Job ID = 10480741 sra ファイルのダウンロード中... Completed: 405344K bytes transferred in 10 seconds (319839K 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 12668505 spots for /home/okishinya/chipatlas/results/dm3/SRX3380800/SRR6278163.sra Written 12668505 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: 00:05:01 12668505 reads; of these: 12668505 (100.00%) were unpaired; of these: 269478 (2.13%) aligned 0 times 9181956 (72.48%) aligned exactly 1 time 3217071 (25.39%) aligned >1 times 97.87% overall alignment rate Time searching: 00:05:01 Overall time: 00:05:01 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] 1901183 / 12399027 = 0.1533 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, 16 Mar 2018 07:55:14: # Command line: callpeak -t SRX3380800.bam -f BAM -g dm -n SRX3380800.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3380800.05 # format = BAM # ChIP-seq file = ['SRX3380800.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, 16 Mar 2018 07:55:14: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:55:14: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:55:14: # Command line: callpeak -t SRX3380800.bam -f BAM -g dm -n SRX3380800.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3380800.10 # format = BAM # ChIP-seq file = ['SRX3380800.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, 16 Mar 2018 07:55:14: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:55:14: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:55:14: # Command line: callpeak -t SRX3380800.bam -f BAM -g dm -n SRX3380800.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3380800.20 # format = BAM # ChIP-seq file = ['SRX3380800.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, 16 Mar 2018 07:55:14: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:55:14: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:55:21: 1000000 INFO @ Fri, 16 Mar 2018 07:55:22: 1000000 INFO @ Fri, 16 Mar 2018 07:55:22: 1000000 INFO @ Fri, 16 Mar 2018 07:55:28: 2000000 INFO @ Fri, 16 Mar 2018 07:55:29: 2000000 INFO @ Fri, 16 Mar 2018 07:55:29: 2000000 INFO @ Fri, 16 Mar 2018 07:55:35: 3000000 INFO @ Fri, 16 Mar 2018 07:55:37: 3000000 INFO @ Fri, 16 Mar 2018 07:55:37: 3000000 INFO @ Fri, 16 Mar 2018 07:55:42: 4000000 INFO @ Fri, 16 Mar 2018 07:55:44: 4000000 INFO @ Fri, 16 Mar 2018 07:55:44: 4000000 INFO @ Fri, 16 Mar 2018 07:55:49: 5000000 INFO @ Fri, 16 Mar 2018 07:55:52: 5000000 INFO @ Fri, 16 Mar 2018 07:55:52: 5000000 INFO @ Fri, 16 Mar 2018 07:55:56: 6000000 INFO @ Fri, 16 Mar 2018 07:55:59: 6000000 INFO @ Fri, 16 Mar 2018 07:56:00: 6000000 INFO @ Fri, 16 Mar 2018 07:56:03: 7000000 INFO @ Fri, 16 Mar 2018 07:56:07: 7000000 INFO @ Fri, 16 Mar 2018 07:56:07: 7000000 INFO @ Fri, 16 Mar 2018 07:56:10: 8000000 INFO @ Fri, 16 Mar 2018 07:56:15: 8000000 INFO @ Fri, 16 Mar 2018 07:56:15: 8000000 INFO @ Fri, 16 Mar 2018 07:56:17: 9000000 INFO @ Fri, 16 Mar 2018 07:56:22: 9000000 INFO @ Fri, 16 Mar 2018 07:56:23: 9000000 INFO @ Fri, 16 Mar 2018 07:56:24: 10000000 INFO @ Fri, 16 Mar 2018 07:56:28: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:56:28: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:56:28: #1 total tags in treatment: 10497844 INFO @ Fri, 16 Mar 2018 07:56:28: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:56:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:56:28: #1 tags after filtering in treatment: 10497844 INFO @ Fri, 16 Mar 2018 07:56:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:56:28: #1 finished! INFO @ Fri, 16 Mar 2018 07:56:28: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:56:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:56:29: #2 number of paired peaks: 1209 INFO @ Fri, 16 Mar 2018 07:56:29: start model_add_line... INFO @ Fri, 16 Mar 2018 07:56:29: start X-correlation... INFO @ Fri, 16 Mar 2018 07:56:29: end of X-cor INFO @ Fri, 16 Mar 2018 07:56:29: #2 finished! INFO @ Fri, 16 Mar 2018 07:56:29: #2 predicted fragment length is 138 bps INFO @ Fri, 16 Mar 2018 07:56:29: #2 alternative fragment length(s) may be 138 bps INFO @ Fri, 16 Mar 2018 07:56:29: #2.2 Generate R script for model : SRX3380800.10_model.r INFO @ Fri, 16 Mar 