Job ID = 9162293 sra ファイルのダウンロード中... Completed: 571108K bytes transferred in 10 seconds (462878K 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 4721017 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1872722/SRR3713195.sra Written 4721017 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: 00:06:23 4721017 reads; of these: 4721017 (100.00%) were paired; of these: 1049274 (22.23%) aligned concordantly 0 times 3118228 (66.05%) aligned concordantly exactly 1 time 553515 (11.72%) aligned concordantly >1 times ---- 1049274 pairs aligned concordantly 0 times; of these: 427101 (40.70%) aligned discordantly 1 time ---- 622173 pairs aligned 0 times concordantly or discordantly; of these: 1244346 mates make up the pairs; of these: 964895 (77.54%) aligned 0 times 95311 (7.66%) aligned exactly 1 time 184140 (14.80%) aligned >1 times 89.78% overall alignment rate Time searching: 00:06:23 Overall time: 00:06:23 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] 57162 / 4056147 = 0.0141 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 07:24:40: # Command line: callpeak -t SRX1872722.bam -f BAM -g 12100000 -n SRX1872722.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1872722.20 # format = BAM # ChIP-seq file = ['SRX1872722.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 07:24:40: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:24:40: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:24:40: # Command line: callpeak -t SRX1872722.bam -f BAM -g 12100000 -n SRX1872722.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1872722.10 # format = BAM # ChIP-seq file = ['SRX1872722.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 07:24:40: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:24:40: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:24:40: # Command line: callpeak -t SRX1872722.bam -f BAM -g 12100000 -n SRX1872722.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1872722.05 # format = BAM # ChIP-seq file = ['SRX1872722.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 07:24:40: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:24:40: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:24:47: 1000000 INFO @ Wed, 28 Jun 2017 07:24:47: 1000000 INFO @ Wed, 28 Jun 2017 07:24:47: 1000000 INFO @ Wed, 28 Jun 2017 07:24:54: 2000000 INFO @ Wed, 28 Jun 2017 07:24:54: 2000000 INFO @ Wed, 28 Jun 2017 07:24:54: 2000000 INFO @ Wed, 28 Jun 2017 07:25:00: 3000000 INFO @ Wed, 28 Jun 2017 07:25:01: 3000000 INFO @ Wed, 28 Jun 2017 07:25:01: 3000000 INFO @ Wed, 28 Jun 2017 07:25:07: 4000000 INFO @ Wed, 28 Jun 2017 07:25:08: 4000000 INFO @ Wed, 28 Jun 2017 07:25:08: 4000000 INFO @ Wed, 28 Jun 2017 07:25:13: 5000000 INFO @ Wed, 28 Jun 2017 07:25:15: 5000000 INFO @ Wed, 28 Jun 2017 07:25:16: 5000000 INFO @ Wed, 28 Jun 2017 07:25:20: 6000000 INFO @ Wed, 28 Jun 2017 07:25:22: 6000000 INFO @ Wed, 28 Jun 2017 07:25:23: 6000000 INFO @ Wed, 28 Jun 2017 07:25:26: 7000000 INFO @ Wed, 28 Jun 2017 07:25:29: 7000000 INFO @ Wed, 28 Jun 2017 07:25:30: 7000000 INFO @ Wed, 28 Jun 2017 07:25:33: 8000000 INFO @ Wed, 28 Jun 2017 07:25:35: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:25:35: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:25:35: #1 total tags in treatment: 3620620 INFO @ Wed, 28 Jun 2017 07:25:35: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:25:35: #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 07:25:36: #1 tags after filtering in treatment: 2812220 INFO @ Wed, 28 Jun 2017 07:25:36: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 28 Jun 2017 07:25:36: #1 finished! INFO @ Wed, 28 Jun 2017 07:25:36: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:25:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:25:36: #2 number of paired peaks: 176 WARNING @ Wed, 28 Jun 2017 07:25:36: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Wed, 28 Jun 2017 07:25:36: start model_add_line... INFO @ Wed, 28 Jun 2017 07:25:36: start X-correlation... INFO @ Wed, 28 Jun 2017 07:25:36: end of X-cor INFO @ Wed, 28 Jun 2017 07:25:36: #2 finished! INFO @ Wed, 28 Jun 2017 07:25:36: #2 predicted fragment length is 128 bps INFO @ Wed, 28 Jun 2017 07:25:36: #2 alternative fragment length(s) may be 34,65,101,128,146,162,179,228,266,290,330,336,360,382,427,468,503,537,573,592 bps INFO @ Wed, 28 Jun 2017 07:25:36: #2.2 Generate R script for model : SRX1872722.10_model.r WARNING @ Wed, 28 Jun 2017 07:25:36: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 07:25:36: #2 You may need to consider one of the other alternative d(s): 