Job ID = 9162299 sra ファイルのダウンロード中... Completed: 448208K bytes transferred in 11 seconds (330679K bits/sec), in 1 file, 2 directories. 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 3704992 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1872734/SRR3713207.sra Written 3704992 spots total 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: 00:04:59 3704992 reads; of these: 3704992 (100.00%) were paired; of these: 852606 (23.01%) aligned concordantly 0 times 2402470 (64.84%) aligned concordantly exactly 1 time 449916 (12.14%) aligned concordantly >1 times ---- 852606 pairs aligned concordantly 0 times; of these: 335360 (39.33%) aligned discordantly 1 time ---- 517246 pairs aligned 0 times concordantly or discordantly; of these: 1034492 mates make up the pairs; of these: 813498 (78.64%) aligned 0 times 71666 (6.93%) aligned exactly 1 time 149328 (14.43%) aligned >1 times 89.02% overall alignment rate Time searching: 00:04:59 Overall time: 00:04:59 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] 35217 / 3156054 = 0.0112 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 @ Wed, 28 Jun 2017 07:22:25: # Command line: callpeak -t SRX1872734.bam -f BAM -g 12100000 -n SRX1872734.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1872734.10 # format = BAM # ChIP-seq file = ['SRX1872734.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 @ Wed, 28 Jun 2017 07:22:25: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:22:25: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:22:25: # Command line: callpeak -t SRX1872734.bam -f BAM -g 12100000 -n SRX1872734.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1872734.20 # format = BAM # ChIP-seq file = ['SRX1872734.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 @ Wed, 28 Jun 2017 07:22:25: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:22:25: # Command line: callpeak -t SRX1872734.bam -f BAM -g 12100000 -n SRX1872734.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1872734.05 # format = BAM # ChIP-seq file = ['SRX1872734.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 @ Wed, 28 Jun 2017 07:22:25: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:22:25: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:22:25: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:22:33: 1000000 INFO @ Wed, 28 Jun 2017 07:22:34: 1000000 INFO @ Wed, 28 Jun 2017 07:22:34: 1000000 INFO @ Wed, 28 Jun 2017 07:22:42: 2000000 INFO @ Wed, 28 Jun 2017 07:22:43: 2000000 INFO @ Wed, 28 Jun 2017 07:22:43: 2000000 INFO @ Wed, 28 Jun 2017 07:22:50: 3000000 INFO @ Wed, 28 Jun 2017 07:22:52: 3000000 INFO @ Wed, 28 Jun 2017 07:22:52: 3000000 INFO @ Wed, 28 Jun 2017 07:22:58: 4000000 INFO @ Wed, 28 Jun 2017 07:23:00: 4000000 INFO @ Wed, 28 Jun 2017 07:23:00: 4000000 INFO @ Wed, 28 Jun 2017 07:23:06: 5000000 INFO @ Wed, 28 Jun 2017 07:23:09: 5000000 INFO @ Wed, 28 Jun 2017 07:23:09: 5000000 INFO @ Wed, 28 Jun 2017 07:23:15: 6000000 INFO @ Wed, 28 Jun 2017 07:23:18: 6000000 INFO @ Wed, 28 Jun 2017 07:23:18: 6000000 INFO @ Wed, 28 Jun 2017 07:23:19: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:23:19: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:23:19: #1 total tags in treatment: 2820715 INFO @ Wed, 28 Jun 2017 07:23:19: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:23:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 07:23:19: #1 tags after filtering in treatment: 2276728 INFO @ Wed, 28 Jun 2017 07:23:19: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 28 Jun 2017 07:23:19: #1 finished! INFO @ Wed, 28 Jun 2017 07:23:19: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:23:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:23:19: #2 number of paired peaks: 178 WARNING @ Wed, 28 Jun 2017 07:23:19: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Wed, 28 Jun 2017 07:23:19: start model_add_line... INFO @ Wed, 28 Jun 2017 07:23:19: start X-correlation... INFO @ Wed, 28 Jun 2017 07:23:19: end of X-cor INFO @ Wed, 28 Jun 2017 07:23:19: #2 finished! INFO @ Wed, 28 Jun 2017 07:23:19: #2 predicted fragment length is 178 bps INFO @ Wed, 28 Jun 2017 07:23:19: #2 alternative fragment length(s) may be 10,64,86,118,131,134,146,178,192,217,238,262,279,304,328,407,454,470,490,493,517,547,581,583,593 bps INFO @ Wed, 28 Jun 2017 07:23:19: #2.2 Generate R script for model : SRX1872734.10_model.r WARNING @ Wed, 28 Jun 2017 07:23:19: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 07:23:19: #2 You may need to consider one of the other alternative d(s): 10,64,86,118,131,134,146,178,192,217,238,262,279,304,328,407,454,470,490,493,517,547,581,583,593 WARNING @ Wed, 28 Jun 2017 07:23:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 07:23:19: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:23:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 