Job ID = 11244992 sra ファイルのダウンロード中... Completed: 195397K bytes transferred in 7 seconds (215649K 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 5794236 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554706/SRR7696379.sra Written 5794236 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554706/SRR7696379.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: 00:03:18 5794236 reads; of these: 5794236 (100.00%) were paired; of these: 3274205 (56.51%) aligned concordantly 0 times 1476683 (25.49%) aligned concordantly exactly 1 time 1043348 (18.01%) aligned concordantly >1 times ---- 3274205 pairs aligned concordantly 0 times; of these: 1622 (0.05%) aligned discordantly 1 time ---- 3272583 pairs aligned 0 times concordantly or discordantly; of these: 6545166 mates make up the pairs; of these: 4640798 (70.90%) aligned 0 times 1204589 (18.40%) aligned exactly 1 time 699779 (10.69%) aligned >1 times 59.95% overall alignment rate Time searching: 00:03:18 Overall time: 00:03:18 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] 658772 / 2521302 = 0.2613 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 23:06:51: # Command line: callpeak -t SRX4554706.bam -f BAM -g 12100000 -n SRX4554706.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554706.05 # format = BAM # ChIP-seq file = ['SRX4554706.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 23:06:51: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:06:51: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:06:51: # Command line: callpeak -t SRX4554706.bam -f BAM -g 12100000 -n SRX4554706.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554706.10 # format = BAM # ChIP-seq file = ['SRX4554706.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 23:06:51: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:06:51: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:06:51: # Command line: callpeak -t SRX4554706.bam -f BAM -g 12100000 -n SRX4554706.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554706.20 # format = BAM # ChIP-seq file = ['SRX4554706.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 23:06:51: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:06:51: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:06:58: 1000000 INFO @ Tue, 09 Oct 2018 23:06:58: 1000000 INFO @ Tue, 09 Oct 2018 23:06:59: 1000000 INFO @ Tue, 09 Oct 2018 23:07:05: 2000000 INFO @ Tue, 09 Oct 2018 23:07:06: 2000000 INFO @ Tue, 09 Oct 2018 23:07:06: 2000000 INFO @ Tue, 09 Oct 2018 23:07:12: 3000000 INFO @ Tue, 09 Oct 2018 23:07:14: 3000000 INFO @ Tue, 09 Oct 2018 23:07:14: 3000000 INFO @ Tue, 09 Oct 2018 23:07:18: 4000000 INFO @ Tue, 09 Oct 2018 23:07:21: 4000000 INFO @ Tue, 09 Oct 2018 23:07:22: 4000000 INFO @ Tue, 09 Oct 2018 23:07:25: 5000000 INFO @ Tue, 09 Oct 2018 23:07:29: 5000000 INFO @ Tue, 09 Oct 2018 23:07:29: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:07:29: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:07:29: #1 total tags in treatment: 1861293 INFO @ Tue, 09 Oct 2018 23:07:29: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:07:29: #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 23:07:29: #1 tags after filtering in treatment: 1026012 INFO @ Tue, 09 Oct 2018 23:07:29: #1 Redundant rate of treatment: 0.45 INFO @ Tue, 09 Oct 2018 23:07:29: #1 finished! INFO @ Tue, 09 Oct 2018 23:07:29: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:07:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:07:29: #2 number of paired peaks: 141 WARNING @ Tue, 09 Oct 2018 23:07:29: Fewer paired peaks (141) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 141 pairs to build model! INFO @ Tue, 09 Oct 2018 23:07:29: start model_add_line... INFO @ Tue, 09 Oct 2018 23:07:29: start X-correlation... INFO @ Tue, 09 Oct 2018 23:07:29: end of X-cor INFO @ Tue, 09 Oct 2018 23:07:29: #2 finished! INFO @ Tue, 09 Oct 2018 23:07:29: #2 predicted fragment length is 290 bps INFO @ Tue, 09 Oct 2018 23:07:29: #2 alternative fragment length(s) may be 290,311 bps INFO @ Tue, 09 Oct 2018 23:07:29: #2.2 Generate R script for model : SRX4554706.10_model.r INFO @ Tue, 09 Oct 2018 23:07:29: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:07:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:07:31: 5000000 INFO @ Tue, 09 Oct 2018 