Job ID = 9730462 sra ファイルのダウンロード中... Completed: 899375K bytes transferred in 54 seconds (134110K 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 26691839 spots for /home/okishinya/chipatlas/results/dm3/SRX2829101/SRR5569911.sra Written 26691839 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: 00:13:35 26691839 reads; of these: 26691839 (100.00%) were unpaired; of these: 1227339 (4.60%) aligned 0 times 15236058 (57.08%) aligned exactly 1 time 10228442 (38.32%) aligned >1 times 95.40% overall alignment rate Time searching: 00:13:35 Overall time: 00:13:35 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] 18156199 / 25464500 = 0.7130 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 01:15:27: # Command line: callpeak -t SRX2829101.bam -f BAM -g dm -n SRX2829101.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2829101.20 # format = BAM # ChIP-seq file = ['SRX2829101.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 01:15:27: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:15:27: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:15:27: # Command line: callpeak -t SRX2829101.bam -f BAM -g dm -n SRX2829101.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2829101.10 # format = BAM # ChIP-seq file = ['SRX2829101.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 01:15:27: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:15:27: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:15:27: # Command line: callpeak -t SRX2829101.bam -f BAM -g dm -n SRX2829101.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2829101.05 # format = BAM # ChIP-seq file = ['SRX2829101.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 01:15:27: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:15:27: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:15:37: 1000000 INFO @ Sun, 03 Sep 2017 01:15:37: 1000000 INFO @ Sun, 03 Sep 2017 01:15:37: 1000000 INFO @ Sun, 03 Sep 2017 01:15:46: 2000000 INFO @ Sun, 03 Sep 2017 01:15:46: 2000000 INFO @ Sun, 03 Sep 2017 01:15:46: 2000000 INFO @ Sun, 03 Sep 2017 01:15:55: 3000000 INFO @ Sun, 03 Sep 2017 01:15:55: 3000000 INFO @ Sun, 03 Sep 2017 01:15:55: 3000000 INFO @ Sun, 03 Sep 2017 01:16:04: 4000000 INFO @ Sun, 03 Sep 2017 01:16:04: 4000000 INFO @ Sun, 03 Sep 2017 01:16:04: 4000000 INFO @ Sun, 03 Sep 2017 01:16:13: 5000000 INFO @ Sun, 03 Sep 2017 01:16:13: 5000000 INFO @ Sun, 03 Sep 2017 01:16:13: 5000000 INFO @ Sun, 03 Sep 2017 01:16:22: 6000000 INFO @ Sun, 03 Sep 2017 01:16:22: 6000000 INFO @ Sun, 03 Sep 2017 01:16:22: 6000000 INFO @ Sun, 03 Sep 2017 01:16:31: 7000000 INFO @ Sun, 03 Sep 2017 01:16:31: 7000000 INFO @ Sun, 03 Sep 2017 01:16:32: 7000000 INFO @ Sun, 03 Sep 2017 01:16:34: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:16:34: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:16:34: #1 total tags in treatment: 7308301 INFO @ Sun, 03 Sep 2017 01:16:34: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:16:34: #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 01:16:34: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:16:34: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:16:34: #1 total tags in treatment: 7308301 INFO @ Sun, 03 Sep 2017 01:16:34: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:16:34: #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 01:16:34: #1 tags after filtering in treatment: 7308301 INFO @ Sun, 03 Sep 2017 01:16:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:16:34: #1 finished! INFO @ Sun, 03 Sep 2017 01:16:34: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:16:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:16:34: #1 tags after filtering in treatment: 7308301 INFO @ Sun, 03 Sep 2017 01:16:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:16:34: #1 finished! INFO @ Sun, 03 Sep 2017 01:16:34: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:16:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:16:35: #2 number of paired peaks: 4777 INFO @ Sun, 03 Sep 2017 01:16:35: start model_add_line... INFO @ Sun, 03 Sep 2017 01:16:35: #2 number of paired peaks: 4777 INFO @ Sun, 03 Sep 2017 01:16:35: start model_add_line... INFO @ Sun, 03 Sep 2017 01:16:35: start X-correlation... INFO @ Sun, 03 Sep 2017 01:16:35: end of X-cor INFO @ Sun, 03 Sep 2017 01:16:35: #2 finished! INFO @ Sun, 03 Sep 2017 01:16:35: #2 predicted fragment length is 143 bps INFO @ Sun, 03 Sep 2017 01:16:35: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 03 Sep 2017 01:16:35: #2.2 Generate R script for model : SRX2829101.20_model.r INFO @ Sun, 03 Sep 2017 01:16:35: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:16:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:16:35: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:16:35: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:16:35: #1 total tags in treatment: 7308301 INFO @ Sun, 03 Sep 2017 01:16:35: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:16:35: #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 01:16:35: start X-correlation... INFO @ Sun, 03 Sep 2017 01:16:35: end of X-cor INFO @ Sun, 03 Sep 2017 01:16:35: #2 finished! INFO @ Sun, 03 Sep 2017 01:16:35: #2 predicted fragment length is 143 bps INFO @ Sun, 03 Sep 2017 01:16:35: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 03 Sep 2017 01:16:35: #2.2 Generate R script for model : SRX2829101.05_model.r INFO @ Sun, 03 Sep 2017 01:16:35: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:16:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:16:35: #1 tags after filtering in treatment: 7308301 INFO @ Sun, 03 Sep 2017 01:16:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:16:35: #1 finished! INFO @ Sun, 03 Sep 2017 01:16:35: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:16:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:16:36: #2 number of paired peaks: 4777 INFO @ Sun, 03 Sep 2017 01:16:36: start model_add_line... INFO @ Sun, 03 Sep 2017 01:16:36: start X-correlation... INFO @ Sun, 03 Sep 2017 01:16:36: end of X-cor INFO @ Sun, 03 Sep 2017 01:16:36: #2 finished! INFO @ Sun, 03 Sep 2017 01:16:36: #2 predicted fragment length is 143 bps INFO @ Sun, 03 Sep 2017 01:16:36: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 03 Sep 2017 01:16:36: #2.2 Generate R script for model : SRX2829101.10_model.r INFO @ Sun, 03 Sep 2017 01:16:36: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:16:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:16:56: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:16:57: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:16:58: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:17:08: #4 Write output xls file... SRX2829101.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:17:08: #4 Write peak in narrowPeak format file... SRX2829101.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:17:08: #4 Write summits bed file... SRX2829101.05_summits.bed INFO @ Sun, 03 Sep 2017 01:17:08: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11379 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:17:09: #4 Write output xls file... SRX2829101.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:17:09: #4 Write peak in narrowPeak format file... SRX2829101.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:17:09: #4 Write summits bed file... SRX2829101.20_summits.bed INFO @ Sun, 03 Sep 2017 01:17:09: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (4713 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:17:10: #4 Write output xls file... SRX2829101.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:17:10: #4 Write peak in narrowPeak format file... SRX2829101.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:17:10: #4 Write summits bed file... SRX2829101.10_summits.bed INFO @ Sun, 03 Sep 2017 01:17:10: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7890 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。