Job ID = 11245004 sra ファイルのダウンロード中... Completed: 93597K bytes transferred in 4 seconds (166951K 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 1898461 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554720/SRR7696393.sra Written 1898461 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554720/SRR7696393.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: 00:00:57 1898461 reads; of these: 1898461 (100.00%) were paired; of these: 928011 (48.88%) aligned concordantly 0 times 833333 (43.90%) aligned concordantly exactly 1 time 137117 (7.22%) aligned concordantly >1 times ---- 928011 pairs aligned concordantly 0 times; of these: 4834 (0.52%) aligned discordantly 1 time ---- 923177 pairs aligned 0 times concordantly or discordantly; of these: 1846354 mates make up the pairs; of these: 1815835 (98.35%) aligned 0 times 24104 (1.31%) aligned exactly 1 time 6415 (0.35%) aligned >1 times 52.18% overall alignment rate Time searching: 00:00:57 Overall time: 00:00:57 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] 93166 / 973819 = 0.0957 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 23:05:08: # Command line: callpeak -t SRX4554720.bam -f BAM -g 12100000 -n SRX4554720.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554720.05 # format = BAM # ChIP-seq file = ['SRX4554720.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 23:05:08: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:05:08: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:05:08: # Command line: callpeak -t SRX4554720.bam -f BAM -g 12100000 -n SRX4554720.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554720.10 # format = BAM # ChIP-seq file = ['SRX4554720.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 23:05:08: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:05:08: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:05:08: # Command line: callpeak -t SRX4554720.bam -f BAM -g 12100000 -n SRX4554720.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554720.20 # format = BAM # ChIP-seq file = ['SRX4554720.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 23:05:08: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:05:08: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:05:13: 1000000 INFO @ Tue, 09 Oct 2018 23:05:13: 1000000 INFO @ Tue, 09 Oct 2018 23:05:13: 1000000 INFO @ Tue, 09 Oct 2018 23:05:17: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:05:17: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:05:17: #1 total tags in treatment: 877421 INFO @ Tue, 09 Oct 2018 23:05:17: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:05:17: #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 23:05:17: #1 tags after filtering in treatment: 595382 INFO @ Tue, 09 Oct 2018 23:05:17: #1 Redundant rate of treatment: 0.32 INFO @ Tue, 09 Oct 2018 23:05:17: #1 finished! INFO @ Tue, 09 Oct 2018 23:05:17: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:05:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:05:18: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:05:18: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:05:18: #1 total tags in treatment: 877421 INFO @ Tue, 09 Oct 2018 23:05:18: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:05:18: #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 23:05:18: #2 number of paired peaks: 934 WARNING @ Tue, 09 Oct 2018 23:05:18: Fewer paired peaks (934) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 934 pairs to build model! INFO @ Tue, 09 Oct 2018 23:05:18: start model_add_line... INFO @ Tue, 09 Oct 2018 23:05:18: #1 tags after filtering in treatment: 595382 INFO @ Tue, 09 Oct 2018 23:05:18: #1 Redundant rate of treatment: 0.32 INFO @ Tue, 09 Oct 2018 23:05:18: #1 finished! INFO @ Tue, 09 Oct 2018 23:05:18: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:05:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:05:18: start X-correlation... INFO @ Tue, 09 Oct 2018 23:05:18: end of X-cor INFO @ Tue, 09 Oct 2018 23:05:18: #2 finished! INFO @ Tue, 09 Oct 2018 23:05:18: #2 predicted fragment length is 145 bps INFO @ Tue, 09 Oct 2018 23:05:18: #2 alternative fragment length(s) may be 0,145,195,234,260,293 bps INFO @ Tue, 09 Oct 2018 23:05:18: #2.2 Generate R script for model : SRX4554720.05_model.r INFO @ Tue, 09 Oct 2018 23:05:18: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:05:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:05:18: #2 number of paired peaks: 934 WARNING @ Tue, 09 Oct 2018 23:05:18: Fewer paired peaks (934) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 934 pairs to build model! INFO @ Tue, 09 Oct 2018 23:05:18: start model_add_line... INFO @ Tue, 09 Oct 2018 23:05:18: start X-correlation... INFO @ Tue, 09 Oct 2018 23:05:18: end of X-cor INFO @ Tue, 09 Oct 2018 23:05:18: #2 finished! INFO @ Tue, 09 Oct 2018 23:05:18: #2 predicted fragment length is 145 bps INFO @ Tue, 09 Oct 2018 23:05:18: #2 alternative fragment length(s) may be 0,145,195,234,260,293 bps INFO @ Tue, 09 Oct 2018 23:05:18: #2.2 Generate R script for model : SRX4554720.10_model.r INFO @ Tue, 09 Oct 2018 23:05:18: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:05:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:05:18: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:05:18: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:05:18: #1 total tags in treatment: 877421 INFO @ Tue, 09 Oct 2018 23:05:18: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:05:18: #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 23:05:18: #1 tags after filtering in treatment: 595382 INFO @ Tue, 09 Oct 2018 23:05:18: #1 Redundant rate of treatment: 0.32 INFO @ Tue, 09 Oct 2018 23:05:18: #1 finished! INFO @ Tue, 09 Oct 2018 23:05:18: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:05:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:05:18: #2 number of paired peaks: 934 WARNING @ Tue, 09 Oct 2018 23:05:18: Fewer paired peaks (934) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 934 pairs to build model! INFO @ Tue, 09 Oct 2018 23:05:18: start model_add_line... INFO @ Tue, 09 Oct 2018 23:05:18: start X-correlation... INFO @ Tue, 09 Oct 2018 23:05:18: end of X-cor INFO @ Tue, 09 Oct 2018 23:05:18: #2 finished! INFO @ Tue, 09 Oct 2018 23:05:18: #2 predicted fragment length is 145 bps INFO @ Tue, 09 Oct 2018 23:05:18: #2 alternative fragment length(s) may be 0,145,195,234,260,293 bps INFO @ Tue, 09 Oct 2018 23:05:18: #2.2 Generate R script for model : SRX4554720.20_model.r INFO @ Tue, 09 Oct 2018 23:05:18: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:05:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:05:21: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:05:21: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:05:21: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:05:21: #4 Write output xls file... SRX4554720.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:05:21: #4 Write peak in narrowPeak format file... SRX4554720.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:05:21: #4 Write summits bed file... SRX4554720.05_summits.bed INFO @ Tue, 09 Oct 2018 23:05:21: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (534 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:05:21: #4 Write output xls file... SRX4554720.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:05:21: #4 Write peak in narrowPeak format file... SRX4554720.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:05:21: #4 Write summits bed file... SRX4554720.10_summits.bed INFO @ Tue, 09 Oct 2018 23:05:21: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (400 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:05:22: #4 Write output xls file... SRX4554720.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:05:22: #4 Write peak in narrowPeak format file... SRX4554720.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:05:22: #4 Write summits bed file... SRX4554720.20_summits.bed INFO @ Tue, 09 Oct 2018 23:05:22: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (146 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。