Job ID = 11171281 sra ファイルのダウンロード中... Completed: 97401K bytes transferred in 17 seconds (46887K bits/sec), in 1 file. Completed: 96395K bytes transferred in 6 seconds (123932K bits/sec), in 1 file. Completed: 96421K bytes transferred in 6 seconds (120863K bits/sec), in 1 file. Completed: 95933K bytes transferred in 7 seconds (103690K 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... Read 5045893 spots for /home/okishinya/chipatlas/results/dm3/SRX3020547/SRR5850451.sra Written 5045893 spots for /home/okishinya/chipatlas/results/dm3/SRX3020547/SRR5850451.sra Read 5081782 spots for /home/okishinya/chipatlas/results/dm3/SRX3020547/SRR5850449.sra Written 5081782 spots for /home/okishinya/chipatlas/results/dm3/SRX3020547/SRR5850449.sra Read 5076028 spots for /home/okishinya/chipatlas/results/dm3/SRX3020547/SRR5850450.sra Written 5076028 spots for /home/okishinya/chipatlas/results/dm3/SRX3020547/SRR5850450.sra Read 5127237 spots for /home/okishinya/chipatlas/results/dm3/SRX3020547/SRR5850448.sra Written 5127237 spots for /home/okishinya/chipatlas/results/dm3/SRX3020547/SRR5850448.sra 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 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: 00:07:39 20330940 reads; of these: 20330940 (100.00%) were unpaired; of these: 539735 (2.65%) aligned 0 times 14433468 (70.99%) aligned exactly 1 time 5357737 (26.35%) aligned >1 times 97.35% overall alignment rate Time searching: 00:07:39 Overall time: 00:07:39 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] 3520635 / 19791205 = 0.1779 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 @ Sat, 08 Sep 2018 13:38:36: # Command line: callpeak -t SRX3020547.bam -f BAM -g dm -n SRX3020547.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3020547.05 # format = BAM # ChIP-seq file = ['SRX3020547.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 @ Sat, 08 Sep 2018 13:38:36: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:38:36: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:38:36: # Command line: callpeak -t SRX3020547.bam -f BAM -g dm -n SRX3020547.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3020547.20 # format = BAM # ChIP-seq file = ['SRX3020547.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 @ Sat, 08 Sep 2018 13:38:36: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:38:36: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:38:36: # Command line: callpeak -t SRX3020547.bam -f BAM -g dm -n SRX3020547.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3020547.10 # format = BAM # ChIP-seq file = ['SRX3020547.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 @ Sat, 08 Sep 2018 13:38:36: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:38:36: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:38:43: 1000000 INFO @ Sat, 08 Sep 2018 13:38:43: 1000000 INFO @ Sat, 08 Sep 2018 13:38:43: 1000000 INFO @ Sat, 08 Sep 2018 13:38:49: 2000000 INFO @ Sat, 08 Sep 2018 13:38:49: 2000000 INFO @ Sat, 08 Sep 2018 13:38:50: 2000000 INFO @ Sat, 08 Sep 2018 13:38:56: 3000000 INFO @ Sat, 08 Sep 2018 13:38:56: 3000000 INFO @ Sat, 08 Sep 2018 13:38:56: 3000000 INFO @ Sat, 08 Sep 2018 13:39:02: 4000000 INFO @ Sat, 08 Sep 2018 13:39:03: 4000000 INFO @ Sat, 08 Sep 2018 13:39:03: 4000000 INFO @ Sat, 08 Sep 2018 13:39:08: 5000000 INFO @ Sat, 08 Sep 2018 13:39:09: 5000000 INFO @ Sat, 08 Sep 2018 13:39:09: 5000000 INFO @ Sat, 08 Sep 2018 13:39:15: 6000000 INFO @ Sat, 08 Sep 2018 13:39:16: 6000000 INFO @ Sat, 08 Sep 2018 13:39:16: 6000000 INFO @ Sat, 08 Sep 2018 13:39:21: 7000000 INFO @ Sat, 08 Sep 2018 13:39:22: 7000000 INFO @ Sat, 08 Sep 2018 13:39:22: 7000000 INFO @ Sat, 08 Sep 2018 13:39:27: 8000000 INFO @ Sat, 08 Sep 2018 13:39:28: 8000000 INFO @ Sat, 08 Sep 2018 13:39:29: 8000000 INFO @ Sat, 08 Sep 2018 13:39:34: 9000000 INFO @ Sat, 08 Sep 2018 13:39:35: 9000000 INFO @ Sat, 08 Sep 2018 13:39:36: 9000000 INFO @ Sat, 08 Sep 2018 13:39:40: 10000000 INFO @ Sat, 08 Sep 2018 13:39:41: 10000000 INFO @ Sat, 08 Sep 2018 13:39:42: 10000000 INFO @ Sat, 08 Sep 2018 13:39:47: 11000000 INFO @ Sat, 08 Sep 2018 13:39:48: 11000000 INFO @ Sat, 08 Sep 2018 13:39:49: 11000000 INFO @ Sat, 08 Sep 2018 13:39:53: 12000000 INFO @ Sat, 08 Sep 2018 13:39:54: 12000000 INFO @ Sat, 08 Sep 2018 13:39:55: 12000000 INFO @ Sat, 08 Sep 2018 13:39:59: 13000000 INFO @ Sat, 08 Sep 2018 13:40:00: 13000000 INFO @ Sat, 08 Sep 2018 13:40:02: 13000000 INFO @ Sat, 08 Sep 2018 13:40:06: 14000000 INFO @ Sat, 08 Sep 2018 13:40:07: 14000000 INFO @ Sat, 08 Sep 2018 13:40:08: 14000000 INFO @ Sat, 08 Sep 2018 13:40:12: 15000000 INFO @ Sat, 08 Sep 2018 13:40:13: 15000000 INFO @ Sat, 08 Sep 2018 13:40:15: 15000000 INFO @ Sat, 08 Sep 2018 13:40:19: 16000000 INFO @ Sat, 08 Sep 2018 13:40:19: 16000000 INFO @ Sat, 08 Sep 2018 13:40:20: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:40:20: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:40:20: #1 total tags in treatment: 16270570 INFO @ Sat, 08 Sep 2018 