Job ID = 9730457 sra ファイルのダウンロード中... Completed: 633773K bytes transferred in 36 seconds (140825K 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 20266485 spots for /home/okishinya/chipatlas/results/dm3/SRX2829097/SRR5569907.sra Written 20266485 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:09 20266485 reads; of these: 20266485 (100.00%) were unpaired; of these: 3524699 (17.39%) aligned 0 times 14352610 (70.82%) aligned exactly 1 time 2389176 (11.79%) aligned >1 times 82.61% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:10 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] 7394338 / 16741786 = 0.4417 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 @ Sun, 03 Sep 2017 01:04:59: # Command line: callpeak -t SRX2829097.bam -f BAM -g dm -n SRX2829097.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2829097.05 # format = BAM # ChIP-seq file = ['SRX2829097.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 @ Sun, 03 Sep 2017 01:04:59: # Command line: callpeak -t SRX2829097.bam -f BAM -g dm -n SRX2829097.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2829097.20 # format = BAM # ChIP-seq file = ['SRX2829097.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 @ Sun, 03 Sep 2017 01:04:59: # Command line: callpeak -t SRX2829097.bam -f BAM -g dm -n SRX2829097.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2829097.10 # format = BAM # ChIP-seq file = ['SRX2829097.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 @ Sun, 03 Sep 2017 01:04:59: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:04:59: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:04:59: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:04:59: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:04:59: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:04:59: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:05:05: 1000000 INFO @ Sun, 03 Sep 2017 01:05:05: 1000000 INFO @ Sun, 03 Sep 2017 01:05:05: 1000000 INFO @ Sun, 03 Sep 2017 01:05:11: 2000000 INFO @ Sun, 03 Sep 2017 01:05:11: 2000000 INFO @ Sun, 03 Sep 2017 01:05:11: 2000000 INFO @ Sun, 03 Sep 2017 01:05:17: 3000000 INFO @ Sun, 03 Sep 2017 01:05:17: 3000000 INFO @ Sun, 03 Sep 2017 01:05:17: 3000000 INFO @ Sun, 03 Sep 2017 01:05:24: 4000000 INFO @ Sun, 03 Sep 2017 01:05:24: 4000000 INFO @ Sun, 03 Sep 2017 01:05:24: 4000000 INFO @ Sun, 03 Sep 2017 01:05:30: 5000000 INFO @ Sun, 03 Sep 2017 01:05:30: 5000000 INFO @ Sun, 03 Sep 2017 01:05:30: 5000000 INFO @ Sun, 03 Sep 2017 01:05:36: 6000000 INFO @ Sun, 03 Sep 2017 01:05:37: 6000000 INFO @ Sun, 03 Sep 2017 01:05:37: 6000000 INFO @ Sun, 03 Sep 2017 01:05:43: 7000000 INFO @ Sun, 03 Sep 2017 01:05:43: 7000000 INFO @ Sun, 03 Sep 2017 01:05:43: 7000000 INFO @ Sun, 03 Sep 2017 01:05:50: 8000000 INFO @ Sun, 03 Sep 2017 01:05:50: 8000000 INFO @ Sun, 03 Sep 2017 01:05:50: 8000000 INFO @ Sun, 03 Sep 2017 01:05:56: 9000000 INFO @ Sun, 03 Sep 2017 01:05:56: 9000000 INFO @ Sun, 03 Sep 2017 01:05:56: 9000000 INFO @ Sun, 03 Sep 2017 01:05:58: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:05:58: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:05:58: #1 total tags in treatment: 9347448 INFO @ Sun, 03 Sep 2017 01:05:58: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:05:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:05:58: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:05:58: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:05:58: #1 total tags in treatment: 9347448 INFO @ Sun, 03 Sep 2017 01:05:58: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:05:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:05:58: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:05:58: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:05:58: #1 total tags in treatment: 9347448 INFO @ Sun, 03 Sep 2017 01:05:58: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:05:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:05:58: #1 tags after filtering in treatment: 9347448 INFO @ Sun, 03 Sep 2017 01:05:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:05:58: #1 finished! INFO @ Sun, 03 Sep 2017 