Job ID = 9371921 sra ファイルのダウンロード中... Completed: 338210K bytes transferred in 13 seconds (198713K bits/sec), in 1 file, 2 directories. 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 12815914 spots for /home/okishinya/chipatlas/results/dm3/SRX2520645/SRR5206764.sra Written 12815914 spots total 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: 00:04:01 12815914 reads; of these: 12815914 (100.00%) were unpaired; of these: 176292 (1.38%) aligned 0 times 10416995 (81.28%) aligned exactly 1 time 2222627 (17.34%) aligned >1 times 98.62% overall alignment rate Time searching: 00:04:02 Overall time: 00:04:02 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 8 files... [bam_rmdupse_core] 4179261 / 12639622 = 0.3306 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 Aug 2017 14:56:57: # Command line: callpeak -t SRX2520645.bam -f BAM -g dm -n SRX2520645.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2520645.20 # format = BAM # ChIP-seq file = ['SRX2520645.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 Aug 2017 14:56:57: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:56:57: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:56:57: # Command line: callpeak -t SRX2520645.bam -f BAM -g dm -n SRX2520645.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2520645.05 # format = BAM # ChIP-seq file = ['SRX2520645.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 Aug 2017 14:56:57: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:56:57: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:56:57: # Command line: callpeak -t SRX2520645.bam -f BAM -g dm -n SRX2520645.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2520645.10 # format = BAM # ChIP-seq file = ['SRX2520645.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 Aug 2017 14:56:57: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:56:57: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:57:03: 1000000 INFO @ Fri, 04 Aug 2017 14:57:03: 1000000 INFO @ Fri, 04 Aug 2017 14:57:04: 1000000 INFO @ Fri, 04 Aug 2017 14:57:09: 2000000 INFO @ Fri, 04 Aug 2017 14:57:10: 2000000 INFO @ Fri, 04 Aug 2017 14:57:12: 2000000 INFO @ Fri, 04 Aug 2017 14:57:16: 3000000 INFO @ Fri, 04 Aug 2017 14:57:17: 3000000 INFO @ Fri, 04 Aug 2017 14:57:20: 3000000 INFO @ Fri, 04 Aug 2017 14:57:22: 4000000 INFO @ Fri, 04 Aug 2017 14:57:24: 4000000 INFO @ Fri, 04 Aug 2017 14:57:29: 4000000 INFO @ Fri, 04 Aug 2017 14:57:30: 5000000 INFO @ Fri, 04 Aug 2017 14:57:32: 5000000 INFO @ Fri, 04 Aug 2017 14:57:38: 5000000 INFO @ Fri, 04 Aug 2017 14:57:38: 6000000 INFO @ Fri, 04 Aug 2017 14:57:40: 6000000 INFO @ Fri, 04 Aug 2017 14:57:45: 7000000 INFO @ Fri, 04 Aug 2017 14:57:46: 6000000 INFO @ Fri, 04 Aug 2017 14:57:47: 7000000 INFO @ Fri, 04 Aug 2017 14:57:51: 8000000 INFO @ Fri, 04 Aug 2017 14:57:54: 8000000 INFO @ Fri, 04 Aug 2017 14:57:54: 7000000 INFO @ Fri, 04 Aug 2017 14:57:54: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 14:57:54: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 14:57:54: #1 total tags in treatment: 8460361 INFO @ Fri, 04 Aug 2017 14:57:54: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:57:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 14:57:54: #1 tags after filtering in treatment: 8460361 INFO @ Fri, 04 Aug 2017 14:57:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 14:57:54: #1 finished! INFO @ Fri, 04 Aug 2017 14:57:54: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:57:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:57:55: #2 number of paired peaks: 2010 INFO @ Fri, 04 Aug 2017 14:57:55: start model_add_line... INFO @ Fri, 04 Aug 2017 14:57:55: start X-correlation... INFO @ Fri, 04 Aug 2017 14:57:55: end of X-cor INFO @ Fri, 04 Aug 2017 14:57:55: #2 finished! INFO @ Fri, 04 Aug 2017 14:57:55: #2 predicted fragment length is 125 bps INFO @ Fri, 04 Aug 2017 14:57:55: #2 alternative fragment length(s) may be 47,125,272 bps INFO @ Fri, 04 Aug 2017 14:57:55: #2.2 Generate R script for model : SRX2520645.20_model.r INFO @ Fri, 04 Aug 2017 