Job ID = 10609515 sra ファイルのダウンロード中... Completed: 970883K bytes transferred in 25 seconds (311466K 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 54047251 spots for /home/okishinya/chipatlas/results/dm3/SRX3011244/SRR5834721.sra Written 54047251 spots for /home/okishinya/chipatlas/results/dm3/SRX3011244/SRR5834721.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 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:50 54047251 reads; of these: 54047251 (100.00%) were unpaired; of these: 395112 (0.73%) aligned 0 times 52625844 (97.37%) aligned exactly 1 time 1026295 (1.90%) aligned >1 times 99.27% overall alignment rate Time searching: 00:08:51 Overall time: 00:08:51 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 24 files... [bam_rmdupse_core] 40356565 / 53652139 = 0.7522 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 @ Mon, 07 May 2018 11:15:47: # Command line: callpeak -t SRX3011244.bam -f BAM -g dm -n SRX3011244.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3011244.20 # format = BAM # ChIP-seq file = ['SRX3011244.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 @ Mon, 07 May 2018 11:15:47: #1 read tag files... INFO @ Mon, 07 May 2018 11:15:47: #1 read treatment tags... INFO @ Mon, 07 May 2018 11:15:47: # Command line: callpeak -t SRX3011244.bam -f BAM -g dm -n SRX3011244.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3011244.10 # format = BAM # ChIP-seq file = ['SRX3011244.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 @ Mon, 07 May 2018 11:15:47: #1 read tag files... INFO @ Mon, 07 May 2018 11:15:47: #1 read treatment tags... INFO @ Mon, 07 May 2018 11:15:47: # Command line: callpeak -t SRX3011244.bam -f BAM -g dm -n SRX3011244.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3011244.05 # format = BAM # ChIP-seq file = ['SRX3011244.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 @ Mon, 07 May 2018 11:15:47: #1 read tag files... INFO @ Mon, 07 May 2018 11:15:47: #1 read treatment tags... INFO @ Mon, 07 May 2018 11:15:53: 1000000 INFO @ Mon, 07 May 2018 11:15:53: 1000000 INFO @ Mon, 07 May 2018 11:15:53: 1000000 INFO @ Mon, 07 May 2018 11:15:59: 2000000 INFO @ Mon, 07 May 2018 11:15:59: 2000000 INFO @ Mon, 07 May 2018 11:15:59: 2000000 INFO @ Mon, 07 May 2018 11:16:05: 3000000 INFO @ Mon, 07 May 2018 11:16:05: 3000000 INFO @ Mon, 07 May 2018 11:16:05: 3000000 INFO @ Mon, 07 May 2018 11:16:10: 4000000 INFO @ Mon, 07 May 2018 11:16:11: 4000000 INFO @ Mon, 07 May 2018 11:16:11: 4000000 INFO @ Mon, 07 May 2018 11:16:16: 5000000 INFO @ Mon, 07 May 2018 11:16:17: 5000000 INFO @ Mon, 07 May 2018 11:16:17: 5000000 INFO @ Mon, 07 May 2018 11:16:22: 6000000 INFO @ Mon, 07 May 2018 11:16:23: 6000000 INFO @ Mon, 07 May 2018 11:16:23: 6000000 INFO @ Mon, 07 May 2018 11:16:28: 7000000 INFO @ Mon, 07 May 2018 11:16:29: 7000000 INFO @ Mon, 07 May 2018 11:16:29: 7000000 INFO @ Mon, 07 May 2018 11:16:34: 8000000 INFO @ Mon, 07 May 2018 11:16:35: 8000000 INFO @ Mon, 07 May 2018 11:16:35: 8000000 INFO @ Mon, 07 May 2018 11:16:40: 9000000 INFO @ Mon, 07 May 2018 11:16:41: 9000000 INFO @ Mon, 07 May 2018 11:16:41: 9000000 INFO @ Mon, 07 May 2018 11:16:46: 10000000 INFO @ Mon, 07 May 2018 11:16:47: 10000000 INFO @ Mon, 07 May 2018 11:16:47: 10000000 INFO @ Mon, 07 May 2018 11:16:51: 11000000 INFO @ Mon, 07 May 2018 11:16:53: 11000000 INFO @ Mon, 07 May 2018 11:16:53: 11000000 INFO @ Mon, 07 May 2018 11:16:57: 12000000 INFO @ Mon, 07 May 2018 11:16:59: 12000000 INFO @ Mon, 07 May 2018 11:16:59: 12000000 INFO @ Mon, 07 May 2018 11:17:03: 13000000 INFO @ Mon, 07 May 2018 11:17:05: #1 tag size is determined as 50 bps INFO @ Mon, 07 May 2018 11:17:05: #1 tag size = 50 INFO @ Mon, 07 May 2018 11:17:05: #1 total tags in treatment: 13295574 INFO @ Mon, 07 May 2018 11:17:05: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 11:17:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 11:17:05: 13000000 INFO @ Mon, 07 May 2018 11:17:05: #1 tags after filtering in treatment: 13295574 INFO @ Mon, 07 May 2018 11:17:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 11:17:05: #1 finished! INFO @ Mon, 07 May 2018 11:17:05: #2 Build Peak Model... INFO @ Mon, 07 May 2018 11:17:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 11:17:05: 13000000 INFO @ Mon, 07 May 2018 11:17:07: #2 number of paired peaks: 8616 INFO @ Mon, 07 May 2018 11:17:07: start model_add_line... INFO @ Mon, 07 May 2018 11:17:07: #1 tag size is determined