Job ID = 10536355 sra ファイルのダウンロード中... Completed: 754771K bytes transferred in 16 seconds (376537K 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... Written 23115604 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3433218/SRR6333859.sra Written 23115604 spots total 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: 00:08:43 23115604 reads; of these: 23115604 (100.00%) were paired; of these: 13650078 (59.05%) aligned concordantly 0 times 8675570 (37.53%) aligned concordantly exactly 1 time 789956 (3.42%) aligned concordantly >1 times ---- 13650078 pairs aligned concordantly 0 times; of these: 23653 (0.17%) aligned discordantly 1 time ---- 13626425 pairs aligned 0 times concordantly or discordantly; of these: 27252850 mates make up the pairs; of these: 26914132 (98.76%) aligned 0 times 301273 (1.11%) aligned exactly 1 time 37445 (0.14%) aligned >1 times 41.78% overall alignment rate Time searching: 00:08:43 Overall time: 00:08:43 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_sort_core] merging from 8 files... [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] 8302105 / 9470244 = 0.8767 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 @ Thu, 05 Apr 2018 09:00:55: # Command line: callpeak -t SRX3433218.bam -f BAM -g 12100000 -n SRX3433218.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3433218.10 # format = BAM # ChIP-seq file = ['SRX3433218.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 @ Thu, 05 Apr 2018 09:00:55: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:00:55: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:00:55: # Command line: callpeak -t SRX3433218.bam -f BAM -g 12100000 -n SRX3433218.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3433218.05 # format = BAM # ChIP-seq file = ['SRX3433218.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 @ Thu, 05 Apr 2018 09:00:55: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:00:55: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:00:55: # Command line: callpeak -t SRX3433218.bam -f BAM -g 12100000 -n SRX3433218.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3433218.20 # format = BAM # ChIP-seq file = ['SRX3433218.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 @ Thu, 05 Apr 2018 09:00:55: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:00:55: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:01:02: 1000000 INFO @ Thu, 05 Apr 2018 09:01:02: 1000000 INFO @ Thu, 05 Apr 2018 09:01:03: 1000000 INFO @ Thu, 05 Apr 2018 09:01:09: 2000000 INFO @ Thu, 05 Apr 2018 09:01:09: 2000000 INFO @ Thu, 05 Apr 2018 09:01:10: 2000000 INFO @ Thu, 05 Apr 2018 09:01:13: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:01:13: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:01:13: #1 total tags in treatment: 1166274 INFO @ Thu, 05 Apr 2018 09:01:13: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:01:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:01:13: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:01:13: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:01:13: #1 total tags in treatment: 1166274 INFO @ Thu, 05 Apr 2018 09:01:13: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:01:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:01:13: #1 tags after filtering in treatment: 1086524 INFO @ Thu, 05 Apr 2018 09:01:13: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 05 Apr 2018 09:01:13: #1 finished! INFO @ Thu, 05 Apr 2018 09:01:13: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:01:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:01:13: #1 tags after filtering in treatment: 1086524 INFO @ Thu, 05 Apr 2018 09:01:13: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 05 Apr 2018 09:01:13: #1 finished! INFO @ Thu, 05 Apr 2018 09:01:13: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:01:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:01:13: #2 number of paired peaks: 213 WARNING @ Thu, 05 Apr 2018 09:01:13: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Thu, 05 Apr 2018 09:01:13: start model_add_line... INFO @ Thu, 05 Apr 2018 09:01:13: #2 number of paired peaks: 213 WARNING @ Thu, 05 Apr 2018 09:01:13: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Thu, 05 Apr 2018 09:01:13: start model_add_line... INFO @ Thu, 05 Apr 2018 09:01:13: start X-correlation... INFO @ Thu, 05 Apr 2018 09:01:13: end of X-cor INFO @ Thu, 05 Apr 2018 09:01:13: #2 finished! INFO @ Thu, 05 Apr 2018 09:01:13: #2 predicted fragment length is 134 bps INFO @ Thu, 05 Apr 2018 09:01:13: #2 alternative fragment length(s) may be 4,97,101,134,175 bps INFO @ Thu, 05 Apr 2018 09:01:13: #2.2 Generate R script for model : SRX3433218.20_model.r INFO @ Thu, 05 Apr 2018 09:01:13: start X-correlation... INFO @ Thu, 05 Apr 2018 09:01:13: end of X-cor INFO @ Thu, 05 Apr 2018 09:01:13: #2 finished! INFO @ Thu, 05 Apr 2018 09:01:13: #2 predicted fragment length is 134 bps INFO @ Thu, 05 Apr 2018 09:01:13: #2 alternative fragment length(s) may be 4,97,101,134,175 bps INFO @ Thu, 05 Apr 2018 09:01:13: #2.2 Generate R script for model : SRX3433218.05_model.r INFO @ Thu, 05 Apr 2018 09:01:13: #3 Call peaks... INFO @ Thu, 05 Apr 2018 09:01:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 09:01:13: #3 Call peaks... INFO @ Thu, 05 Apr 2018 09:01:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 09:01:15: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:01:15: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:01:15: #1 total tags in treatment: 1166274 INFO @ Thu, 05 Apr 2018 09:01:15: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:01:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:01:15: #1 tags after filtering in treatment: 1086524 INFO @ Thu, 05 Apr 2018 09:01:15: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 05 Apr 2018 09:01:15: #1 finished! INFO @ Thu, 05 Apr 2018 09:01:15: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:01:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:01:15: #2 number of paired peaks: 213 WARNING @ Thu, 05 Apr 2018 09:01:15: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Thu, 05 Apr 2018 09:01:15: start model_add_line... INFO @ Thu, 05 Apr 2018 09:01:15: start X-correlation... INFO @ Thu, 05 Apr 2018 09:01:15: end of X-cor INFO @ Thu, 05 Apr 2018 09:01:15: #2 finished! INFO @ Thu, 05 Apr 2018 09:01:15: #2 predicted fragment length is 134 bps INFO @ Thu, 05 Apr 2018 09:01:15: #2 alternative fragment length(s) may be 4,97,101,134,175 bps INFO @ Thu, 05 Apr 2018 09:01:15: #2.2 Generate R script for model : SRX3433218.10_model.r INFO @ Thu, 05 Apr 2018 09:01:15: #3 Call peaks... INFO @ Thu, 05 Apr 2018 09:01:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 09:01:16: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 09:01:17: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 09:01:18: #4 Write output xls file... SRX3433218.05_peaks.xls INFO @ Thu, 05 Apr 2018 09:01:18: #4 Write peak in narrowPeak format file... SRX3433218.05_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 09:01:18: #4 Write summits bed file... SRX3433218.05_summits.bed INFO @ Thu, 05 Apr 2018 09:01:18: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (737 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Apr 2018 09:01:18: #4 Write output xls file... SRX3433218.20_peaks.xls INFO @ Thu, 05 Apr 2018 09:01:18: #4 Write peak in narrowPeak format file... SRX3433218.20_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 09:01:18: #4 Write summits bed file... SRX3433218.20_summits.bed INFO @ Thu, 05 Apr 2018 09:01:18: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (158 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 05 Apr 2018 09:01:19: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 09:01:20: #4 Write output xls file... SRX3433218.10_peaks.xls INFO @ Thu, 05 Apr 2018 09:01:20: #4 Write peak in narrowPeak format file... SRX3433218.10_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 09:01:20: #4 Write summits bed file... SRX3433218.10_summits.bed INFO @ Thu, 05 Apr 2018 09:01:20: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (389 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。