14:57:55: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:57:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:57:57: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 14:57:57: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 14:57:57: #1 total tags in treatment: 8460361 INFO @ Fri, 04 Aug 2017 14:57:57: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:57:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 14:57:57: #1 tags after filtering in treatment: 8460361 INFO @ Fri, 04 Aug 2017 14:57:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 14:57:57: #1 finished! INFO @ Fri, 04 Aug 2017 14:57:57: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:57:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:57:58: #2 number of paired peaks: 2010 INFO @ Fri, 04 Aug 2017 14:57:58: start model_add_line... INFO @ Fri, 04 Aug 2017 14:57:58: start X-correlation... INFO @ Fri, 04 Aug 2017 14:57:58: end of X-cor INFO @ Fri, 04 Aug 2017 14:57:58: #2 finished! INFO @ Fri, 04 Aug 2017 14:57:58: #2 predicted fragment length is 125 bps INFO @ Fri, 04 Aug 2017 14:57:58: #2 alternative fragment length(s) may be 47,125,272 bps INFO @ Fri, 04 Aug 2017 14:57:58: #2.2 Generate R script for model : SRX2520645.05_model.r INFO @ Fri, 04 Aug 2017 14:57:58: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:57:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:58:01: 8000000 INFO @ Fri, 04 Aug 2017 14:58:04: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 14:58:04: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 14:58:04: #1 total tags in treatment: 8460361 INFO @ Fri, 04 Aug 2017 14:58:04: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:58:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 14:58:04: #1 tags after filtering in treatment: 8460361 INFO @ Fri, 04 Aug 2017 14:58:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 14:58:04: #1 finished! INFO @ Fri, 04 Aug 2017 14:58:04: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:58:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:58:05: #2 number of paired peaks: 2010 INFO @ Fri, 04 Aug 2017 14:58:05: start model_add_line... INFO @ Fri, 04 Aug 2017 14:58:05: start X-correlation... INFO @ Fri, 04 Aug 2017 14:58:05: end of X-cor INFO @ Fri, 04 Aug 2017 14:58:05: #2 finished! INFO @ Fri, 04 Aug 2017 14:58:05: #2 predicted fragment length is 125 bps INFO @ Fri, 04 Aug 2017 14:58:05: #2 alternative fragment length(s) may be 47,125,272 bps INFO @ Fri, 04 Aug 2017 14:58:05: #2.2 Generate R script for model : SRX2520645.10_model.r INFO @ Fri, 04 Aug 2017 14:58:05: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:58:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:58:17: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:58:19: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:58:26: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:58:28: #4 Write output xls file... SRX2520645.20_peaks.xls INFO @ Fri, 04 Aug 2017 14:58:28: #4 Write peak in narrowPeak format file... SRX2520645.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 14:58:28: #4 Write summits bed file... SRX2520645.20_summits.bed INFO @ Fri, 04 Aug 2017 14:58:28: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (303 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 14:58:32: #4 Write output xls file... SRX2520645.05_peaks.xls INFO @ Fri, 04 Aug 2017 14:58:32: #4 Write peak in narrowPeak format file... SRX2520645.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 14:58:32: #4 Write summits bed file... SRX2520645.05_summits.bed INFO @ Fri, 04 Aug 2017 14:58:32: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4921 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 14:58:38: #4 Write output xls file... SRX2520645.10_peaks.xls INFO @ Fri, 04 Aug 2017 14:58:38: #4 Write peak in narrowPeak format file... SRX2520645.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 14:58:38: #4 Write summits bed file... SRX2520645.10_summits.bed INFO @ Fri, 04 Aug 2017 14:58:38: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1322 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。