13:40:20: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:40:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:40:21: #1 tags after filtering in treatment: 16270570 INFO @ Sat, 08 Sep 2018 13:40:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:40:21: #1 finished! INFO @ Sat, 08 Sep 2018 13:40:21: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:40:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:40:21: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:40:21: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:40:21: #1 total tags in treatment: 16270570 INFO @ Sat, 08 Sep 2018 13:40:21: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:40:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:40:22: #1 tags after filtering in treatment: 16270570 INFO @ Sat, 08 Sep 2018 13:40:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:40:22: #1 finished! INFO @ Sat, 08 Sep 2018 13:40:22: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:40:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:40:22: 16000000 INFO @ Sat, 08 Sep 2018 13:40:22: #2 number of paired peaks: 2338 INFO @ Sat, 08 Sep 2018 13:40:22: start model_add_line... INFO @ Sat, 08 Sep 2018 13:40:22: start X-correlation... INFO @ Sat, 08 Sep 2018 13:40:23: end of X-cor INFO @ Sat, 08 Sep 2018 13:40:23: #2 finished! INFO @ Sat, 08 Sep 2018 13:40:23: #2 predicted fragment length is 146 bps INFO @ Sat, 08 Sep 2018 13:40:23: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 08 Sep 2018 13:40:23: #2.2 Generate R script for model : SRX3020547.20_model.r INFO @ Sat, 08 Sep 2018 13:40:23: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:40:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:40:23: #2 number of paired peaks: 2338 INFO @ Sat, 08 Sep 2018 13:40:23: start model_add_line... INFO @ Sat, 08 Sep 2018 13:40:23: start X-correlation... INFO @ Sat, 08 Sep 2018 13:40:23: end of X-cor INFO @ Sat, 08 Sep 2018 13:40:23: #2 finished! INFO @ Sat, 08 Sep 2018 13:40:23: #2 predicted fragment length is 146 bps INFO @ Sat, 08 Sep 2018 13:40:23: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 08 Sep 2018 13:40:23: #2.2 Generate R script for model : SRX3020547.10_model.r INFO @ Sat, 08 Sep 2018 13:40:23: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:40:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:40:23: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:40:23: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:40:23: #1 total tags in treatment: 16270570 INFO @ Sat, 08 Sep 2018 13:40:23: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:40:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:40:24: #1 tags after filtering in treatment: 16270570 INFO @ Sat, 08 Sep 2018 13:40:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:40:24: #1 finished! INFO @ Sat, 08 Sep 2018 13:40:24: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:40:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:40:25: #2 number of paired peaks: 2338 INFO @ Sat, 08 Sep 2018 13:40:25: start model_add_line... INFO @ Sat, 08 Sep 2018 13:40:26: start X-correlation... INFO @ Sat, 08 Sep 2018 13:40:26: end of X-cor INFO @ Sat, 08 Sep 2018 13:40:26: #2 finished! INFO @ Sat, 08 Sep 2018 13:40:26: #2 predicted fragment length is 146 bps INFO @ Sat, 08 Sep 2018 13:40:26: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 08 Sep 2018 13:40:26: #2.2 Generate R script for model : SRX3020547.05_model.r INFO @ Sat, 08 Sep 2018 13:40:26: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:40:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:41:01: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:41:01: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:41:07: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:41:21: #4 Write output xls file... SRX3020547.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:41:21: #4 Write peak in narrowPeak format file... SRX3020547.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:41:22: #4 Write summits bed file... SRX3020547.10_summits.bed INFO @ Sat, 08 Sep 2018 13:41:22: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7384 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:41:23: #4 Write output xls file... SRX3020547.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:41:23: #4 Write peak in narrowPeak format file... SRX3020547.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:41:23: #4 Write summits bed file... SRX3020547.20_summits.bed INFO @ Sat, 08 Sep 2018 13:41:23: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4918 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:41:27: #4 Write output xls file... SRX3020547.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:41:28: #4 Write peak in narrowPeak format file... SRX3020547.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:41:28: #4 Write summits bed file... SRX3020547.05_summits.bed INFO @ Sat, 08 Sep 2018 13:41:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9048 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。