Job ID = 10450894 sra ファイルのダウンロード中... Completed: 314432K bytes transferred in 9 seconds (276443K 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 16204495 spots for /home/okishinya/chipatlas/results/dm3/SRX3404031/SRR6303508.sra Written 16204495 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: 00:05:13 16204495 reads; of these: 16204495 (100.00%) were unpaired; of these: 712388 (4.40%) aligned 0 times 12613408 (77.84%) aligned exactly 1 time 2878699 (17.76%) aligned >1 times 95.60% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4363143 / 15492107 = 0.2816 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, 07 Feb 2018 15:23:19: # Command line: callpeak -t SRX3404031.bam -f BAM -g dm -n SRX3404031.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404031.05 # format = BAM # ChIP-seq file = ['SRX3404031.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 @ Wed, 07 Feb 2018 15:23:19: #1 read tag files... INFO @ Wed, 07 Feb 2018 15:23:19: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 15:23:19: # Command line: callpeak -t SRX3404031.bam -f BAM -g dm -n SRX3404031.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404031.10 # format = BAM # ChIP-seq file = ['SRX3404031.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 @ Wed, 07 Feb 2018 15:23:19: #1 read tag files... INFO @ Wed, 07 Feb 2018 15:23:19: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 15:23:19: # Command line: callpeak -t SRX3404031.bam -f BAM -g dm -n SRX3404031.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404031.20 # format = BAM # ChIP-seq file = ['SRX3404031.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 @ Wed, 07 Feb 2018 15:23:19: #1 read tag files... INFO @ Wed, 07 Feb 2018 15:23:19: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 15:23:26: 1000000 INFO @ Wed, 07 Feb 2018 15:23:26: 1000000 INFO @ Wed, 07 Feb 2018 15:23:27: 1000000 INFO @ Wed, 07 Feb 2018 15:23:33: 2000000 INFO @ Wed, 07 Feb 2018 15:23:34: 2000000 INFO @ Wed, 07 Feb 2018 15:23:34: 2000000 INFO @ Wed, 07 Feb 2018 15:23:39: 3000000 INFO @ Wed, 07 Feb 2018 15:23:41: 3000000 INFO @ Wed, 07 Feb 2018 15:23:41: 3000000 INFO @ Wed, 07 Feb 2018 15:23:46: 4000000 INFO @ Wed, 07 Feb 2018 15:23:49: 4000000 INFO @ Wed, 07 Feb 2018 15:23:49: 4000000 INFO @ Wed, 07 Feb 2018 15:23:52: 5000000 INFO @ Wed, 07 Feb 2018 15:23:56: 5000000 INFO @ Wed, 07 Feb 2018 15:23:56: 5000000 INFO @ Wed, 07 Feb 2018 15:23:58: 6000000 INFO @ Wed, 07 Feb 2018 15:24:03: 6000000 INFO @ Wed, 07 Feb 2018 15:24:04: 6000000 INFO @ Wed, 07 Feb 2018 15:24:05: 7000000 INFO @ Wed, 07 Feb 2018 15:24:11: 7000000 INFO @ Wed, 07 Feb 2018 15:24:11: 7000000 INFO @ Wed, 07 Feb 2018 15:24:11: 8000000 INFO @ Wed, 07 Feb 2018 15:24:17: 9000000 INFO @ Wed, 07 Feb 2018 15:24:18: 8000000 INFO @ Wed, 07 Feb 2018 15:24:18: 8000000 INFO @ Wed, 07 Feb 2018 15:24:24: 10000000 INFO @ Wed, 07 Feb 2018 15:24:25: 9000000 INFO @ Wed, 07 Feb 2018 15:24:25: 9000000 INFO @ Wed, 07 Feb 2018 15:24:30: 11000000 INFO @ Wed, 07 Feb 2018 15:24:31: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 15:24:31: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 15:24:31: #1 total tags in treatment: 11128964 INFO @ Wed, 07 Feb 2018 15:24:31: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 15:24:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 15:24:31: #1 tags after filtering in treatment: 11128964 INFO @ Wed, 07 Feb 2018 15:24:31: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 15:24:31: #1 finished! INFO @ Wed, 07 Feb 2018 15:24:31: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 15:24:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 15:24:32: #2 number of paired peaks: 1971 INFO @ Wed, 07 Feb 2018 15:24:32: start model_add_line... INFO @ Wed, 07 Feb 2018 15:24:32: start X-correlation... INFO @ Wed, 07 Feb 2018 15:24:32: end of X-cor INFO @ Wed, 07 Feb 2018 15:24:32: #2 finished! INFO @ Wed, 07 Feb 2018 15:24:32: #2 predicted fragment length is 251 bps INFO @ Wed, 07 Feb 2018 15:24:32: #2 alternative fragment length(s) may be 251 bps INFO @ Wed, 07 Feb 2018 15:24:32: #2.2 Generate R script for model : SRX3404031.20_model.r INFO @ Wed, 07 Feb 2018 15:24:32: #3 Call peaks... INFO @ Wed, 07 Feb 2018 