Job ID = 10937539 sra ファイルのダウンロード中... Completed: 406670K bytes transferred in 52 seconds (63627K 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 4171324 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010331/SRR5833330.sra Written 4171324 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010331/SRR5833330.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: 00:05:27 4171324 reads; of these: 4171324 (100.00%) were paired; of these: 625828 (15.00%) aligned concordantly 0 times 3013245 (72.24%) aligned concordantly exactly 1 time 532251 (12.76%) aligned concordantly >1 times ---- 625828 pairs aligned concordantly 0 times; of these: 42015 (6.71%) aligned discordantly 1 time ---- 583813 pairs aligned 0 times concordantly or discordantly; of these: 1167626 mates make up the pairs; of these: 1106268 (94.75%) aligned 0 times 38915 (3.33%) aligned exactly 1 time 22443 (1.92%) aligned >1 times 86.74% overall alignment rate Time searching: 00:05:27 Overall time: 00:05:27 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] 91028 / 3580085 = 0.0254 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 @ Fri, 10 Aug 2018 02:41:20: # Command line: callpeak -t SRX3010331.bam -f BAM -g 12100000 -n SRX3010331.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3010331.05 # format = BAM # ChIP-seq file = ['SRX3010331.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 @ Fri, 10 Aug 2018 02:41:20: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:41:20: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:41:20: # Command line: callpeak -t SRX3010331.bam -f BAM -g 12100000 -n SRX3010331.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3010331.20 # format = BAM # ChIP-seq file = ['SRX3010331.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 @ Fri, 10 Aug 2018 02:41:20: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:41:20: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:41:20: # Command line: callpeak -t SRX3010331.bam -f BAM -g 12100000 -n SRX3010331.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3010331.10 # format = BAM # ChIP-seq file = ['SRX3010331.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 @ Fri, 10 Aug 2018 02:41:20: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:41:20: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:41:29: 1000000 INFO @ Fri, 10 Aug 2018 02:41:30: 1000000 INFO @ Fri, 10 Aug 2018 02:41:30: 1000000 INFO @ Fri, 10 Aug 2018 02:41:38: 2000000 INFO @ Fri, 10 Aug 2018 02:41:39: 2000000 INFO @ Fri, 10 Aug 2018 02:41:39: 2000000 INFO @ Fri, 10 Aug 2018 02:41:48: 3000000 INFO @ Fri, 10 Aug 2018 02:41:48: 3000000 INFO @ Fri, 10 Aug 2018 02:41:48: 3000000 INFO @ Fri, 10 Aug 2018 02:41:56: 4000000 INFO @ Fri, 10 Aug 2018 02:41:56: 4000000 INFO @ Fri, 10 Aug 2018 02:41:58: 4000000 INFO @ Fri, 10 Aug 2018 02:42:04: 5000000 INFO @ Fri, 10 Aug 2018 02:42:05: 5000000 INFO @ Fri, 10 Aug 2018 02:42:07: 5000000 INFO @ Fri, 10 Aug 2018 02:42:12: 6000000 INFO @ Fri, 10 Aug 2018 02:42:12: 6000000 INFO @ Fri, 10 Aug 2018 02:42:18: 6000000 INFO @ Fri, 10 Aug 2018 02:42:22: 7000000 INFO @ Fri, 10 Aug 2018 02:42:23: 7000000 INFO @ Fri, 10 Aug 2018 02:42:23: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:42:23: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:42:23: #1 total tags in treatment: 3454789 INFO @ Fri, 10 Aug 2018 02:42:23: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:42:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:42:23: #1 tags after filtering in treatment: 2844644 INFO @ Fri, 10 Aug 2018 02:42:23: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 10 Aug 2018 02:42:23: #1 finished! INFO @ Fri, 10 Aug 2018 02:42:23: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:42:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:42:23: #2 number of paired peaks: 132 WARNING @ Fri, 10 Aug 2018 02:42:23: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Fri, 10 Aug 2018 02:42:23: start model_add_line... INFO @ Fri, 10 Aug 2018 02:42:23: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:42:23: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:42:23: #1 total tags in treatment: 3454789 INFO @ Fri, 10 Aug 2018 02:42:23: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:42:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:42:23: start X-correlation... INFO @ Fri, 10 Aug 2018 02:42:23: end of X-cor INFO @ Fri, 10 Aug 2018 02:42:23: #2 finished! INFO @ Fri, 10 Aug 2018 02:42:23: #2 predicted fragment length is 191 bps INFO @ Fri, 10 Aug 2018 02:42:23: #2 alternative fragment length(s) may be 0,59,85,98,126,148,164,191,207,252,297,326,550,569 bps INFO @ Fri, 10 Aug 2018 02:42:23: #2.2 Generate R script for model : SRX3010331.20_model.r WARNING @ Fri, 10 Aug 2018 02:42:23: #2 Since the d (191) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 02:42:23: #2 