Job ID = 11244947 sra ファイルのダウンロード中... Completed: 369306K bytes transferred in 7 seconds (395012K 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 11294697 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554678/SRR7696351.sra Written 11294697 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554678/SRR7696351.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: 00:04:55 11294697 reads; of these: 11294697 (100.00%) were paired; of these: 5404304 (47.85%) aligned concordantly 0 times 4176301 (36.98%) aligned concordantly exactly 1 time 1714092 (15.18%) aligned concordantly >1 times ---- 5404304 pairs aligned concordantly 0 times; of these: 157647 (2.92%) aligned discordantly 1 time ---- 5246657 pairs aligned 0 times concordantly or discordantly; of these: 10493314 mates make up the pairs; of these: 10162621 (96.85%) aligned 0 times 135864 (1.29%) aligned exactly 1 time 194829 (1.86%) aligned >1 times 55.01% overall alignment rate Time searching: 00:04:55 Overall time: 00:04:55 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] 689489 / 6014717 = 0.1146 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 23:03:00: # Command line: callpeak -t SRX4554678.bam -f BAM -g 12100000 -n SRX4554678.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554678.10 # format = BAM # ChIP-seq file = ['SRX4554678.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 23:03:00: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:03:00: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:03:00: # Command line: callpeak -t SRX4554678.bam -f BAM -g 12100000 -n SRX4554678.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554678.05 # format = BAM # ChIP-seq file = ['SRX4554678.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 23:03:00: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:03:00: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:03:00: # Command line: callpeak -t SRX4554678.bam -f BAM -g 12100000 -n SRX4554678.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554678.20 # format = BAM # ChIP-seq file = ['SRX4554678.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 23:03:00: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:03:00: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:03:06: 1000000 INFO @ Tue, 09 Oct 2018 23:03:06: 1000000 INFO @ Tue, 09 Oct 2018 23:03:06: 1000000 INFO @ Tue, 09 Oct 2018 23:03:12: 2000000 INFO @ Tue, 09 Oct 2018 23:03:12: 2000000 INFO @ Tue, 09 Oct 2018 23:03:12: 2000000 INFO @ Tue, 09 Oct 2018 23:03:17: 3000000 INFO @ Tue, 09 Oct 2018 23:03:18: 3000000 INFO @ Tue, 09 Oct 2018 23:03:18: 3000000 INFO @ Tue, 09 Oct 2018 23:03:23: 4000000 INFO @ Tue, 09 Oct 2018 23:03:24: 4000000 INFO @ Tue, 09 Oct 2018 23:03:24: 4000000 INFO @ Tue, 09 Oct 2018 23:03:29: 5000000 INFO @ Tue, 09 Oct 2018 23:03:30: 5000000 INFO @ Tue, 09 Oct 2018 23:03:30: 5000000 INFO @ Tue, 09 Oct 2018 23:03:35: 6000000 INFO @ Tue, 09 Oct 2018 23:03:36: 6000000 INFO @ Tue, 09 Oct 2018 23:03:36: 6000000 INFO @ Tue, 09 Oct 2018 23:03:41: 7000000 INFO @ Tue, 09 Oct 2018 23:03:42: 7000000 INFO @ Tue, 09 Oct 2018 23:03:42: 7000000 INFO @ Tue, 09 Oct 2018 23:03:46: 8000000 INFO @ Tue, 09 Oct 2018 23:03:47: 8000000 INFO @ Tue, 09 Oct 2018 23:03:48: 8000000 INFO @ Tue, 09 Oct 2018 23:03:52: 9000000 INFO @ Tue, 09 Oct 2018 23:03:53: 9000000 INFO @ Tue, 09 Oct 2018 23:03:54: 9000000 INFO @ Tue, 09 Oct 2018 23:03:58: 10000000 INFO @ Tue, 09 Oct 2018 23:03:59: 10000000 INFO @ Tue, 09 Oct 2018 23:04:00: 10000000 INFO @ Tue, 09 Oct 2018 23:04:03: 11000000 INFO @ Tue, 09 Oct 2018 23:04:04: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:04:04: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:04:04: #1 total tags in treatment: 5211000 INFO @ Tue, 09 Oct 2018 23:04:04: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:04:04: #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 23:04:04: #1 tags after filtering in treatment: 2703340 INFO @ Tue, 09 Oct 2018 23:04:04: #1 Redundant rate of treatment: 0.48 INFO @ Tue, 09 Oct 2018 23:04:04: #1 finished! INFO @ Tue, 09 Oct 2018 23:04:04: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:04:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:04:04: #2 number of paired peaks: 600 WARNING @ Tue, 09 Oct 2018 23:04:04: Fewer paired peaks (600) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 600 pairs to build model! INFO @ Tue, 09 Oct 2018 23:04:04: start model_add_line... INFO @ Tue, 09 Oct 2018 23:04:04: start X-correlation... INFO @ Tue, 09 Oct 2018 23:04:04: end of X-cor INFO @ Tue, 09 Oct 2018 23:04:04: #2 finished! INFO @ Tue, 09 Oct 2018 23:04:04: #2 predicted fragment length is 254 bps INFO @ Tue, 09 Oct 2018 23:04:04: #2 