2018 07:56:29: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:56:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:56:30: 10000000 INFO @ Fri, 16 Mar 2018 07:56:31: 10000000 INFO @ Fri, 16 Mar 2018 07:56:34: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:56:34: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:56:34: #1 total tags in treatment: 10497844 INFO @ Fri, 16 Mar 2018 07:56:34: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:56:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:56:34: #1 tags after filtering in treatment: 10497844 INFO @ Fri, 16 Mar 2018 07:56:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:56:34: #1 finished! INFO @ Fri, 16 Mar 2018 07:56:34: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:56:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:56:35: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:56:35: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:56:35: #1 total tags in treatment: 10497844 INFO @ Fri, 16 Mar 2018 07:56:35: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:56:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:56:35: #1 tags after filtering in treatment: 10497844 INFO @ Fri, 16 Mar 2018 07:56:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:56:35: #1 finished! INFO @ Fri, 16 Mar 2018 07:56:35: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:56:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:56:35: #2 number of paired peaks: 1209 INFO @ Fri, 16 Mar 2018 07:56:35: start model_add_line... INFO @ Fri, 16 Mar 2018 07:56:35: start X-correlation... INFO @ Fri, 16 Mar 2018 07:56:35: end of X-cor INFO @ Fri, 16 Mar 2018 07:56:35: #2 finished! INFO @ Fri, 16 Mar 2018 07:56:35: #2 predicted fragment length is 138 bps INFO @ Fri, 16 Mar 2018 07:56:35: #2 alternative fragment length(s) may be 138 bps INFO @ Fri, 16 Mar 2018 07:56:35: #2.2 Generate R script for model : SRX3380800.05_model.r INFO @ Fri, 16 Mar 2018 07:56:35: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:56:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:56:36: #2 number of paired peaks: 1209 INFO @ Fri, 16 Mar 2018 07:56:36: start model_add_line... INFO @ Fri, 16 Mar 2018 07:56:36: start X-correlation... INFO @ Fri, 16 Mar 2018 07:56:36: end of X-cor INFO @ Fri, 16 Mar 2018 07:56:36: #2 finished! INFO @ Fri, 16 Mar 2018 07:56:36: #2 predicted fragment length is 138 bps INFO @ Fri, 16 Mar 2018 07:56:36: #2 alternative fragment length(s) may be 138 bps INFO @ Fri, 16 Mar 2018 07:56:36: #2.2 Generate R script for model : SRX3380800.20_model.r INFO @ Fri, 16 Mar 2018 07:56:36: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:56:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:56:54: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:57:01: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:57:02: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:57:08: #4 Write output xls file... SRX3380800.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:57:08: #4 Write peak in narrowPeak format file... SRX3380800.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:57:08: #4 Write summits bed file... SRX3380800.10_summits.bed INFO @ Fri, 16 Mar 2018 07:57:08: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5417 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:57:16: #4 Write output xls file... SRX3380800.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:57:16: #4 Write peak in narrowPeak format file... SRX3380800.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:57:16: #4 Write summits bed file... SRX3380800.20_summits.bed INFO @ Fri, 16 Mar 2018 07:57:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2115 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:57:18: #4 Write output xls file... SRX3380800.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:57:18: #4 Write peak in narrowPeak format file... SRX3380800.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:57:18: #4 Write summits bed file... SRX3380800.05_summits.bed INFO @ Fri, 16 Mar 2018 07:57:18: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (12108 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。