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。