Job ID = 10450725 sra ファイルのダウンロード中... Completed: 491814K bytes transferred in 36 seconds (111342K 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 25924790 spots for /home/okishinya/chipatlas/results/dm3/SRX3404015/SRR6303492.sra Written 25924790 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:08 25924790 reads; of these: 25924790 (100.00%) were unpaired; of these: 6271648 (24.19%) aligned 0 times 14570035 (56.20%) aligned exactly 1 time 5083107 (19.61%) aligned >1 times 75.81% overall alignment rate Time searching: 00:08:08 Overall time: 00:08:08 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] 4486082 / 19653142 = 0.2283 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 13:41:31: # Command line: callpeak -t SRX3404015.bam -f BAM -g dm -n SRX3404015.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404015.10 # format = BAM # ChIP-seq file = ['SRX3404015.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 13:41:31: #1 read tag files... INFO @ Wed, 07 Feb 2018 13:41:31: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 13:41:31: # Command line: callpeak -t SRX3404015.bam -f BAM -g dm -n SRX3404015.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404015.05 # format = BAM # ChIP-seq file = ['SRX3404015.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 13:41:31: #1 read tag files... INFO @ Wed, 07 Feb 2018 13:41:31: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 13:41:31: # Command line: callpeak -t SRX3404015.bam -f BAM -g dm -n SRX3404015.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404015.20 # format = BAM # ChIP-seq file = ['SRX3404015.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 13:41:31: #1 read tag files... INFO @ Wed, 07 Feb 2018 13:41:31: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 13:41:38: 1000000 INFO @ Wed, 07 Feb 2018 13:41:38: 1000000 INFO @ Wed, 07 Feb 2018 13:41:38: 1000000 INFO @ Wed, 07 Feb 2018 13:41:44: 2000000 INFO @ Wed, 07 Feb 2018 13:41:44: 2000000 INFO @ Wed, 07 Feb 2018 13:41:44: 2000000 INFO @ Wed, 07 Feb 2018 13:41:50: 3000000 INFO @ Wed, 07 Feb 2018 13:41:51: 3000000 INFO @ Wed, 07 Feb 2018 13:41:51: 3000000 INFO @ Wed, 07 Feb 2018 13:41:57: 4000000 INFO @ Wed, 07 Feb 2018 13:41:58: 4000000 INFO @ Wed, 07 Feb 2018 13:41:58: 4000000 INFO @ Wed, 07 Feb 2018 13:42:03: 5000000 INFO @ Wed, 07 Feb 2018 13:42:04: 5000000 INFO @ Wed, 07 Feb 2018 13:42:04: 5000000 INFO @ Wed, 07 Feb 2018 13:42:09: 6000000 INFO @ Wed, 07 Feb 2018 13:42:11: 6000000 INFO @ Wed, 07 Feb 2018 13:42:11: 6000000 INFO @ Wed, 07 Feb 2018 13:42:15: 7000000 INFO @ Wed, 07 Feb 2018 13:42:18: 7000000 INFO @ Wed, 07 Feb 2018 13:42:18: 7000000 INFO @ Wed, 07 Feb 2018 13:42:22: 8000000 INFO @ Wed, 07 Feb 2018 13:42:24: 8000000 INFO @ Wed, 07 Feb 2018 13:42:25: 8000000 INFO @ Wed, 07 Feb 2018 13:42:28: 9000000 INFO @ Wed, 07 Feb 2018 13:42:31: 9000000 INFO @ Wed, 07 Feb 2018 13:42:31: 9000000 INFO @ Wed, 07 Feb 2018 13:42:34: 10000000 INFO @ Wed, 07 Feb 2018 13:42:38: 10000000 INFO @ Wed, 07 Feb 2018 13:42:38: 10000000 INFO @ Wed, 07 Feb 2018 13:42:41: 11000000 INFO @ Wed, 07 Feb 2018 13:42:45: 11000000 INFO @ Wed, 07 Feb 2018 13:42:45: 11000000 INFO @ Wed, 07 Feb 2018 13:42:47: 12000000 INFO @ Wed, 07 Feb 2018 13:42:52: 12000000 INFO @ Wed, 07 Feb 2018 13:42:52: 12000000 INFO @ Wed, 07 Feb 2018 13:42:53: 13000000 INFO @ Wed, 07 Feb 2018 13:42:59: 13000000 INFO @ Wed, 07 Feb 2018 13:42:59: 14000000 INFO @ Wed, 07 Feb 2018 13:43:00: 13000000 INFO @ Wed, 07 Feb 2018 13:43:06: 14000000 INFO @ Wed, 07 Feb 2018 13:43:06: 15000000 INFO @ Wed, 07 Feb 2018 13:43:07: 14000000 INFO @ Wed, 07 Feb 2018 13:43:07: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 13:43:07: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 13:43:07: #1 total tags in treatment: 15167060 INFO @ Wed, 07 Feb 2018 13:43:07: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 13:43:07: #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 13:43:07: #1 tags after filtering in treatment: 15167060 INFO @ Wed, 07 Feb 2018 13:43:07: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 13:43:07: #1 finished! INFO @ Wed, 07 Feb 2018 13:43:07: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 13:43:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 13:43:09: #2 number of paired peaks: 1358 INFO @ Wed, 07 Feb 2018 13:43:09: start model_add_line... INFO @ Wed, 07 Feb 2018 13:43:09: start X-correlation... INFO @ Wed, 07 Feb 2018 13:43:09: end of X-cor INFO @ Wed, 07 Feb 