You may need to consider one of the other alternative d(s): 0,59,85,98,126,148,164,191,207,252,297,326,550,569 WARNING @ Fri, 10 Aug 2018 02:42:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 02:42:23: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:42:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:42:23: #1 tags after filtering in treatment: 2844644 INFO @ Fri, 10 Aug 2018 02:42:23: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 10 Aug 2018 02:42:23: #1 finished! INFO @ Fri, 10 Aug 2018 02:42:23: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:42:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:42:24: #2 number of paired peaks: 132 WARNING @ Fri, 10 Aug 2018 02:42:24: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Fri, 10 Aug 2018 02:42:24: start model_add_line... INFO @ Fri, 10 Aug 2018 02:42:24: start X-correlation... INFO @ Fri, 10 Aug 2018 02:42:24: end of X-cor INFO @ Fri, 10 Aug 2018 02:42:24: #2 finished! INFO @ Fri, 10 Aug 2018 02:42:24: #2 predicted fragment length is 191 bps INFO @ Fri, 10 Aug 2018 02:42:24: #2 alternative fragment length(s) may be 0,59,85,98,126,148,164,191,207,252,297,326,550,569 bps INFO @ Fri, 10 Aug 2018 02:42:24: #2.2 Generate R script for model : SRX3010331.10_model.r WARNING @ Fri, 10 Aug 2018 02:42:24: #2 Since the d (191) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 02:42:24: #2 You may need to consider one of the other alternative d(s): 0,59,85,98,126,148,164,191,207,252,297,326,550,569 WARNING @ Fri, 10 Aug 2018 02:42:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 02:42:24: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:42:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:42:28: 7000000 INFO @ Fri, 10 Aug 2018 02:42:29: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:42:29: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:42:29: #1 total tags in treatment: 3454789 INFO @ Fri, 10 Aug 2018 02:42:29: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:42:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:42:29: #1 tags after filtering in treatment: 2844644 INFO @ Fri, 10 Aug 2018 02:42:29: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 10 Aug 2018 02:42:29: #1 finished! INFO @ Fri, 10 Aug 2018 02:42:29: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:42:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:42:29: #2 number of paired peaks: 132 WARNING @ Fri, 10 Aug 2018 02:42:29: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Fri, 10 Aug 2018 02:42:29: start model_add_line... INFO @ Fri, 10 Aug 2018 02:42:29: start X-correlation... INFO @ Fri, 10 Aug 2018 02:42:29: end of X-cor INFO @ Fri, 10 Aug 2018 02:42:29: #2 finished! INFO @ Fri, 10 Aug 2018 02:42:29: #2 predicted fragment length is 191 bps INFO @ Fri, 10 Aug 2018 02:42:29: #2 alternative fragment length(s) may be 0,59,85,98,126,148,164,191,207,252,297,326,550,569 bps INFO @ Fri, 10 Aug 2018 02:42:29: #2.2 Generate R script for model : SRX3010331.05_model.r WARNING @ Fri, 10 Aug 2018 02:42:29: #2 Since the d (191) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 02:42:29: #2 You may need to consider one of the other alternative d(s): 0,59,85,98,126,148,164,191,207,252,297,326,550,569 WARNING @ Fri, 10 Aug 2018 02:42:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 02:42:29: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:42:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:42:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:42:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:42:34: #4 Write output xls file... SRX3010331.10_peaks.xls INFO @ Fri, 10 Aug 2018 02:42:34: #4 Write peak in narrowPeak format file... SRX3010331.10_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:42:34: #4 Write summits bed file... SRX3010331.10_summits.bed INFO @ Fri, 10 Aug 2018 02:42:34: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (77 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:42:34: #4 Write output xls file... SRX3010331.20_peaks.xls INFO @ Fri, 10 Aug 2018 02:42:34: #4 Write peak in narrowPeak format file... SRX3010331.20_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:42:34: #4 Write summits bed file... SRX3010331.20_summits.bed INFO @ Fri, 10 Aug 2018 02:42:34: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (11 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:42:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:42:39: #4 Write output xls file... SRX3010331.05_peaks.xls INFO @ Fri, 10 Aug 2018 02:42:39: #4 Write peak in narrowPeak format file... SRX3010331.05_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:42:39: #4 Write summits bed file... SRX3010331.05_summits.bed INFO @ Fri, 10 Aug 2018 02:42:39: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (388 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。