alternative fragment length(s) may be 0,201,231,254,274 bps INFO @ Tue, 09 Oct 2018 23:04:04: #2.2 Generate R script for model : SRX4554678.05_model.r INFO @ Tue, 09 Oct 2018 23:04:04: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:04:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:04:05: 11000000 INFO @ Tue, 09 Oct 2018 23:04:05: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:04:05: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:04:05: #1 total tags in treatment: 5211000 INFO @ Tue, 09 Oct 2018 23:04:05: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:04:05: #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 23:04:05: 11000000 INFO @ Tue, 09 Oct 2018 23:04:06: #1 tags after filtering in treatment: 2703340 INFO @ Tue, 09 Oct 2018 23:04:06: #1 Redundant rate of treatment: 0.48 INFO @ Tue, 09 Oct 2018 23:04:06: #1 finished! INFO @ Tue, 09 Oct 2018 23:04:06: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:04:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:04:06: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:04:06: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:04:06: #1 total tags in treatment: 5211000 INFO @ Tue, 09 Oct 2018 23:04:06: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:04:06: #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 23:04:06: #2 number of paired peaks: 600 WARNING @ Tue, 09 Oct 2018 23:04:06: Fewer paired peaks (600) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 600 pairs to build model! INFO @ Tue, 09 Oct 2018 23:04:06: start model_add_line... INFO @ Tue, 09 Oct 2018 23:04:06: start X-correlation... INFO @ Tue, 09 Oct 2018 23:04:06: #1 tags after filtering in treatment: 2703340 INFO @ Tue, 09 Oct 2018 23:04:06: #1 Redundant rate of treatment: 0.48 INFO @ Tue, 09 Oct 2018 23:04:06: #1 finished! INFO @ Tue, 09 Oct 2018 23:04:06: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:04:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:04:06: end of X-cor INFO @ Tue, 09 Oct 2018 23:04:06: #2 finished! INFO @ Tue, 09 Oct 2018 23:04:06: #2 predicted fragment length is 254 bps INFO @ Tue, 09 Oct 2018 23:04:06: #2 alternative fragment length(s) may be 0,201,231,254,274 bps INFO @ Tue, 09 Oct 2018 23:04:06: #2.2 Generate R script for model : SRX4554678.20_model.r INFO @ Tue, 09 Oct 2018 23:04:06: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:04:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:04:06: #2 number of paired peaks: 600 WARNING @ Tue, 09 Oct 2018 23:04:06: Fewer paired peaks (600) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 600 pairs to build model! INFO @ Tue, 09 Oct 2018 23:04:06: start model_add_line... INFO @ Tue, 09 Oct 2018 23:04:06: start X-correlation... INFO @ Tue, 09 Oct 2018 23:04:06: end of X-cor INFO @ Tue, 09 Oct 2018 23:04:06: #2 finished! INFO @ Tue, 09 Oct 2018 23:04:06: #2 predicted fragment length is 254 bps INFO @ Tue, 09 Oct 2018 23:04:06: #2 alternative fragment length(s) may be 0,201,231,254,274 bps INFO @ Tue, 09 Oct 2018 23:04:06: #2.2 Generate R script for model : SRX4554678.10_model.r INFO @ Tue, 09 Oct 2018 23:04:06: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:04:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:04:24: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:04:26: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:04:27: #4 Write output xls file... SRX4554678.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:04:27: #4 Write peak in narrowPeak format file... SRX4554678.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:04:27: #4 Write summits bed file... SRX4554678.05_summits.bed INFO @ Tue, 09 Oct 2018 23:04:27: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (576 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:04:27: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 09 Oct 2018 23:04:29: #4 Write output xls file... SRX4554678.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:04:29: #4 Write peak in narrowPeak format file... SRX4554678.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:04:29: #4 Write summits bed file... SRX4554678.20_summits.bed INFO @ Tue, 09 Oct 2018 23:04:29: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (64 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:04:30: #4 Write output xls file... SRX4554678.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:04:30: #4 Write peak in narrowPeak format file... SRX4554678.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:04:30: #4 Write summits bed file... SRX4554678.10_summits.bed INFO @ Tue, 09 Oct 2018 23:04:30: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (232 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。