07:23:22: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:23:22: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:23:22: #1 total tags in treatment: 2820715 INFO @ Wed, 28 Jun 2017 07:23:22: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:23:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 07:23:22: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:23:22: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:23:22: #1 total tags in treatment: 2820715 INFO @ Wed, 28 Jun 2017 07:23:22: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:23:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 07:23:22: #1 tags after filtering in treatment: 2276728 INFO @ Wed, 28 Jun 2017 07:23:22: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 28 Jun 2017 07:23:22: #1 finished! INFO @ Wed, 28 Jun 2017 07:23:22: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:23:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:23:22: #1 tags after filtering in treatment: 2276728 INFO @ Wed, 28 Jun 2017 07:23:22: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 28 Jun 2017 07:23:22: #1 finished! INFO @ Wed, 28 Jun 2017 07:23:22: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:23:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:23:23: #2 number of paired peaks: 178 WARNING @ Wed, 28 Jun 2017 07:23:23: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Wed, 28 Jun 2017 07:23:23: start model_add_line... INFO @ Wed, 28 Jun 2017 07:23:23: #2 number of paired peaks: 178 WARNING @ Wed, 28 Jun 2017 07:23:23: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Wed, 28 Jun 2017 07:23:23: start model_add_line... INFO @ Wed, 28 Jun 2017 07:23:23: start X-correlation... INFO @ Wed, 28 Jun 2017 07:23:23: start X-correlation... INFO @ Wed, 28 Jun 2017 07:23:23: end of X-cor INFO @ Wed, 28 Jun 2017 07:23:23: #2 finished! INFO @ Wed, 28 Jun 2017 07:23:23: #2 predicted fragment length is 178 bps INFO @ Wed, 28 Jun 2017 07:23:23: #2 alternative fragment length(s) may be 10,64,86,118,131,134,146,178,192,217,238,262,279,304,328,407,454,470,490,493,517,547,581,583,593 bps INFO @ Wed, 28 Jun 2017 07:23:23: #2.2 Generate R script for model : SRX1872734.20_model.r INFO @ Wed, 28 Jun 2017 07:23:23: end of X-cor INFO @ Wed, 28 Jun 2017 07:23:23: #2 finished! INFO @ Wed, 28 Jun 2017 07:23:23: #2 predicted fragment length is 178 bps INFO @ Wed, 28 Jun 2017 07:23:23: #2 alternative fragment length(s) may be 10,64,86,118,131,134,146,178,192,217,238,262,279,304,328,407,454,470,490,493,517,547,581,583,593 bps INFO @ Wed, 28 Jun 2017 07:23:23: #2.2 Generate R script for model : SRX1872734.05_model.r WARNING @ Wed, 28 Jun 2017 07:23:23: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 07:23:23: #2 You may need to consider one of the other alternative d(s): 10,64,86,118,131,134,146,178,192,217,238,262,279,304,328,407,454,470,490,493,517,547,581,583,593 WARNING @ Wed, 28 Jun 2017 07:23:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 07:23:23: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:23:23: #3 Pre-compute pvalue-qvalue table... WARNING @ Wed, 28 Jun 2017 07:23:23: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 07:23:23: #2 You may need to consider one of the other alternative d(s): 10,64,86,118,131,134,146,178,192,217,238,262,279,304,328,407,454,470,490,493,517,547,581,583,593 WARNING @ Wed, 28 Jun 2017 07:23:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 07:23:23: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:23:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 07:23:24: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 07:23:26: #4 Write output xls file... SRX1872734.10_peaks.xls INFO @ Wed, 28 Jun 2017 07:23:26: #4 Write peak in narrowPeak format file... SRX1872734.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 07:23:26: #4 Write summits bed file... SRX1872734.10_summits.bed INFO @ Wed, 28 Jun 2017 07:23:26: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (16 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 07:23:27: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 07:23:28: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 07:23:29: #4 Write output xls file... SRX1872734.20_peaks.xls INFO @ Wed, 28 Jun 2017 07:23:29: #4 Write peak in narrowPeak format file... SRX1872734.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 07:23:29: #4 Write summits bed file... SRX1872734.20_summits.bed INFO @ Wed, 28 Jun 2017 07:23:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 07:23:30: #4 Write output xls file... SRX1872734.05_peaks.xls INFO @ Wed, 28 Jun 2017 07:23:30: #4 Write peak in narrowPeak format file... SRX1872734.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 07:23:30: #4 Write summits bed file... SRX1872734.05_summits.bed INFO @ Wed, 28 Jun 2017 07:23:30: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (26 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。