23:07:33: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:07:33: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:07:33: #1 total tags in treatment: 1861293 INFO @ Tue, 09 Oct 2018 23:07:33: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:07:33: #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 23:07:33: #1 tags after filtering in treatment: 1026012 INFO @ Tue, 09 Oct 2018 23:07:33: #1 Redundant rate of treatment: 0.45 INFO @ Tue, 09 Oct 2018 23:07:33: #1 finished! INFO @ Tue, 09 Oct 2018 23:07:33: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:07:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:07:33: #2 number of paired peaks: 141 WARNING @ Tue, 09 Oct 2018 23:07:33: Fewer paired peaks (141) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 141 pairs to build model! INFO @ Tue, 09 Oct 2018 23:07:33: start model_add_line... INFO @ Tue, 09 Oct 2018 23:07:33: start X-correlation... INFO @ Tue, 09 Oct 2018 23:07:33: end of X-cor INFO @ Tue, 09 Oct 2018 23:07:33: #2 finished! INFO @ Tue, 09 Oct 2018 23:07:33: #2 predicted fragment length is 290 bps INFO @ Tue, 09 Oct 2018 23:07:33: #2 alternative fragment length(s) may be 290,311 bps INFO @ Tue, 09 Oct 2018 23:07:33: #2.2 Generate R script for model : SRX4554706.20_model.r INFO @ Tue, 09 Oct 2018 23:07:33: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:07:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:07:35: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:07:36: #4 Write output xls file... SRX4554706.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:07:36: #4 Write peak in narrowPeak format file... SRX4554706.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:07:36: #4 Write summits bed file... SRX4554706.10_summits.bed INFO @ Tue, 09 Oct 2018 23:07:36: Done! INFO @ Tue, 09 Oct 2018 23:07:36: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:07:36: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:07:36: #1 total tags in treatment: 1861293 INFO @ Tue, 09 Oct 2018 23:07:36: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:07:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (12 chroms): 4 millis pass2 - checking and writing primary data (26 records, 4 fields): 3 millis INFO @ Tue, 09 Oct 2018 23:07:36: #1 tags after filtering in treatment: 1026012 INFO @ Tue, 09 Oct 2018 23:07:36: #1 Redundant rate of treatment: 0.45 INFO @ Tue, 09 Oct 2018 23:07:36: #1 finished! INFO @ Tue, 09 Oct 2018 23:07:36: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:07:36: #2 looking for paired plus/minus strand peaks... CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:07:36: #2 number of paired peaks: 141 WARNING @ Tue, 09 Oct 2018 23:07:36: Fewer paired peaks (141) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 141 pairs to build model! INFO @ Tue, 09 Oct 2018 23:07:36: start model_add_line... INFO @ Tue, 09 Oct 2018 23:07:36: start X-correlation... INFO @ Tue, 09 Oct 2018 23:07:36: end of X-cor INFO @ Tue, 09 Oct 2018 23:07:36: #2 finished! INFO @ Tue, 09 Oct 2018 23:07:36: #2 predicted fragment length is 290 bps INFO @ Tue, 09 Oct 2018 23:07:36: #2 alternative fragment length(s) may be 290,311 bps INFO @ Tue, 09 Oct 2018 23:07:36: #2.2 Generate R script for model : SRX4554706.05_model.r INFO @ Tue, 09 Oct 2018 23:07:36: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:07:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:07:39: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:07:41: #4 Write output xls file... SRX4554706.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:07:41: #4 Write peak in narrowPeak format file... SRX4554706.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:07:41: #4 Write summits bed file... SRX4554706.20_summits.bed INFO @ Tue, 09 Oct 2018 23:07:41: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:07:42: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:07:44: #4 Write output xls file... SRX4554706.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:07:44: #4 Write peak in narrowPeak format file... SRX4554706.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:07:44: #4 Write summits bed file... SRX4554706.05_summits.bed INFO @ Tue, 09 Oct 2018 23:07:44: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (83 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。