Job ID = 11171181 sra ファイルのダウンロード中... Completed: 404629K bytes transferred in 19 seconds (168253K 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 20287959 spots for /home/okishinya/chipatlas/results/dm3/SRX2618496/SRR5319050.sra Written 20287959 spots for /home/okishinya/chipatlas/results/dm3/SRX2618496/SRR5319050.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:53 20287959 reads; of these: 20287959 (100.00%) were unpaired; of these: 6203483 (30.58%) aligned 0 times 12375991 (61.00%) aligned exactly 1 time 1708485 (8.42%) aligned >1 times 69.42% overall alignment rate Time searching: 00:04:53 Overall time: 00:04:53 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] 1478485 / 14084476 = 0.1050 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 12:40:22: # Command line: callpeak -t SRX2618496.bam -f BAM -g dm -n SRX2618496.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2618496.10 # format = BAM # ChIP-seq file = ['SRX2618496.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 12:40:22: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:40:22: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:40:22: # Command line: callpeak -t SRX2618496.bam -f BAM -g dm -n SRX2618496.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2618496.05 # format = BAM # ChIP-seq file = ['SRX2618496.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 12:40:22: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:40:22: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:40:22: # Command line: callpeak -t SRX2618496.bam -f BAM -g dm -n SRX2618496.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2618496.20 # format = BAM # ChIP-seq file = ['SRX2618496.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 12:40:22: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:40:22: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:40:28: 1000000 INFO @ Sat, 08 Sep 2018 12:40:28: 1000000 INFO @ Sat, 08 Sep 2018 12:40:28: 1000000 INFO @ Sat, 08 Sep 2018 12:40:35: 2000000 INFO @ Sat, 08 Sep 2018 12:40:35: 2000000 INFO @ Sat, 08 Sep 2018 12:40:35: 2000000 INFO @ Sat, 08 Sep 2018 12:40:41: 3000000 INFO @ Sat, 08 Sep 2018 12:40:41: 3000000 INFO @ Sat, 08 Sep 2018 12:40:41: 3000000 INFO @ Sat, 08 Sep 2018 12:40:47: 4000000 INFO @ Sat, 08 Sep 2018 12:40:47: 4000000 INFO @ Sat, 08 Sep 2018 12:40:48: 4000000 INFO @ Sat, 08 Sep 2018 12:40:54: 5000000 INFO @ Sat, 08 Sep 2018 12:40:54: 5000000 INFO @ Sat, 08 Sep 2018 12:40:54: 5000000 INFO @ Sat, 08 Sep 2018 12:41:00: 6000000 INFO @ Sat, 08 Sep 2018 12:41:00: 6000000 INFO @ Sat, 08 Sep 2018 12:41:01: 6000000 INFO @ Sat, 08 Sep 2018 12:41:06: 7000000 INFO @ Sat, 08 Sep 2018 12:41:06: 7000000 INFO @ Sat, 08 Sep 2018 12:41:07: 7000000 INFO @ Sat, 08 Sep 2018 12:41:12: 8000000 INFO @ Sat, 08 Sep 2018 12:41:13: 8000000 INFO @ Sat, 08 Sep 2018 12:41:13: 8000000 INFO @ Sat, 08 Sep 2018 12:41:19: 9000000 INFO @ Sat, 08 Sep 2018 12:41:19: 9000000 INFO @ Sat, 08 Sep 2018 12:41:20: 9000000 INFO @ Sat, 08 Sep 2018 12:41:25: 10000000 INFO @ Sat, 08 Sep 2018 12:41:25: 10000000 INFO @ Sat, 08 Sep 2018 12:41:26: 10000000 INFO @ Sat, 08 Sep 2018 12:41:31: 11000000 INFO @ Sat, 08 Sep 2018 12:41:32: 11000000 INFO @ Sat, 08 Sep 2018 12:41:33: 11000000 INFO @ Sat, 08 Sep 2018 12:41:38: 12000000 INFO @ Sat, 08 Sep 2018 12:41:38: 12000000 INFO @ Sat, 08 Sep 2018 12:41:39: 12000000 INFO @ Sat, 08 Sep 2018 12:41:42: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 12:41:42: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 12:41:42: #1 total tags in treatment: 12605991 INFO @ Sat, 08 Sep 2018 12:41:42: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:41:42: #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 12:41:42: #1 tags after filtering in treatment: 12605991 INFO @ Sat, 08 Sep 2018 12:41:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:41:42: #1 finished! INFO @ Sat, 08 Sep 2018 12:41:42: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:41:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:41:42: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 12:41:42: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 12:41:42: #1 total tags in treatment: 12605991 INFO @ Sat, 08 Sep 2018 12:41:42: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:41:42: #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 