Job ID = 10609012 sra ファイルのダウンロード中... Completed: 250363K bytes transferred in 8 seconds (238244K 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 2553492 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3063099/SRR5901529.sra Written 2553492 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: 00:03:19 2553492 reads; of these: 2553492 (100.00%) were paired; of these: 108294 (4.24%) aligned concordantly 0 times 2195494 (85.98%) aligned concordantly exactly 1 time 249704 (9.78%) aligned concordantly >1 times ---- 108294 pairs aligned concordantly 0 times; of these: 17135 (15.82%) aligned discordantly 1 time ---- 91159 pairs aligned 0 times concordantly or discordantly; of these: 182318 mates make up the pairs; of these: 144021 (78.99%) aligned 0 times 29772 (16.33%) aligned exactly 1 time 8525 (4.68%) aligned >1 times 97.18% overall alignment rate Time searching: 00:03:19 Overall time: 00:03:19 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] 152519 / 2444301 = 0.0624 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, 03 May 2018 23:10:13: # Command line: callpeak -t SRX3063099.bam -f BAM -g 12100000 -n SRX3063099.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3063099.05 # format = BAM # ChIP-seq file = ['SRX3063099.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, 03 May 2018 23:10:13: #1 read tag files... INFO @ Thu, 03 May 2018 23:10:13: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:10:13: # Command line: callpeak -t SRX3063099.bam -f BAM -g 12100000 -n SRX3063099.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3063099.20 # format = BAM # ChIP-seq file = ['SRX3063099.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, 03 May 2018 23:10:13: #1 read tag files... INFO @ Thu, 03 May 2018 23:10:13: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:10:13: # Command line: callpeak -t SRX3063099.bam -f BAM -g 12100000 -n SRX3063099.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3063099.10 # format = BAM # ChIP-seq file = ['SRX3063099.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, 03 May 2018 23:10:13: #1 read tag files... INFO @ Thu, 03 May 2018 23:10:13: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:10:22: 1000000 INFO @ Thu, 03 May 2018 23:10:23: 1000000 INFO @ Thu, 03 May 2018 23:10:23: 1000000 INFO @ Thu, 03 May 2018 23:10:31: 2000000 INFO @ Thu, 03 May 2018 23:10:33: 2000000 INFO @ Thu, 03 May 2018 23:10:33: 2000000 INFO @ Thu, 03 May 2018 23:10:40: 3000000 INFO @ Thu, 03 May 2018 23:10:43: 3000000 INFO @ Thu, 03 May 2018 23:10:43: 3000000 INFO @ Thu, 03 May 2018 23:10:49: 4000000 INFO @ Thu, 03 May 2018 23:10:53: 4000000 INFO @ Thu, 03 May 2018 23:10:53: 4000000 INFO @ Thu, 03 May 2018 23:10:55: #1 tag size is determined as 101 bps INFO @ Thu, 03 May 2018 23:10:55: #1 tag size = 101 INFO @ Thu, 03 May 2018 23:10:55: #1 total tags in treatment: 2293028 INFO @ Thu, 03 May 2018 23:10:55: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:10:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:10:55: #1 tags after filtering in treatment: 2058841 INFO @ Thu, 03 May 2018 23:10:55: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 03 May 2018 23:10:55: #1 finished! INFO @ Thu, 03 May 2018 23:10:55: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:10:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:10:55: #2 number of paired peaks: 138 WARNING @ Thu, 03 May 2018 23:10:55: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Thu, 03 May 2018 23:10:55: start model_add_line... INFO @ Thu, 03 May 2018 23:10:55: start X-correlation... INFO @ Thu, 03 May 2018 23:10:55: end of X-cor INFO @ Thu, 03 May 2018 23:10:55: #2 finished! INFO @ Thu, 03 May 2018 23:10:55: #2 predicted fragment length is 92 bps INFO @ Thu, 03 May 2018 23:10:55: #2 alternative fragment length(s) may be 3,92,121,130 bps INFO @ Thu, 03 May 2018 23:10:55: #2.2 Generate R script for model : SRX3063099.20_model.r WARNING @ Thu, 03 May 2018 23:10:55: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 23:10:55: #2 You may need to consider one of the other alternative d(s): 3,92,121,130 WARNING @ Thu, 03 May 2018 23:10:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 23:10:55: #3 Call peaks... INFO @ Thu, 03 May 2018 23:10:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 23:10:59: #1 tag size is determined as 101 bps INFO @ Thu, 03 May 2018 23:10:59: #1 tag size = 101 INFO @ Thu, 03 May 2018 23:10:59: #1 total