Job ID = 11240732 sra ファイルのダウンロード中... Completed: 542303K bytes transferred in 16 seconds (270127K 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 30240617 spots for /home/okishinya/chipatlas/results/dm3/SRX4669016/SRR7817541.sra Written 30240617 spots for /home/okishinya/chipatlas/results/dm3/SRX4669016/SRR7817541.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: 00:08:17 30240617 reads; of these: 30240617 (100.00%) were unpaired; of these: 2743583 (9.07%) aligned 0 times 22412630 (74.11%) aligned exactly 1 time 5084404 (16.81%) aligned >1 times 90.93% overall alignment rate Time searching: 00:08:17 Overall time: 00:08:17 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] 10653931 / 27497034 = 0.3875 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, 07 Oct 2018 20:43:55: # Command line: callpeak -t SRX4669016.bam -f BAM -g dm -n SRX4669016.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669016.10 # format = BAM # ChIP-seq file = ['SRX4669016.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, 07 Oct 2018 20:43:55: # Command line: callpeak -t SRX4669016.bam -f BAM -g dm -n SRX4669016.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669016.05 # format = BAM # ChIP-seq file = ['SRX4669016.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, 07 Oct 2018 20:43:55: # Command line: callpeak -t SRX4669016.bam -f BAM -g dm -n SRX4669016.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669016.20 # format = BAM # ChIP-seq file = ['SRX4669016.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, 07 Oct 2018 20:43:55: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:43:55: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:43:55: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:43:55: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:43:55: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:43:55: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:44:02: 1000000 INFO @ Sun, 07 Oct 2018 20:44:02: 1000000 INFO @ Sun, 07 Oct 2018 20:44:02: 1000000 INFO @ Sun, 07 Oct 2018 20:44:08: 2000000 INFO @ Sun, 07 Oct 2018 20:44:09: 2000000 INFO @ Sun, 07 Oct 2018 20:44:09: 2000000 INFO @ Sun, 07 Oct 2018 20:44:15: 3000000 INFO @ Sun, 07 Oct 2018 20:44:16: 3000000 INFO @ Sun, 07 Oct 2018 20:44:16: 3000000 INFO @ Sun, 07 Oct 2018 20:44:22: 4000000 INFO @ Sun, 07 Oct 2018 20:44:23: 4000000 INFO @ Sun, 07 Oct 2018 20:44:23: 4000000 INFO @ Sun, 07 Oct 2018 20:44:28: 5000000 INFO @ Sun, 07 Oct 2018 20:44:29: 5000000 INFO @ Sun, 07 Oct 2018 20:44:30: 5000000 INFO @ Sun, 07 Oct 2018 20:44:35: 6000000 INFO @ Sun, 07 Oct 2018 20:44:36: 6000000 INFO @ Sun, 07 Oct 2018 20:44:36: 6000000 INFO @ Sun, 07 Oct 2018 20:44:42: 7000000 INFO @ Sun, 07 Oct 2018 20:44:43: 7000000 INFO @ Sun, 07 Oct 2018 20:44:43: 7000000 INFO @ Sun, 07 Oct 2018 20:44:48: 8000000 INFO @ Sun, 07 Oct 2018 20:44:50: 8000000 INFO @ Sun, 07 Oct 2018 20:44:50: 8000000 INFO @ Sun, 07 Oct 2018 20:44:55: 9000000 INFO @ Sun, 07 Oct 2018 20:44:57: 9000000 INFO @ Sun, 07 Oct 2018 20:44:57: 9000000 INFO @ Sun, 07 Oct 2018 20:45:02: 10000000 INFO @ Sun, 07 Oct 2018 20:45:04: 10000000 INFO @ Sun, 07 Oct 2018 20:45:04: 10000000 INFO @ Sun, 07 Oct 2018 20:45:09: 11000000 INFO @ Sun, 07 Oct 2018 20:45:11: 11000000 INFO @ Sun, 07 Oct 2018 20:45:11: 11000000 INFO @ Sun, 07 Oct 2018 20:45:16: 12000000 INFO @ Sun, 07 Oct 2018 20:45:18: 12000000 INFO @ Sun, 07 Oct 2018 20:45:18: 12000000 INFO @ Sun, 07 Oct 2018 20:45:23: 13000000 INFO @ Sun, 07 Oct 2018 20:45:25: 13000000 INFO @ Sun, 07 Oct 2018 20:45:25: 13000000 INFO @ Sun, 07 Oct 2018 20:45:31: 14000000 INFO @ Sun, 07 Oct 2018 20:45:31: 14000000 INFO @ Sun, 07 Oct 2018 20:45:32: 14000000 INFO @ Sun, 07 Oct 2018 20:45:38: 15000000 INFO @ Sun, 07 Oct 2018 20:45:38: 15000000 INFO @ Sun, 07 Oct 2018 20:45:39: 15000000 INFO @ Sun, 07 Oct 2018 20:45:45: 16000000 INFO @ Sun, 07 Oct 2018 20:45:45: 16000000 INFO @ Sun, 07 Oct 2018 20:45:47: 16000000 INFO @ Sun, 07 Oct 2018 20:45:51: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:45:51: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:45:51: #1 total tags in treatment: 16843103 INFO @ Sun, 07 Oct 2018 20:45:51: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:45:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:45:51: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:45:51: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:45:51: #1 total tags in treatment: 16843103 INFO @ Sun, 07 Oct 2018 20:45:51: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:45:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:45:51: #1 tags after filtering in treatment: 16843103 INFO @ Sun, 07 Oct 2018 20:45:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:45:51: #1 finished! INFO @ Sun, 07 Oct 2018 20:45:51: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:45:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:45:51: #1 tags after filtering in treatment: 16843103 INFO @ Sun, 07 Oct 2018 20:45:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:45:51: #1 finished! INFO @ Sun, 07 Oct 2018 20:45:51: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:45:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:45:52: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:45:52: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:45:52: #1 total tags in treatment: 16843103 INFO @ Sun, 07 Oct 2018 20:45:52: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:45:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:45:53: #2 number of paired peaks: 1772 INFO @ Sun, 07 Oct 2018 20:45:53: start model_add_line... INFO @ Sun, 07 Oct 2018 20:45:53: #1 tags after filtering in treatment: 16843103 INFO @ Sun, 07 Oct 2018 20:45:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:45:53: #1 finished! INFO @ Sun, 07 Oct 2018 20:45:53: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:45:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:45:53: #2 number of paired peaks: 1772 INFO @ Sun, 07 Oct 2018 20:45:53: start model_add_line... INFO @ Sun, 07 Oct 2018 20:45:53: start X-correlation... INFO @ Sun, 07 Oct 2018 20:45:53: end of X-cor INFO @ Sun, 07 Oct 2018 20:45:53: #2 finished! INFO @ Sun, 07 Oct 2018 20:45:53: #2 predicted fragment length is 156 bps INFO @ Sun, 07 Oct 2018 20:45:53: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 07 Oct 2018 20:45:53: #2.2 Generate R script for model : SRX4669016.20_model.r INFO @ Sun, 07 Oct 2018 20:45:53: start X-correlation... INFO @ Sun, 07 Oct 2018 20:45:53: end of X-cor INFO @ Sun, 07 Oct 2018 20:45:53: #2 finished! INFO @ Sun, 07 Oct 2018 20:45:53: #2 predicted fragment length is 156 bps INFO @ Sun, 07 Oct 2018 20:45:53: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 07 Oct 2018 20:45:53: #2.2 Generate R script for model : SRX4669016.10_model.r INFO @ Sun, 07 Oct 2018 20:45:53: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:45:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:45:54: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:45:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:45:54: #2 number of paired peaks: 1772 INFO @ Sun, 07 Oct 2018 20:45:54: start model_add_line... INFO @ Sun, 07 Oct 2018 20:45:54: start X-correlation... INFO @ Sun, 07 Oct 2018 20:45:54: end of X-cor INFO @ Sun, 07 Oct 2018 20:45:54: #2 finished! INFO @ Sun, 07 Oct 2018 20:45:54: #2 predicted fragment length is 156 bps INFO @ Sun, 07 Oct 2018 20:45:54: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 07 Oct 2018 20:45:54: #2.2 Generate R script for model : SRX4669016.05_model.r INFO @ Sun, 07 Oct 2018 20:45:54: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:45:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:46:35: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:46:36: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:46:37: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:46:58: #4 Write output xls file... SRX4669016.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:46:58: #4 Write peak in narrowPeak format file... SRX4669016.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:46:58: #4 Write summits bed file... SRX4669016.10_summits.bed INFO @ Sun, 07 Oct 2018 20:46:59: Done! INFO @ Sun, 07 Oct 2018 20:46:59: #4 Write output xls file... SRX4669016.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:46:59: #4 Write peak in narrowPeak format file... SRX4669016.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:46:59: #4 Write summits bed file... SRX4669016.20_summits.bed INFO @ Sun, 07 Oct 2018 20:47:00: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (10384 records, 4 fields): 14 millis pass1 - making usageList (13 chroms): 2 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (6216 records, 4 fields): 278 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:47:02: #4 Write output xls file... SRX4669016.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:47:02: #4 Write peak in narrowPeak format file... SRX4669016.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:47:02: #4 Write summits bed file... SRX4669016.05_summits.bed INFO @ Sun, 07 Oct 2018 20:47:02: Done! pass1 - making usageList (15 chroms): 8 millis pass2 - checking and writing primary data (14976 records, 4 fields): 27 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。