12:41:42: #1 tags after filtering in treatment: 12605991 INFO @ Sat, 08 Sep 2018 12:41:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:41:42: #1 finished! INFO @ Sat, 08 Sep 2018 12:41:42: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:41:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:41:43: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 12:41:43: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 12:41:43: #1 total tags in treatment: 12605991 INFO @ Sat, 08 Sep 2018 12:41:43: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:41:43: #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 12:41:43: #2 number of paired peaks: 1180 INFO @ Sat, 08 Sep 2018 12:41:43: start model_add_line... INFO @ Sat, 08 Sep 2018 12:41:43: start X-correlation... INFO @ Sat, 08 Sep 2018 12:41:43: end of X-cor INFO @ Sat, 08 Sep 2018 12:41:43: #2 finished! INFO @ Sat, 08 Sep 2018 12:41:43: #2 predicted fragment length is 173 bps INFO @ Sat, 08 Sep 2018 12:41:43: #2 alternative fragment length(s) may be 173 bps INFO @ Sat, 08 Sep 2018 12:41:43: #2.2 Generate R script for model : SRX2618496.10_model.r INFO @ Sat, 08 Sep 2018 12:41:43: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:41:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:41:43: #1 tags after filtering in treatment: 12605991 INFO @ Sat, 08 Sep 2018 12:41:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:41:43: #1 finished! INFO @ Sat, 08 Sep 2018 12:41:43: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:41:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:41:43: #2 number of paired peaks: 1180 INFO @ Sat, 08 Sep 2018 12:41:43: start model_add_line... INFO @ Sat, 08 Sep 2018 12:41:44: start X-correlation... INFO @ Sat, 08 Sep 2018 12:41:44: end of X-cor INFO @ Sat, 08 Sep 2018 12:41:44: #2 finished! INFO @ Sat, 08 Sep 2018 12:41:44: #2 predicted fragment length is 173 bps INFO @ Sat, 08 Sep 2018 12:41:44: #2 alternative fragment length(s) may be 173 bps INFO @ Sat, 08 Sep 2018 12:41:44: #2.2 Generate R script for model : SRX2618496.05_model.r INFO @ Sat, 08 Sep 2018 12:41:44: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:41:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:41:44: #2 number of paired peaks: 1180 INFO @ Sat, 08 Sep 2018 12:41:44: start model_add_line... INFO @ Sat, 08 Sep 2018 12:41:44: start X-correlation... INFO @ Sat, 08 Sep 2018 12:41:44: end of X-cor INFO @ Sat, 08 Sep 2018 12:41:44: #2 finished! INFO @ Sat, 08 Sep 2018 12:41:44: #2 predicted fragment length is 173 bps INFO @ Sat, 08 Sep 2018 12:41:44: #2 alternative fragment length(s) may be 173 bps INFO @ Sat, 08 Sep 2018 12:41:44: #2.2 Generate R script for model : SRX2618496.20_model.r INFO @ Sat, 08 Sep 2018 12:41:44: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:41:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:42:15: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:42:15: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:42:15: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:42:31: #4 Write output xls file... SRX2618496.10_peaks.xls INFO @ Sat, 08 Sep 2018 12:42:31: #4 Write peak in narrowPeak format file... SRX2618496.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:42:31: #4 Write summits bed file... SRX2618496.10_summits.bed INFO @ Sat, 08 Sep 2018 12:42:31: Done! INFO @ Sat, 08 Sep 2018 12:42:31: #4 Write output xls file... SRX2618496.05_peaks.xls pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (5375 records, 4 fields): 9 millis INFO @ Sat, 08 Sep 2018 12:42:31: #4 Write peak in narrowPeak format file... SRX2618496.05_peaks.narrowPeak CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:42:32: #4 Write summits bed file... SRX2618496.05_summits.bed INFO @ Sat, 08 Sep 2018 12:42:32: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (8026 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:42:32: #4 Write output xls file... SRX2618496.20_peaks.xls INFO @ Sat, 08 Sep 2018 12:42:32: #4 Write peak in narrowPeak format file... SRX2618496.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:42:32: #4 Write summits bed file... SRX2618496.20_summits.bed INFO @ Sat, 08 Sep 2018 12:42:32: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2371 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。