15:24:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 15:24:33: 10000000 INFO @ Wed, 07 Feb 2018 15:24:33: 10000000 INFO @ Wed, 07 Feb 2018 15:24:40: 11000000 INFO @ Wed, 07 Feb 2018 15:24:40: 11000000 INFO @ Wed, 07 Feb 2018 15:24:41: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 15:24:41: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 15:24:41: #1 total tags in treatment: 11128964 INFO @ Wed, 07 Feb 2018 15:24:41: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 15:24:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 15:24:41: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 15:24:41: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 15:24:41: #1 total tags in treatment: 11128964 INFO @ Wed, 07 Feb 2018 15:24:41: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 15:24:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 15:24:41: #1 tags after filtering in treatment: 11128964 INFO @ Wed, 07 Feb 2018 15:24:41: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 15:24:41: #1 finished! INFO @ Wed, 07 Feb 2018 15:24:41: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 15:24:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 15:24:41: #1 tags after filtering in treatment: 11128964 INFO @ Wed, 07 Feb 2018 15:24:41: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 15:24:41: #1 finished! INFO @ Wed, 07 Feb 2018 15:24:41: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 15:24:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 15:24:42: #2 number of paired peaks: 1971 INFO @ Wed, 07 Feb 2018 15:24:42: start model_add_line... INFO @ Wed, 07 Feb 2018 15:24:42: #2 number of paired peaks: 1971 INFO @ Wed, 07 Feb 2018 15:24:42: start model_add_line... INFO @ Wed, 07 Feb 2018 15:24:42: start X-correlation... INFO @ Wed, 07 Feb 2018 15:24:42: end of X-cor INFO @ Wed, 07 Feb 2018 15:24:42: #2 finished! INFO @ Wed, 07 Feb 2018 15:24:42: #2 predicted fragment length is 251 bps INFO @ Wed, 07 Feb 2018 15:24:42: #2 alternative fragment length(s) may be 251 bps INFO @ Wed, 07 Feb 2018 15:24:42: #2.2 Generate R script for model : SRX3404031.05_model.r INFO @ Wed, 07 Feb 2018 15:24:42: start X-correlation... INFO @ Wed, 07 Feb 2018 15:24:42: end of X-cor INFO @ Wed, 07 Feb 2018 15:24:42: #2 finished! INFO @ Wed, 07 Feb 2018 15:24:42: #2 predicted fragment length is 251 bps INFO @ Wed, 07 Feb 2018 15:24:42: #2 alternative fragment length(s) may be 251 bps INFO @ Wed, 07 Feb 2018 15:24:42: #2.2 Generate R script for model : SRX3404031.10_model.r INFO @ Wed, 07 Feb 2018 15:24:42: #3 Call peaks... INFO @ Wed, 07 Feb 2018 15:24:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 15:24:42: #3 Call peaks... INFO @ Wed, 07 Feb 2018 15:24:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 15:25:11: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 15:25:16: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 15:25:18: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 15:25:30: #4 Write output xls file... SRX3404031.20_peaks.xls INFO @ Wed, 07 Feb 2018 15:25:30: #4 Write peak in narrowPeak format file... SRX3404031.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 15:25:30: #4 Write summits bed file... SRX3404031.20_summits.bed INFO @ Wed, 07 Feb 2018 15:25:30: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3735 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 15:25:34: #4 Write output xls file... SRX3404031.10_peaks.xls INFO @ Wed, 07 Feb 2018 15:25:34: #4 Write peak in narrowPeak format file... SRX3404031.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 15:25:34: #4 Write summits bed file... SRX3404031.10_summits.bed INFO @ Wed, 07 Feb 2018 15:25:34: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10241 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 15:25:36: #4 Write output xls file... SRX3404031.05_peaks.xls INFO @ Wed, 07 Feb 2018 15:25:36: #4 Write peak in narrowPeak format file... SRX3404031.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 15:25:36: #4 Write summits bed file... SRX3404031.05_summits.bed INFO @ Wed, 07 Feb 2018 15:25:36: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (19973 records, 4 fields): 24 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。