Job ID = 10714581 sra ファイルのダウンロード中... Completed: 56697K bytes transferred in 3 seconds (133954K 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 3596931 spots for /home/okishinya/chipatlas/results/dm3/SRX4053335/SRR7132378.sra Written 3596931 spots for /home/okishinya/chipatlas/results/dm3/SRX4053335/SRR7132378.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: 00:00:50 3596931 reads; of these: 3596931 (100.00%) were unpaired; of these: 470860 (13.09%) aligned 0 times 2919714 (81.17%) aligned exactly 1 time 206357 (5.74%) aligned >1 times 86.91% overall alignment rate Time searching: 00:00:51 Overall time: 00:00:51 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_rmdupse_core] 636403 / 3126071 = 0.2036 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, 03 Jun 2018 13:36:41: # Command line: callpeak -t SRX4053335.bam -f BAM -g dm -n SRX4053335.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4053335.20 # format = BAM # ChIP-seq file = ['SRX4053335.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, 03 Jun 2018 13:36:41: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:36:41: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:36:41: # Command line: callpeak -t SRX4053335.bam -f BAM -g dm -n SRX4053335.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4053335.05 # format = BAM # ChIP-seq file = ['SRX4053335.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, 03 Jun 2018 13:36:41: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:36:41: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:36:41: # Command line: callpeak -t SRX4053335.bam -f BAM -g dm -n SRX4053335.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4053335.10 # format = BAM # ChIP-seq file = ['SRX4053335.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, 03 Jun 2018 13:36:41: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:36:41: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:36:47: 1000000 INFO @ Sun, 03 Jun 2018 13:36:48: 1000000 INFO @ Sun, 03 Jun 2018 13:36:48: 1000000 INFO @ Sun, 03 Jun 2018 13:36:53: 2000000 INFO @ Sun, 03 Jun 2018 13:36:54: 2000000 INFO @ Sun, 03 Jun 2018 13:36:54: 2000000 INFO @ Sun, 03 Jun 2018 13:36:56: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:36:56: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:36:56: #1 total tags in treatment: 2489668 INFO @ Sun, 03 Jun 2018 13:36:56: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:36:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:36:56: #1 tags after filtering in treatment: 2489668 INFO @ Sun, 03 Jun 2018 13:36:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:36:56: #1 finished! INFO @ Sun, 03 Jun 2018 13:36:56: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:36:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:36:56: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:36:56: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:36:56: #1 total tags in treatment: 2489668 INFO @ Sun, 03 Jun 2018 13:36:56: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:36:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:36:57: #1 tags after filtering in treatment: 2489668 INFO @ Sun, 03 Jun 2018 13:36:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:36:57: #1 finished! INFO @ Sun, 03 Jun 2018 13:36:57: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:36:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:36:57: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:36:57: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:36:57: #1 total tags in treatment: 2489668 INFO @ Sun, 03 Jun 2018 13:36:57: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:36:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:36:57: #1 tags after filtering in treatment: 2489668 INFO @ Sun, 03 Jun 2018 13:36:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:36:57: #1 finished! INFO @ Sun, 03 Jun 2018 13:36:57: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:36:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:36:57: #2 number of paired peaks: 9377 INFO @ Sun, 03 Jun 2018 13:36:57: start model_add_line... INFO @ Sun, 03 Jun 2018 13:36:57: start X-correlation... INFO @ Sun, 03 Jun 2018 13:36:57: end of X-cor INFO @ Sun, 03 Jun 2018 13:36:57: #2 finished! INFO @ Sun, 03 Jun 2018 13:36:57: #2 predicted fragment length is 198 bps INFO @ Sun, 03 Jun 2018 13:36:57: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 03 Jun 2018 13:36:57: #2.2 Generate R script for model : SRX4053335.05_model.r INFO @ Sun, 03 Jun 2018 13:36:57: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:36:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:36:57: #2 number of paired peaks: 9377 INFO @ Sun, 03 Jun 2018 13:36:57: start model_add_line... INFO @ Sun, 03 Jun 2018 13:36:57: start X-correlation... INFO @ Sun, 03 Jun 2018 13:36:57: end of X-cor INFO @ Sun, 03 Jun 2018 13:36:57: #2 finished! INFO @ Sun, 03 Jun 2018 13:36:57: #2 predicted fragment length is 198 bps INFO @ Sun, 03 Jun 2018 13:36:57: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 03 Jun 2018 13:36:57: #2.2 Generate R script for model : SRX4053335.10_model.r INFO @ Sun, 03 Jun 2018 13:36:57: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:36:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:36:57: #2 number of paired peaks: 9377 INFO @ Sun, 03 Jun 2018 13:36:57: start model_add_line... INFO @ Sun, 03 Jun 2018 13:36:57: start X-correlation... INFO @ Sun, 03 Jun 2018 13:36:57: end of X-cor INFO @ Sun, 03 Jun 2018 13:36:57: #2 finished! INFO @ Sun, 03 Jun 2018 13:36:57: #2 predicted fragment length is 198 bps INFO @ Sun, 03 Jun 2018 13:36:57: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 03 Jun 2018 13:36:57: #2.2 Generate R script for model : SRX4053335.20_model.r INFO @ Sun, 03 Jun 2018 13:36:57: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:36:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:37:04: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:37:04: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:37:05: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:37:07: #4 Write output xls file... SRX4053335.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:37:07: #4 Write peak in narrowPeak format file... SRX4053335.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:37:07: #4 Write summits bed file... SRX4053335.05_summits.bed INFO @ Sun, 03 Jun 2018 13:37:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5643 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:37:08: #4 Write output xls file... SRX4053335.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:37:08: #4 Write peak in narrowPeak format file... SRX4053335.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:37:08: #4 Write summits bed file... SRX4053335.10_summits.bed INFO @ Sun, 03 Jun 2018 13:37:08: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5258 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:37:08: #4 Write output xls file... SRX4053335.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:37:09: #4 Write peak in narrowPeak format file... SRX4053335.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:37:09: #4 Write summits bed file... SRX4053335.20_summits.bed INFO @ Sun, 03 Jun 2018 13:37:09: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (4304 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。