tags in treatment: 2293028 INFO @ Thu, 03 May 2018 23:10:59: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:10:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:10:59: #1 tag size is determined as 101 bps INFO @ Thu, 03 May 2018 23:10:59: #1 tag size = 101 INFO @ Thu, 03 May 2018 23:10:59: #1 total tags in treatment: 2293028 INFO @ Thu, 03 May 2018 23:10:59: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:10:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:10:59: #1 tags after filtering in treatment: 2058841 INFO @ Thu, 03 May 2018 23:10:59: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 03 May 2018 23:10:59: #1 finished! INFO @ Thu, 03 May 2018 23:10:59: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:10:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:10:59: #1 tags after filtering in treatment: 2058841 INFO @ Thu, 03 May 2018 23:10:59: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 03 May 2018 23:10:59: #1 finished! INFO @ Thu, 03 May 2018 23:10:59: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:10:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:10:59: #2 number of paired peaks: 138 WARNING @ Thu, 03 May 2018 23:10:59: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Thu, 03 May 2018 23:10:59: start model_add_line... INFO @ Thu, 03 May 2018 23:10:59: start X-correlation... INFO @ Thu, 03 May 2018 23:10:59: end of X-cor INFO @ Thu, 03 May 2018 23:10:59: #2 finished! INFO @ Thu, 03 May 2018 23:10:59: #2 predicted fragment length is 92 bps INFO @ Thu, 03 May 2018 23:10:59: #2 alternative fragment length(s) may be 3,92,121,130 bps INFO @ Thu, 03 May 2018 23:10:59: #2.2 Generate R script for model : SRX3063099.05_model.r WARNING @ Thu, 03 May 2018 23:10:59: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 23:10:59: #2 You may need to consider one of the other alternative d(s): 3,92,121,130 WARNING @ Thu, 03 May 2018 23:10:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 23:10:59: #3 Call peaks... INFO @ Thu, 03 May 2018 23:10:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 23:10:59: #2 number of paired peaks: 138 WARNING @ Thu, 03 May 2018 23:10:59: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Thu, 03 May 2018 23:10:59: start model_add_line... INFO @ Thu, 03 May 2018 23:10:59: start X-correlation... INFO @ Thu, 03 May 2018 23:10:59: end of X-cor INFO @ Thu, 03 May 2018 23:10:59: #2 finished! INFO @ Thu, 03 May 2018 23:10:59: #2 predicted fragment length is 92 bps INFO @ Thu, 03 May 2018 23:10:59: #2 alternative fragment length(s) may be 3,92,121,130 bps INFO @ Thu, 03 May 2018 23:10:59: #2.2 Generate R script for model : SRX3063099.10_model.r WARNING @ Thu, 03 May 2018 23:10:59: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 23:10:59: #2 You may need to consider one of the other alternative d(s): 3,92,121,130 WARNING @ Thu, 03 May 2018 23:10:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 23:10:59: #3 Call peaks... INFO @ Thu, 03 May 2018 23:10:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 23:11:01: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 23:11:03: #4 Write output xls file... SRX3063099.20_peaks.xls INFO @ Thu, 03 May 2018 23:11:03: #4 Write peak in narrowPeak format file... SRX3063099.20_peaks.narrowPeak INFO @ Thu, 03 May 2018 23:11:03: #4 Write summits bed file... SRX3063099.20_summits.bed INFO @ Thu, 03 May 2018 23:11:03: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (163 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 23:11:05: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 23:11:05: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 23:11:07: #4 Write output xls file... SRX3063099.10_peaks.xls INFO @ Thu, 03 May 2018 23:11:07: #4 Write peak in narrowPeak format file... SRX3063099.10_peaks.narrowPeak INFO @ Thu, 03 May 2018 23:11:07: #4 Write summits bed file... SRX3063099.10_summits.bed INFO @ Thu, 03 May 2018 23:11:07: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (443 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 23:11:07: #4 Write output xls file... SRX3063099.05_peaks.xls INFO @ Thu, 03 May 2018 23:11:07: #4 Write peak in narrowPeak format file... SRX3063099.05_peaks.narrowPeak INFO @ Thu, 03 May 2018 23:11:07: #4 Write summits bed file... SRX3063099.05_summits.bed INFO @ Thu, 03 May 2018 23:11:07: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (816 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。