Job ID = 11244990 sra ファイルのダウンロード中... Completed: 245650K bytes transferred in 12 seconds (164519K 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 7776654 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554702/SRR7696375.sra Written 7776654 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554702/SRR7696375.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: 00:03:01 7776654 reads; of these: 7776654 (100.00%) were paired; of these: 6237959 (80.21%) aligned concordantly 0 times 1324562 (17.03%) aligned concordantly exactly 1 time 214133 (2.75%) aligned concordantly >1 times ---- 6237959 pairs aligned concordantly 0 times; of these: 1467 (0.02%) aligned discordantly 1 time ---- 6236492 pairs aligned 0 times concordantly or discordantly; of these: 12472984 mates make up the pairs; of these: 9842743 (78.91%) aligned 0 times 2294409 (18.40%) aligned exactly 1 time 335832 (2.69%) aligned >1 times 36.72% overall alignment rate Time searching: 00:03:01 Overall time: 00:03:01 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] 521785 / 1539533 = 0.3389 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 23:06:02: # Command line: callpeak -t SRX4554702.bam -f BAM -g 12100000 -n SRX4554702.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554702.10 # format = BAM # ChIP-seq file = ['SRX4554702.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 23:06:02: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:06:02: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:06:02: # Command line: callpeak -t SRX4554702.bam -f BAM -g 12100000 -n SRX4554702.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554702.05 # format = BAM # ChIP-seq file = ['SRX4554702.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 23:06:02: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:06:02: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:06:02: # Command line: callpeak -t SRX4554702.bam -f BAM -g 12100000 -n SRX4554702.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554702.20 # format = BAM # ChIP-seq file = ['SRX4554702.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 23:06:02: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:06:02: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:06:07: 1000000 INFO @ Tue, 09 Oct 2018 23:06:07: 1000000 INFO @ Tue, 09 Oct 2018 23:06:07: 1000000 INFO @ Tue, 09 Oct 2018 23:06:12: 2000000 INFO @ Tue, 09 Oct 2018 23:06:13: 2000000 INFO @ Tue, 09 Oct 2018 23:06:13: 2000000 INFO @ Tue, 09 Oct 2018 23:06:17: 3000000 INFO @ Tue, 09 Oct 2018 23:06:18: 3000000 INFO @ Tue, 09 Oct 2018 23:06:18: 3000000 INFO @ Tue, 09 Oct 2018 23:06:22: 4000000 INFO @ Tue, 09 Oct 2018 23:06:23: 4000000 INFO @ Tue, 09 Oct 2018 23:06:23: 4000000 INFO @ Tue, 09 Oct 2018 23:06:26: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:06:26: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:06:26: #1 total tags in treatment: 1016956 INFO @ Tue, 09 Oct 2018 23:06:26: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:06:26: #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 23:06:26: #1 tags after filtering in treatment: 745917 INFO @ Tue, 09 Oct 2018 23:06:26: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 09 Oct 2018 23:06:26: #1 finished! INFO @ Tue, 09 Oct 2018 23:06:26: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:06:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:06:26: #2 number of paired peaks: 184 WARNING @ Tue, 09 Oct 2018 23:06:26: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 09 Oct 2018 23:06:26: start model_add_line... INFO @ Tue, 09 Oct 2018 23:06:26: start X-correlation... INFO @ Tue, 09 Oct 2018 23:06:26: end of X-cor INFO @ Tue, 09 Oct 2018 23:06:26: #2 finished! INFO @ Tue, 09 Oct 2018 23:06:26: #2 predicted fragment length is 193 bps INFO @ Tue, 09 Oct 2018 23:06:26: #2 alternative fragment length(s) may be 18,41,63,104,157,163,193,218,239,258,303,347,443,505,508,517,541,590 bps INFO @ Tue, 09 Oct 2018 23:06:26: #2.2 Generate R script for model : SRX4554702.20_model.r INFO @ Tue, 09 Oct 2018 23:06:26: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:06:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:06:26: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:06:26: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:06:26: #1 total tags in treatment: 1016956 INFO @ Tue, 09 Oct 2018 23:06:26: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:06:26: #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 23:06:26: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:06:26: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:06:26: #1 total tags in treatment: 1016956 INFO @ Tue, 09 Oct 2018 23:06:26: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:06:26: #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 23:06:26: #1 tags after filtering in treatment: 745917 INFO @ Tue, 09 Oct 2018 23:06:26: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 09 Oct 2018 23:06:26: #1 finished! INFO @ Tue, 09 Oct 2018 23:06:26: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:06:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:06:26: #1 tags after filtering in treatment: 745917 INFO @ Tue, 09 Oct 2018 23:06:26: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 09 Oct 2018 23:06:26: #1 finished! INFO @ Tue, 09 Oct 2018 23:06:26: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:06:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:06:26: #2 number of paired peaks: 184 WARNING @ Tue, 09 Oct 2018 23:06:26: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 09 Oct 2018 23:06:26: start model_add_line... INFO @ Tue, 09 Oct 2018 23:06:26: #2 number of paired peaks: 184 WARNING @ Tue, 09 Oct 2018 23:06:26: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 09 Oct 2018 23:06:26: start model_add_line... INFO @ Tue, 09 Oct 2018 23:06:26: start X-correlation... INFO @ Tue, 09 Oct 2018 23:06:26: end of X-cor INFO @ Tue, 09 Oct 2018 23:06:26: #2 finished! INFO @ Tue, 09 Oct 2018 23:06:26: #2 predicted fragment length is 193 bps INFO @ Tue, 09 Oct 2018 23:06:26: #2 alternative fragment length(s) may be 18,41,63,104,157,163,193,218,239,258,303,347,443,505,508,517,541,590 bps INFO @ Tue, 09 Oct 2018 23:06:26: #2.2 Generate R script for model : SRX4554702.05_model.r INFO @ Tue, 09 Oct 2018 23:06:26: start X-correlation... INFO @ Tue, 09 Oct 2018 23:06:26: end of X-cor INFO @ Tue, 09 Oct 2018 23:06:26: #2 finished! INFO @ Tue, 09 Oct 2018 23:06:26: #2 predicted fragment length is 193 bps INFO @ Tue, 09 Oct 2018 23:06:26: #2 alternative fragment length(s) may be 18,41,63,104,157,163,193,218,239,258,303,347,443,505,508,517,541,590 bps INFO @ Tue, 09 Oct 2018 23:06:26: #2.2 Generate R script for model : SRX4554702.10_model.r INFO @ Tue, 09 Oct 2018 23:06:26: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:06:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:06:26: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:06:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:06:29: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:06:29: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:06:30: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:06:30: #4 Write output xls file... SRX4554702.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:06:30: #4 Write peak in narrowPeak format file... SRX4554702.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:06:30: #4 Write summits bed file... SRX4554702.20_summits.bed INFO @ Tue, 09 Oct 2018 23:06:30: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:06:30: #4 Write output xls file... SRX4554702.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:06:30: #4 Write peak in narrowPeak format file... SRX4554702.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:06:30: #4 Write summits bed file... SRX4554702.05_summits.bed INFO @ Tue, 09 Oct 2018 23:06:30: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (32 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:06:31: #4 Write output xls file... SRX4554702.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:06:31: #4 Write peak in narrowPeak format file... SRX4554702.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:06:31: #4 Write summits bed file... SRX4554702.10_summits.bed INFO @ Tue, 09 Oct 2018 23:06:31: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。