2018 13:43:09: #2 finished! INFO @ Wed, 07 Feb 2018 13:43:09: #2 predicted fragment length is 157 bps INFO @ Wed, 07 Feb 2018 13:43:09: #2 alternative fragment length(s) may be 157 bps INFO @ Wed, 07 Feb 2018 13:43:09: #2.2 Generate R script for model : SRX3404015.05_model.r INFO @ Wed, 07 Feb 2018 13:43:09: #3 Call peaks... INFO @ Wed, 07 Feb 2018 13:43:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 13:43:13: 15000000 INFO @ Wed, 07 Feb 2018 13:43:14: 15000000 INFO @ Wed, 07 Feb 2018 13:43:14: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 13:43:14: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 13:43:14: #1 total tags in treatment: 15167060 INFO @ Wed, 07 Feb 2018 13:43:14: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 13:43:14: #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 13:43:14: #1 tags after filtering in treatment: 15167060 INFO @ Wed, 07 Feb 2018 13:43:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 13:43:14: #1 finished! INFO @ Wed, 07 Feb 2018 13:43:14: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 13:43:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 13:43:15: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 13:43:15: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 13:43:15: #1 total tags in treatment: 15167060 INFO @ Wed, 07 Feb 2018 13:43:15: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 13:43:15: #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 13:43:15: #1 tags after filtering in treatment: 15167060 INFO @ Wed, 07 Feb 2018 13:43:15: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 13:43:15: #1 finished! INFO @ Wed, 07 Feb 2018 13:43:15: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 13:43:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 13:43:16: #2 number of paired peaks: 1358 INFO @ Wed, 07 Feb 2018 13:43:16: start model_add_line... INFO @ Wed, 07 Feb 2018 13:43:16: start X-correlation... INFO @ Wed, 07 Feb 2018 13:43:16: end of X-cor INFO @ Wed, 07 Feb 2018 13:43:16: #2 finished! INFO @ Wed, 07 Feb 2018 13:43:16: #2 predicted fragment length is 157 bps INFO @ Wed, 07 Feb 2018 13:43:16: #2 alternative fragment length(s) may be 157 bps INFO @ Wed, 07 Feb 2018 13:43:16: #2.2 Generate R script for model : SRX3404015.20_model.r INFO @ Wed, 07 Feb 2018 13:43:16: #3 Call peaks... INFO @ Wed, 07 Feb 2018 13:43:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 13:43:17: #2 number of paired peaks: 1358 INFO @ Wed, 07 Feb 2018 13:43:17: start model_add_line... INFO @ Wed, 07 Feb 2018 13:43:17: start X-correlation... INFO @ Wed, 07 Feb 2018 13:43:17: end of X-cor INFO @ Wed, 07 Feb 2018 13:43:17: #2 finished! INFO @ Wed, 07 Feb 2018 13:43:17: #2 predicted fragment length is 157 bps INFO @ Wed, 07 Feb 2018 13:43:17: #2 alternative fragment length(s) may be 157 bps INFO @ Wed, 07 Feb 2018 13:43:17: #2.2 Generate R script for model : SRX3404015.10_model.r INFO @ Wed, 07 Feb 2018 13:43:17: #3 Call peaks... INFO @ Wed, 07 Feb 2018 13:43:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 13:43:47: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 13:43:54: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 13:43:57: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 13:44:06: #4 Write output xls file... SRX3404015.05_peaks.xls INFO @ Wed, 07 Feb 2018 13:44:06: #4 Write peak in narrowPeak format file... SRX3404015.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 13:44:07: #4 Write summits bed file... SRX3404015.05_summits.bed INFO @ Wed, 07 Feb 2018 13:44:07: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5848 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 13:44:13: #4 Write output xls file... SRX3404015.20_peaks.xls INFO @ Wed, 07 Feb 2018 13:44:13: #4 Write peak in narrowPeak format file... SRX3404015.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 13:44:13: #4 Write summits bed file... SRX3404015.20_summits.bed INFO @ Wed, 07 Feb 2018 13:44:13: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3213 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 13:44:16: #4 Write output xls file... SRX3404015.10_peaks.xls INFO @ Wed, 07 Feb 2018 13:44:16: #4 Write peak in narrowPeak format file... SRX3404015.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 13:44:16: #4 Write summits bed file... SRX3404015.10_summits.bed INFO @ Wed, 07 Feb 2018 13:44:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4466 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。