01:05:58: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:05:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:05:58: #1 tags after filtering in treatment: 9347448 INFO @ Sun, 03 Sep 2017 01:05:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:05:58: #1 finished! INFO @ Sun, 03 Sep 2017 01:05:58: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:05:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:05:58: #1 tags after filtering in treatment: 9347448 INFO @ Sun, 03 Sep 2017 01:05:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:05:58: #1 finished! INFO @ Sun, 03 Sep 2017 01:05:58: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:05:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:06:00: #2 number of paired peaks: 6957 INFO @ Sun, 03 Sep 2017 01:06:00: start model_add_line... INFO @ Sun, 03 Sep 2017 01:06:00: #2 number of paired peaks: 6957 INFO @ Sun, 03 Sep 2017 01:06:00: start model_add_line... INFO @ Sun, 03 Sep 2017 01:06:00: #2 number of paired peaks: 6957 INFO @ Sun, 03 Sep 2017 01:06:00: start model_add_line... INFO @ Sun, 03 Sep 2017 01:06:00: start X-correlation... INFO @ Sun, 03 Sep 2017 01:06:00: start X-correlation... INFO @ Sun, 03 Sep 2017 01:06:00: start X-correlation... INFO @ Sun, 03 Sep 2017 01:06:00: end of X-cor INFO @ Sun, 03 Sep 2017 01:06:00: end of X-cor INFO @ Sun, 03 Sep 2017 01:06:00: #2 finished! INFO @ Sun, 03 Sep 2017 01:06:00: end of X-cor INFO @ Sun, 03 Sep 2017 01:06:00: #2 finished! INFO @ Sun, 03 Sep 2017 01:06:00: #2 finished! INFO @ Sun, 03 Sep 2017 01:06:00: #2 predicted fragment length is 178 bps INFO @ Sun, 03 Sep 2017 01:06:00: #2 predicted fragment length is 178 bps INFO @ Sun, 03 Sep 2017 01:06:00: #2 predicted fragment length is 178 bps INFO @ Sun, 03 Sep 2017 01:06:00: #2 alternative fragment length(s) may be 4,178 bps INFO @ Sun, 03 Sep 2017 01:06:00: #2 alternative fragment length(s) may be 4,178 bps INFO @ Sun, 03 Sep 2017 01:06:00: #2 alternative fragment length(s) may be 4,178 bps INFO @ Sun, 03 Sep 2017 01:06:00: #2.2 Generate R script for model : SRX2829097.20_model.r INFO @ Sun, 03 Sep 2017 01:06:00: #2.2 Generate R script for model : SRX2829097.05_model.r INFO @ Sun, 03 Sep 2017 01:06:00: #2.2 Generate R script for model : SRX2829097.10_model.r INFO @ Sun, 03 Sep 2017 01:06:00: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:06:00: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:06:00: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:06:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:06:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:06:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:06:24: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:06:24: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:06:26: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:06:36: #4 Write output xls file... SRX2829097.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:06:36: #4 Write peak in narrowPeak format file... SRX2829097.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:06:36: #4 Write summits bed file... SRX2829097.20_summits.bed INFO @ Sun, 03 Sep 2017 01:06:36: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2567 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:06:37: #4 Write output xls file... SRX2829097.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:06:37: #4 Write peak in narrowPeak format file... SRX2829097.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:06:37: #4 Write summits bed file... SRX2829097.05_summits.bed INFO @ Sun, 03 Sep 2017 01:06:37: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8950 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:06:38: #4 Write output xls file... SRX2829097.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:06:38: #4 Write peak in narrowPeak format file... SRX2829097.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:06:38: #4 Write summits bed file... SRX2829097.10_summits.bed INFO @ Sun, 03 Sep 2017 01:06:38: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5996 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。