Job ID = 11245027 sra ファイルのダウンロード中... Completed: 87384K bytes transferred in 4 seconds (150558K 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 2903439 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554738/SRR7696410.sra Written 2903439 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554738/SRR7696410.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 2903439 reads; of these: 2903439 (100.00%) were paired; of these: 2366539 (81.51%) aligned concordantly 0 times 509158 (17.54%) aligned concordantly exactly 1 time 27742 (0.96%) aligned concordantly >1 times ---- 2366539 pairs aligned concordantly 0 times; of these: 758 (0.03%) aligned discordantly 1 time ---- 2365781 pairs aligned 0 times concordantly or discordantly; of these: 4731562 mates make up the pairs; of these: 4159420 (87.91%) aligned 0 times 539347 (11.40%) aligned exactly 1 time 32795 (0.69%) aligned >1 times 28.37% overall alignment rate Time searching: 00:00:50 Overall time: 00:00:50 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] 59916 / 537561 = 0.1115 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 23:11:46: # Command line: callpeak -t SRX4554738.bam -f BAM -g 12100000 -n SRX4554738.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554738.10 # format = BAM # ChIP-seq file = ['SRX4554738.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 23:11:46: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:11:46: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:11:46: # Command line: callpeak -t SRX4554738.bam -f BAM -g 12100000 -n SRX4554738.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554738.20 # format = BAM # ChIP-seq file = ['SRX4554738.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 23:11:46: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:11:46: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:11:46: # Command line: callpeak -t SRX4554738.bam -f BAM -g 12100000 -n SRX4554738.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554738.05 # format = BAM # ChIP-seq file = ['SRX4554738.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 23:11:46: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:11:46: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:11:52: 1000000 INFO @ Tue, 09 Oct 2018 23:11:53: 1000000 INFO @ Tue, 09 Oct 2018 23:11:53: 1000000 INFO @ Tue, 09 Oct 2018 23:11:56: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:11:56: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:11:56: #1 total tags in treatment: 476998 INFO @ Tue, 09 Oct 2018 23:11:56: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:11:56: #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 23:11:56: #1 tags after filtering in treatment: 312518 INFO @ Tue, 09 Oct 2018 23:11:56: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 09 Oct 2018 23:11:56: #1 finished! INFO @ Tue, 09 Oct 2018 23:11:56: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:11:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:11:56: #2 number of paired peaks: 649 WARNING @ Tue, 09 Oct 2018 23:11:56: Fewer paired peaks (649) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 649 pairs to build model! INFO @ Tue, 09 Oct 2018 23:11:56: start model_add_line... INFO @ Tue, 09 Oct 2018 23:11:56: start X-correlation... INFO @ Tue, 09 Oct 2018 23:11:56: end of X-cor INFO @ Tue, 09 Oct 2018 23:11:56: #2 finished! INFO @ Tue, 09 Oct 2018 23:11:56: #2 predicted fragment length is 195 bps INFO @ Tue, 09 Oct 2018 23:11:56: #2 alternative fragment length(s) may be 195 bps INFO @ Tue, 09 Oct 2018 23:11:56: #2.2 Generate R script for model : SRX4554738.20_model.r INFO @ Tue, 09 Oct 2018 23:11:56: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:11:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:11:57: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:11:57: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:11:57: #1 total tags in treatment: 476998 INFO @ Tue, 09 Oct 2018 23:11:57: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:11:57: #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 23:11:57: #1 tags after filtering in treatment: 312518 INFO @ Tue, 09 Oct 2018 23:11:57: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 09 Oct 2018 23:11:57: #1 finished! INFO @ Tue, 09 Oct 2018 23:11:57: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:11:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:11:57: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:11:57: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:11:57: #1 total tags in treatment: 476998 INFO @ Tue, 09 Oct 2018 23:11:57: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:11:57: #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 23:11:57: #1 tags after filtering in treatment: 312518 INFO @ Tue, 09 Oct 2018 23:11:57: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 09 Oct 2018 23:11:57: #1 finished! INFO @ Tue, 09 Oct 2018 23:11:57: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:11:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:11:57: #2 number of paired peaks: 649 WARNING @ Tue, 09 Oct 2018 23:11:57: Fewer paired peaks (649) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 649 pairs to build model! INFO @ Tue, 09 Oct 2018 23:11:57: start model_add_line... INFO @ Tue, 09 Oct 2018 23:11:57: start X-correlation... INFO @ Tue, 09 Oct 2018 23:11:57: end of X-cor INFO @ Tue, 09 Oct 2018 23:11:57: #2 finished! INFO @ Tue, 09 Oct 2018 23:11:57: #2 predicted fragment length is 195 bps INFO @ Tue, 09 Oct 2018 23:11:57: #2 alternative fragment length(s) may be 195 bps INFO @ Tue, 09 Oct 2018 23:11:57: #2.2 Generate R script for model : SRX4554738.10_model.r INFO @ Tue, 09 Oct 2018 23:11:57: #2 number of paired peaks: 649 WARNING @ Tue, 09 Oct 2018 23:11:57: Fewer paired peaks (649) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 649 pairs to build model! INFO @ Tue, 09 Oct 2018 23:11:57: start model_add_line... INFO @ Tue, 09 Oct 2018 23:11:57: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:11:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:11:57: start X-correlation... INFO @ Tue, 09 Oct 2018 23:11:57: end of X-cor INFO @ Tue, 09 Oct 2018 23:11:57: #2 finished! INFO @ Tue, 09 Oct 2018 23:11:57: #2 predicted fragment length is 195 bps INFO @ Tue, 09 Oct 2018 23:11:57: #2 alternative fragment length(s) may be 195 bps INFO @ Tue, 09 Oct 2018 23:11:57: #2.2 Generate R script for model : SRX4554738.05_model.r INFO @ Tue, 09 Oct 2018 23:11:57: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:11:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:11:57: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:11:58: #4 Write output xls file... SRX4554738.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:11:58: #4 Write peak in narrowPeak format file... SRX4554738.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:11:58: #4 Write summits bed file... SRX4554738.20_summits.bed INFO @ Tue, 09 Oct 2018 23:11:58: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (195 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:11:59: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:11:59: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:11:59: #4 Write output xls file... SRX4554738.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:11:59: #4 Write peak in narrowPeak format file... SRX4554738.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:11:59: #4 Write summits bed file... SRX4554738.10_summits.bed INFO @ Tue, 09 Oct 2018 23:11:59: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (324 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:11:59: #4 Write output xls file... SRX4554738.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:11:59: #4 Write peak in narrowPeak format file... SRX4554738.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:11:59: #4 Write summits bed file... SRX4554738.05_summits.bed INFO @ Tue, 09 Oct 2018 23:11:59: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (494 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。