Job ID = 11244925 sra ファイルのダウンロード中... Completed: 257752K bytes transferred in 7 seconds (300490K 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 9062138 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554665/SRR7696338.sra Written 9062138 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554665/SRR7696338.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: 00:05:34 9062138 reads; of these: 9062138 (100.00%) were paired; of these: 5400940 (59.60%) aligned concordantly 0 times 3146768 (34.72%) aligned concordantly exactly 1 time 514430 (5.68%) aligned concordantly >1 times ---- 5400940 pairs aligned concordantly 0 times; of these: 31699 (0.59%) aligned discordantly 1 time ---- 5369241 pairs aligned 0 times concordantly or discordantly; of these: 10738482 mates make up the pairs; of these: 5728971 (53.35%) aligned 0 times 4256842 (39.64%) aligned exactly 1 time 752669 (7.01%) aligned >1 times 68.39% overall alignment rate Time searching: 00:05:34 Overall time: 00:05:34 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] 86569 / 3690786 = 0.0235 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 22:59:51: # Command line: callpeak -t SRX4554665.bam -f BAM -g 12100000 -n SRX4554665.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554665.10 # format = BAM # ChIP-seq file = ['SRX4554665.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 22:59:51: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:59:51: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:59:51: # Command line: callpeak -t SRX4554665.bam -f BAM -g 12100000 -n SRX4554665.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554665.05 # format = BAM # ChIP-seq file = ['SRX4554665.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 22:59:51: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:59:51: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:59:51: # Command line: callpeak -t SRX4554665.bam -f BAM -g 12100000 -n SRX4554665.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554665.20 # format = BAM # ChIP-seq file = ['SRX4554665.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 22:59:51: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:59:51: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:59:56: 1000000 INFO @ Tue, 09 Oct 2018 22:59:57: 1000000 INFO @ Tue, 09 Oct 2018 22:59:57: 1000000 INFO @ Tue, 09 Oct 2018 23:00:02: 2000000 INFO @ Tue, 09 Oct 2018 23:00:02: 2000000 INFO @ Tue, 09 Oct 2018 23:00:02: 2000000 INFO @ Tue, 09 Oct 2018 23:00:08: 3000000 INFO @ Tue, 09 Oct 2018 23:00:08: 3000000 INFO @ Tue, 09 Oct 2018 23:00:08: 3000000 INFO @ Tue, 09 Oct 2018 23:00:13: 4000000 INFO @ Tue, 09 Oct 2018 23:00:14: 4000000 INFO @ Tue, 09 Oct 2018 23:00:14: 4000000 INFO @ Tue, 09 Oct 2018 23:00:19: 5000000 INFO @ Tue, 09 Oct 2018 23:00:19: 5000000 INFO @ Tue, 09 Oct 2018 23:00:20: 5000000 INFO @ Tue, 09 Oct 2018 23:00:24: 6000000 INFO @ Tue, 09 Oct 2018 23:00:25: 6000000 INFO @ Tue, 09 Oct 2018 23:00:26: 6000000 INFO @ Tue, 09 Oct 2018 23:00:30: 7000000 INFO @ Tue, 09 Oct 2018 23:00:31: 7000000 INFO @ Tue, 09 Oct 2018 23:00:32: 7000000 INFO @ Tue, 09 Oct 2018 23:00:36: 8000000 INFO @ Tue, 09 Oct 2018 23:00:37: 8000000 INFO @ Tue, 09 Oct 2018 23:00:38: 8000000 INFO @ Tue, 09 Oct 2018 23:00:41: 9000000 INFO @ Tue, 09 Oct 2018 23:00:43: 9000000 INFO @ Tue, 09 Oct 2018 23:00:44: 9000000 INFO @ Tue, 09 Oct 2018 23:00:47: 10000000 INFO @ Tue, 09 Oct 2018 23:00:49: 10000000 INFO @ Tue, 09 Oct 2018 23:00:50: 10000000 INFO @ Tue, 09 Oct 2018 23:00:52: 11000000 INFO @ Tue, 09 Oct 2018 23:00:55: 11000000 INFO @ Tue, 09 Oct 2018 23:00:56: 11000000 INFO @ Tue, 09 Oct 2018 23:00:58: 12000000 INFO @ Tue, 09 Oct 2018 23:00:59: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:00:59: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:00:59: #1 total tags in treatment: 3574928 INFO @ Tue, 09 Oct 2018 23:00:59: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:00:59: #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 23:00:59: #1 tags after filtering in treatment: 2841202 INFO @ Tue, 09 Oct 2018 23:00:59: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 09 Oct 2018 23:00:59: #1 finished! INFO @ Tue, 09 Oct 2018 23:00:59: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:00:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:00:59: #2 number of paired peaks: 159 WARNING @ Tue, 09 Oct 2018 23:00:59: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Tue, 09 Oct 2018 23:00:59: start model_add_line... INFO @ Tue, 09 Oct 2018 23:00:59: start X-correlation... INFO @ Tue, 09 Oct 2018 23:00:59: end of X-cor INFO @ Tue, 09 Oct 2018 23:00:59: #2 finished! INFO @ Tue, 09 Oct 2018 23:00:59: #2 predicted fragment length is 246 bps INFO @ Tue, 09 Oct 2018 23:00:59: #2 alternative fragment length(s) may be 0,80,175,218,246,262,280,337,582 bps INFO @ Tue, 09 Oct 2018 23:00:59: #2.2 Generate R script for model : SRX4554665.10_model.r INFO @ Tue, 09 Oct 2018 23:00:59: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:00:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:01:01: 12000000 INFO @ Tue, 09 Oct 2018 23:01:02: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:01:02: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:01:02: #1 total tags in treatment: 3574928 INFO @ Tue, 09 Oct 2018 23:01:02: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:01:02: #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 23:01:02: #1 tags after filtering in treatment: 2841202 INFO @ Tue, 09 Oct 2018 23:01:02: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 09 Oct 2018 23:01:02: #1 finished! INFO @ Tue, 09 Oct 2018 23:01:02: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:01:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:01:02: #2 number of paired peaks: 159 WARNING @ Tue, 09 Oct 2018 23:01:02: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Tue, 09 Oct 2018 23:01:02: start model_add_line... INFO @ Tue, 09 Oct 2018 23:01:02: start X-correlation... INFO @ Tue, 09 Oct 2018 23:01:02: end of X-cor INFO @ Tue, 09 Oct 2018 23:01:02: #2 finished! INFO @ Tue, 09 Oct 2018 23:01:02: #2 predicted fragment length is 246 bps INFO @ Tue, 09 Oct 2018 23:01:02: #2 alternative fragment length(s) may be 0,80,175,218,246,262,280,337,582 bps INFO @ Tue, 09 Oct 2018 23:01:02: #2.2 Generate R script for model : SRX4554665.20_model.r INFO @ Tue, 09 Oct 2018 23:01:02: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:01:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:01:02: 12000000 INFO @ Tue, 09 Oct 2018 23:01:03: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:01:03: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:01:03: #1 total tags in treatment: 3574928 INFO @ Tue, 09 Oct 2018 23:01:03: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:01:03: #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 23:01:03: #1 tags after filtering in treatment: 2841202 INFO @ Tue, 09 Oct 2018 23:01:03: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 09 Oct 2018 23:01:03: #1 finished! INFO @ Tue, 09 Oct 2018 23:01:03: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:01:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:01:04: #2 number of paired peaks: 159 WARNING @ Tue, 09 Oct 2018 23:01:04: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Tue, 09 Oct 2018 23:01:04: start model_add_line... INFO @ Tue, 09 Oct 2018 23:01:04: start X-correlation... INFO @ Tue, 09 Oct 2018 23:01:04: end of X-cor INFO @ Tue, 09 Oct 2018 23:01:04: #2 finished! INFO @ Tue, 09 Oct 2018 23:01:04: #2 predicted fragment length is 246 bps INFO @ Tue, 09 Oct 2018 23:01:04: #2 alternative fragment length(s) may be 0,80,175,218,246,262,280,337,582 bps INFO @ Tue, 09 Oct 2018 23:01:04: #2.2 Generate R script for model : SRX4554665.05_model.r INFO @ Tue, 09 Oct 2018 23:01:04: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:01:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:01:06: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:01:09: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:01:09: #4 Write output xls file... SRX4554665.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:01:09: #4 Write peak in narrowPeak format file... SRX4554665.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:01:09: #4 Write summits bed file... SRX4554665.10_summits.bed INFO @ Tue, 09 Oct 2018 23:01:09: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (21 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:01:10: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:01:11: #4 Write output xls file... SRX4554665.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:01:11: #4 Write peak in narrowPeak format file... SRX4554665.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:01:11: #4 Write summits bed file... SRX4554665.20_summits.bed INFO @ Tue, 09 Oct 2018 23:01:11: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:01:13: #4 Write output xls file... SRX4554665.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:01:13: #4 Write peak in narrowPeak format file... SRX4554665.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:01:13: #4 Write summits bed file... SRX4554665.05_summits.bed INFO @ Tue, 09 Oct 2018 23:01:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (39 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。