as 50 bps INFO @ Mon, 07 May 2018 11:17:07: #1 tag size = 50 INFO @ Mon, 07 May 2018 11:17:07: #1 total tags in treatment: 13295574 INFO @ Mon, 07 May 2018 11:17:07: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 11:17:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 11:17:07: start X-correlation... INFO @ Mon, 07 May 2018 11:17:07: #1 tags after filtering in treatment: 13295574 INFO @ Mon, 07 May 2018 11:17:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 11:17:07: #1 finished! INFO @ Mon, 07 May 2018 11:17:07: #2 Build Peak Model... INFO @ Mon, 07 May 2018 11:17:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 11:17:07: end of X-cor INFO @ Mon, 07 May 2018 11:17:07: #2 finished! INFO @ Mon, 07 May 2018 11:17:07: #2 predicted fragment length is 201 bps INFO @ Mon, 07 May 2018 11:17:07: #2 alternative fragment length(s) may be 201 bps INFO @ Mon, 07 May 2018 11:17:07: #2.2 Generate R script for model : SRX3011244.20_model.r INFO @ Mon, 07 May 2018 11:17:07: #3 Call peaks... INFO @ Mon, 07 May 2018 11:17:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 11:17:07: #1 tag size is determined as 50 bps INFO @ Mon, 07 May 2018 11:17:07: #1 tag size = 50 INFO @ Mon, 07 May 2018 11:17:07: #1 total tags in treatment: 13295574 INFO @ Mon, 07 May 2018 11:17:07: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 11:17:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 11:17:08: #1 tags after filtering in treatment: 13295574 INFO @ Mon, 07 May 2018 11:17:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 11:17:08: #1 finished! INFO @ Mon, 07 May 2018 11:17:08: #2 Build Peak Model... INFO @ Mon, 07 May 2018 11:17:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 11:17:09: #2 number of paired peaks: 8616 INFO @ Mon, 07 May 2018 11:17:09: start model_add_line... INFO @ Mon, 07 May 2018 11:17:09: start X-correlation... INFO @ Mon, 07 May 2018 11:17:09: end of X-cor INFO @ Mon, 07 May 2018 11:17:09: #2 finished! INFO @ Mon, 07 May 2018 11:17:09: #2 predicted fragment length is 201 bps INFO @ Mon, 07 May 2018 11:17:09: #2 alternative fragment length(s) may be 201 bps INFO @ Mon, 07 May 2018 11:17:09: #2.2 Generate R script for model : SRX3011244.10_model.r INFO @ Mon, 07 May 2018 11:17:09: #3 Call peaks... INFO @ Mon, 07 May 2018 11:17:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 11:17:09: #2 number of paired peaks: 8616 INFO @ Mon, 07 May 2018 11:17:09: start model_add_line... INFO @ Mon, 07 May 2018 11:17:10: start X-correlation... INFO @ Mon, 07 May 2018 11:17:10: end of X-cor INFO @ Mon, 07 May 2018 11:17:10: #2 finished! INFO @ Mon, 07 May 2018 11:17:10: #2 predicted fragment length is 201 bps INFO @ Mon, 07 May 2018 11:17:10: #2 alternative fragment length(s) may be 201 bps INFO @ Mon, 07 May 2018 11:17:10: #2.2 Generate R script for model : SRX3011244.05_model.r INFO @ Mon, 07 May 2018 11:17:10: #3 Call peaks... INFO @ Mon, 07 May 2018 11:17:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 11:18:02: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 11:18:02: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 11:18:04: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 11:18:23: #4 Write output xls file... SRX3011244.10_peaks.xls INFO @ Mon, 07 May 2018 11:18:23: #4 Write peak in narrowPeak format file... SRX3011244.10_peaks.narrowPeak INFO @ Mon, 07 May 2018 11:18:23: #4 Write summits bed file... SRX3011244.10_summits.bed INFO @ Mon, 07 May 2018 11:18:23: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (9711 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 07 May 2018 11:18:24: #4 Write output xls file... SRX3011244.05_peaks.xls INFO @ Mon, 07 May 2018 11:18:24: #4 Write peak in narrowPeak format file... SRX3011244.05_peaks.narrowPeak INFO @ Mon, 07 May 2018 11:18:24: #4 Write summits bed file... SRX3011244.05_summits.bed INFO @ Mon, 07 May 2018 11:18:24: Done! INFO @ Mon, 07 May 2018 11:18:24: #4 Write output xls file... SRX3011244.20_peaks.xls INFO @ Mon, 07 May 2018 11:18:24: #4 Write peak in narrowPeak format file... SRX3011244.20_peaks.narrowPeak INFO @ Mon, 07 May 2018 11:18:24: #4 Write summits bed file... SRX3011244.20_summits.bed INFO @ Mon, 07 May 2018 11:18:24: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (11581 records, 4 fields): 15 millis CompletedMACS2peakCalling pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (7817 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。