Job ID = 11244927 sra ファイルのダウンロード中... Completed: 316335K bytes transferred in 7 seconds (369113K 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: PAIRED fastq に変換中... Read 9785930 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554666/SRR7696339.sra Written 9785930 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554666/SRR7696339.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: 00:03:08 9785930 reads; of these: 9785930 (100.00%) were paired; of these: 6497006 (66.39%) aligned concordantly 0 times 2825883 (28.88%) aligned concordantly exactly 1 time 463041 (4.73%) aligned concordantly >1 times ---- 6497006 pairs aligned concordantly 0 times; of these: 99038 (1.52%) aligned discordantly 1 time ---- 6397968 pairs aligned 0 times concordantly or discordantly; of these: 12795936 mates make up the pairs; of these: 12654293 (98.89%) aligned 0 times 88961 (0.70%) aligned exactly 1 time 52682 (0.41%) aligned >1 times 35.34% overall alignment rate Time searching: 00:03:08 Overall time: 00:03:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 84646 / 3368395 = 0.0251 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 @ Tue, 09 Oct 2018 22:56:34: # Command line: callpeak -t SRX4554666.bam -f BAM -g 12100000 -n SRX4554666.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554666.05 # format = BAM # ChIP-seq file = ['SRX4554666.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Tue, 09 Oct 2018 22:56:34: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:56:34: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:56:34: # Command line: callpeak -t SRX4554666.bam -f BAM -g 12100000 -n SRX4554666.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554666.20 # format = BAM # ChIP-seq file = ['SRX4554666.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Tue, 09 Oct 2018 22:56:34: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:56:34: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:56:34: # Command line: callpeak -t SRX4554666.bam -f BAM -g 12100000 -n SRX4554666.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554666.10 # format = BAM # ChIP-seq file = ['SRX4554666.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Tue, 09 Oct 2018 22:56:34: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:56:34: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:56:39: 1000000 INFO @ Tue, 09 Oct 2018 22:56:39: 1000000 INFO @ Tue, 09 Oct 2018 22:56:40: 1000000 INFO @ Tue, 09 Oct 2018 22:56:44: 2000000 INFO @ Tue, 09 Oct 2018 22:56:45: 2000000 INFO @ Tue, 09 Oct 2018 22:56:45: 2000000 INFO @ Tue, 09 Oct 2018 22:56:49: 3000000 INFO @ Tue, 09 Oct 2018 22:56:50: 3000000 INFO @ Tue, 09 Oct 2018 22:56:50: 3000000 INFO @ Tue, 09 Oct 2018 22:56:54: 4000000 INFO @ Tue, 09 Oct 2018 22:56:55: 4000000 INFO @ Tue, 09 Oct 2018 22:56:55: 4000000 INFO @ Tue, 09 Oct 2018 22:56:59: 5000000 INFO @ Tue, 09 Oct 2018 22:57:00: 5000000 INFO @ Tue, 09 Oct 2018 22:57:00: 5000000 INFO @ Tue, 09 Oct 2018 22:57:04: 6000000 INFO @ Tue, 09 Oct 2018 22:57:06: 6000000 INFO @ Tue, 09 Oct 2018 22:57:06: 6000000 INFO @ Tue, 09 Oct 2018 22:57:08: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:57:08: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:57:08: #1 total tags in treatment: 3207184 INFO @ Tue, 09 Oct 2018 22:57:08: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:57:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:57:08: #1 tags after filtering in treatment: 1658135 INFO @ Tue, 09 Oct 2018 22:57:08: #1 Redundant rate of treatment: 0.48 INFO @ Tue, 09 Oct 2018 22:57:08: #1 finished! INFO @ Tue, 09 Oct 2018 22:57:08: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:57:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:57:09: #2 number of paired peaks: 1243 INFO @ Tue, 09 Oct 2018 22:57:09: start model_add_line... INFO @ Tue, 09 Oct 2018 22:57:09: start X-correlation... INFO @ Tue, 09 Oct 2018 22:57:09: end of X-cor INFO @ Tue, 09 Oct 2018 22:57:09: #2 finished! INFO @ Tue, 09 Oct 2018 22:57:09: #2 predicted fragment length is 169 bps INFO @ Tue, 09 Oct 2018 22:57:09: #2 alternative fragment length(s) may be 0,137,169,192 bps INFO @ Tue, 09 Oct 2018 22:57:09: #2.2 Generate R script for