Job ID = 10480746 sra ファイルのダウンロード中... Completed: 575862K bytes transferred in 14 seconds (330281K 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... Written 21398341 spots for /home/okishinya/chipatlas/results/dm3/SRX3380805/SRR6278168.sra Written 21398341 spots total 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: 00:05:46 21398341 reads; of these: 21398341 (100.00%) were unpaired; of these: 2390356 (11.17%) aligned 0 times 17190091 (80.33%) aligned exactly 1 time 1817894 (8.50%) aligned >1 times 88.83% overall alignment rate Time searching: 00:05:46 Overall time: 00:05:46 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] 13428466 / 19007985 = 0.7065 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 @ Fri, 16 Mar 2018 07:57:17: # Command line: callpeak -t SRX3380805.bam -f BAM -g dm -n SRX3380805.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3380805.10 # format = BAM # ChIP-seq file = ['SRX3380805.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 @ Fri, 16 Mar 2018 07:57:17: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:57:17: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:57:17: # Command line: callpeak -t SRX3380805.bam -f BAM -g dm -n SRX3380805.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3380805.05 # format = BAM # ChIP-seq file = ['SRX3380805.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 @ Fri, 16 Mar 2018 07:57:17: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:57:17: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:57:17: # Command line: callpeak -t SRX3380805.bam -f BAM -g dm -n SRX3380805.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3380805.20 # format = BAM # ChIP-seq file = ['SRX3380805.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 @ Fri, 16 Mar 2018 07:57:17: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:57:17: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:57:24: 1000000 INFO @ Fri, 16 Mar 2018 07:57:24: 1000000 INFO @ Fri, 16 Mar 2018 07:57:24: 1000000 INFO @ Fri, 16 Mar 2018 07:57:31: 2000000 INFO @ Fri, 16 Mar 2018 07:57:31: 2000000 INFO @ Fri, 16 Mar 2018 07:57:31: 2000000 INFO @ Fri, 16 Mar 2018 07:57:38: 3000000 INFO @ Fri, 16 Mar 2018 07:57:38: 3000000 INFO @ Fri, 16 Mar 2018 07:57:38: 3000000 INFO @ Fri, 16 Mar 2018 07:57:44: 4000000 INFO @ Fri, 16 Mar 2018 07:57:45: 4000000 INFO @ Fri, 16 Mar 2018 07:57:45: 4000000 INFO @ Fri, 16 Mar 2018 07:57:51: 5000000 INFO @ Fri, 16 Mar 2018 07:57:52: 5000000 INFO @ Fri, 16 Mar 2018 07:57:52: 5000000 INFO @ Fri, 16 Mar 2018 07:57:55: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:57:55: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:57:55: #1 total tags in treatment: 5579519 INFO @ Fri, 16 Mar 2018 07:57:55: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:57:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:57:55: #1 tags after filtering in treatment: 5579519 INFO @ Fri, 16 Mar 2018 07:57:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:57:55: #1 finished! INFO @ Fri, 16 Mar 2018 07:57:55: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:57:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:57:56: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:57:56: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:57:56: #1 total tags in treatment: 5579519 INFO @ Fri, 16 Mar 2018 07:57:56: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:57:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:57:56: #1 tags after filtering in treatment: 5579519 INFO @ Fri, 16 Mar 2018 07:57:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:57:56: #1 finished! INFO @ Fri, 16 Mar 2018 07:57:56: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:57:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:57:56: #2 number of paired peaks: 5830 INFO @ Fri, 16 Mar 2018 07:57:56: start model_add_line... INFO @ Fri, 16 Mar 2018 07:57:56: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:57:56: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:57:56: #1 total tags in treatment: 5579519 INFO @ Fri, 16 Mar 2018 07:57:56: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:57:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:57:56: start X-correlation... INFO @ Fri, 16 Mar 2018 07:57:56: end of X-cor INFO @ Fri, 16 Mar 2018 07:57:56: #2 finished! INFO @ Fri, 16 Mar 2018 07:57:56: #2 predicted fragment length is 188 bps INFO @ Fri, 16 Mar 2018 07:57:56: #2 alternative fragment length(s) may be 188 bps INFO @ Fri, 16 Mar 2018 07:57:56: #2.2 Generate R script for model : SRX3380805.20_model.r INFO @ Fri, 16 Mar 2018 07:57:56: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:57:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:57:56: #1 tags after filtering in treatment: 5579519 INFO @ Fri, 16 Mar 2018 07:57:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:57:56: #1 finished! INFO @ Fri, 16 Mar 2018 07:57:56: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:57:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:57:57: #2 number of paired peaks: 5830 INFO @ Fri, 16 Mar 2018 07:57:57: start model_add_line... INFO @ Fri, 16 Mar 2018 07:57:57: start X-correlation... INFO @ Fri, 16 Mar 2018 07:57:57: end of X-cor INFO @ Fri, 16 Mar 2018 07:57:57: #2 finished! INFO @ Fri, 16 Mar 2018 07:57:57: #2 predicted fragment length is 188 bps INFO @ Fri, 16 Mar 2018 07:57:57: #2 alternative fragment length(s) may be 188 bps INFO @ Fri, 16 Mar 2018 07:57:57: #2.2 Generate R script for model : SRX3380805.05_model.r INFO @ Fri, 16 Mar 2018 07:57:57: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:57:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:57:57: #2 number of paired peaks: 5830 INFO @ Fri, 16 Mar 2018 07:57:57: start model_add_line... INFO @ Fri, 16 Mar 2018 07:57:57: start X-correlation... INFO @ Fri, 16 Mar 2018 07:57:57: end of X-cor INFO @ Fri, 16 Mar 2018 07:57:57: #2 finished! INFO @ Fri, 16 Mar 2018 07:57:57: #2 predicted fragment length is 188 bps INFO @ Fri, 16 Mar 2018 07:57:57: #2 alternative fragment length(s) may be 188 bps INFO @ Fri, 16 Mar 2018 07:57:57: #2.2 Generate R script for model : SRX3380805.10_model.r INFO @ Fri, 16 Mar 2018 07:57:57: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:57:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:58:12: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:58:13: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:58:13: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:58:19: #4 Write output xls file... SRX3380805.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:58:19: #4 Write peak in narrowPeak format file... SRX3380805.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:58:19: #4 Write summits bed file... SRX3380805.20_summits.bed INFO @ Fri, 16 Mar 2018 07:58:19: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3320 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:58:21: #4 Write output xls file... SRX3380805.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:58:21: #4 Write peak in narrowPeak format file... SRX3380805.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:58:21: #4 Write summits bed file... SRX3380805.05_summits.bed INFO @ Fri, 16 Mar 2018 07:58:21: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9655 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:58:22: #4 Write output xls file... SRX3380805.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:58:22: #4 Write peak in narrowPeak format file... SRX3380805.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:58:22: #4 Write summits bed file... SRX3380805.10_summits.bed INFO @ Fri, 16 Mar 2018 07:58:22: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6700 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。