model : SRX4554666.05_model.r INFO @ Tue, 09 Oct 2018 22:57:09: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:57:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:57:09: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:57:09: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:57:09: #1 total tags in treatment: 3207184 INFO @ Tue, 09 Oct 2018 22:57:09: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:57:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:57:09: #1 tags after filtering in treatment: 1658135 INFO @ Tue, 09 Oct 2018 22:57:09: #1 Redundant rate of treatment: 0.48 INFO @ Tue, 09 Oct 2018 22:57:09: #1 finished! INFO @ Tue, 09 Oct 2018 22:57:09: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:57:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:57:10: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:57:10: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:57:10: #1 total tags in treatment: 3207184 INFO @ Tue, 09 Oct 2018 22:57:10: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:57:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:57:10: #1 tags after filtering in treatment: 1658135 INFO @ Tue, 09 Oct 2018 22:57:10: #1 Redundant rate of treatment: 0.48 INFO @ Tue, 09 Oct 2018 22:57:10: #1 finished! INFO @ Tue, 09 Oct 2018 22:57:10: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:57:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:57:10: #2 number of paired peaks: 1243 INFO @ Tue, 09 Oct 2018 22:57:10: start model_add_line... INFO @ Tue, 09 Oct 2018 22:57:10: start X-correlation... INFO @ Tue, 09 Oct 2018 22:57:10: end of X-cor INFO @ Tue, 09 Oct 2018 22:57:10: #2 finished! INFO @ Tue, 09 Oct 2018 22:57:10: #2 predicted fragment length is 169 bps INFO @ Tue, 09 Oct 2018 22:57:10: #2 alternative fragment length(s) may be 0,137,169,192 bps INFO @ Tue, 09 Oct 2018 22:57:10: #2.2 Generate R script for model : SRX4554666.10_model.r INFO @ Tue, 09 Oct 2018 22:57:10: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:57:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:57:10: #2 number of paired peaks: 1243 INFO @ Tue, 09 Oct 2018 22:57:10: start model_add_line... INFO @ Tue, 09 Oct 2018 22:57:10: start X-correlation... INFO @ Tue, 09 Oct 2018 22:57:10: end of X-cor INFO @ Tue, 09 Oct 2018 22:57:10: #2 finished! INFO @ Tue, 09 Oct 2018 22:57:10: #2 predicted fragment length is 169 bps INFO @ Tue, 09 Oct 2018 22:57:10: #2 alternative fragment length(s) may be 0,137,169,192 bps INFO @ Tue, 09 Oct 2018 22:57:10: #2.2 Generate R script for model : SRX4554666.20_model.r INFO @ Tue, 09 Oct 2018 22:57:10: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:57:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:57:20: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:57:21: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:57:21: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:57:21: #4 Write output xls file... SRX4554666.05_peaks.xls INFO @ Tue, 09 Oct 2018 22:57:21: #4 Write peak in narrowPeak format file... SRX4554666.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:57:21: #4 Write summits bed file... SRX4554666.05_summits.bed INFO @ Tue, 09 Oct 2018 22:57:21: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (564 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 09 Oct 2018 22:57:22: #4 Write output xls file... SRX4554666.20_peaks.xls INFO @ Tue, 09 Oct 2018 22:57:22: #4 Write peak in narrowPeak format file... SRX4554666.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:57:22: #4 Write summits bed file... SRX4554666.20_summits.bed INFO @ Tue, 09 Oct 2018 22:57:22: Done! INFO @ Tue, 09 Oct 2018 22:57:22: #4 Write output xls file... SRX4554666.10_peaks.xls INFO @ Tue, 09 Oct 2018 22:57:22: #4 Write peak in narrowPeak format file... SRX4554666.10_peaks.narrowPeak pass1 - making usageList (17 chroms): 1 millis INFO @ Tue, 09 Oct 2018 22:57:22: #4 Write summits bed file... SRX4554666.10_summits.bed pass2 - checking and writing primary data (290 records, 4 fields): 2 millis INFO @ Tue, 09 Oct 2018 22:57:22: Done! CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (480 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。