34,65,101,128,146,162,179,228,266,290,330,336,360,382,427,468,503,537,573,592 WARNING @ Wed, 28 Jun 2017 07:25:36: #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 07:25:36: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:25:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 07:25:36: 8000000 INFO @ Wed, 28 Jun 2017 07:25:38: 8000000 INFO @ Wed, 28 Jun 2017 07:25:39: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:25:39: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:25:39: #1 total tags in treatment: 3620620 INFO @ Wed, 28 Jun 2017 07:25:39: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:25:39: #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 07:25:39: #1 tags after filtering in treatment: 2812220 INFO @ Wed, 28 Jun 2017 07:25:39: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 28 Jun 2017 07:25:39: #1 finished! INFO @ Wed, 28 Jun 2017 07:25:39: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:25:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:25:39: #2 number of paired peaks: 176 WARNING @ Wed, 28 Jun 2017 07:25:39: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Wed, 28 Jun 2017 07:25:39: start model_add_line... INFO @ Wed, 28 Jun 2017 07:25:39: start X-correlation... INFO @ Wed, 28 Jun 2017 07:25:39: end of X-cor INFO @ Wed, 28 Jun 2017 07:25:39: #2 finished! INFO @ Wed, 28 Jun 2017 07:25:39: #2 predicted fragment length is 128 bps INFO @ Wed, 28 Jun 2017 07:25:39: #2 alternative fragment length(s) may be 34,65,101,128,146,162,179,228,266,290,330,336,360,382,427,468,503,537,573,592 bps INFO @ Wed, 28 Jun 2017 07:25:39: #2.2 Generate R script for model : SRX1872722.20_model.r WARNING @ Wed, 28 Jun 2017 07:25:39: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 07:25:39: #2 You may need to consider one of the other alternative d(s): 34,65,101,128,146,162,179,228,266,290,330,336,360,382,427,468,503,537,573,592 WARNING @ Wed, 28 Jun 2017 07:25:39: #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 07:25:39: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:25:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 07:25:40: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:25:40: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:25:40: #1 total tags in treatment: 3620620 INFO @ Wed, 28 Jun 2017 07:25:40: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:25:40: #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 07:25:40: #1 tags after filtering in treatment: 2812220 INFO @ Wed, 28 Jun 2017 07:25:40: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 28 Jun 2017 07:25:40: #1 finished! INFO @ Wed, 28 Jun 2017 07:25:40: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:25:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:25:40: #2 number of paired peaks: 176 WARNING @ Wed, 28 Jun 2017 07:25:40: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Wed, 28 Jun 2017 07:25:40: start model_add_line... INFO @ Wed, 28 Jun 2017 07:25:40: start X-correlation... INFO @ Wed, 28 Jun 2017 07:25:40: end of X-cor INFO @ Wed, 28 Jun 2017 07:25:40: #2 finished! INFO @ Wed, 28 Jun 2017 07:25:40: #2 predicted fragment length is 128 bps INFO @ Wed, 28 Jun 2017 07:25:40: #2 alternative fragment length(s) may be 34,65,101,128,146,162,179,228,266,290,330,336,360,382,427,468,503,537,573,592 bps INFO @ Wed, 28 Jun 2017 07:25:40: #2.2 Generate R script for model : SRX1872722.05_model.r WARNING @ Wed, 28 Jun 2017 07:25:40: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 07:25:40: #2 You may need to consider one of the other alternative d(s): 34,65,101,128,146,162,179,228,266,290,330,336,360,382,427,468,503,537,573,592 WARNING @ Wed, 28 Jun 2017 07:25:40: #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 07:25:40: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:25:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 07:25:41: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 07:25:43: #4 Write output xls file... SRX1872722.10_peaks.xls INFO @ Wed, 28 Jun 2017 07:25:43: #4 Write peak in narrowPeak format file... SRX1872722.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 07:25:43: #4 Write summits bed file... SRX1872722.10_summits.bed INFO @ Wed, 28 Jun 2017 07:25:43: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (19 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 07:25:45: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 07:25:46: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 07:25:47: #4 Write output xls file... SRX1872722.20_peaks.xls INFO @ Wed, 28 Jun 2017 07:25:47: #4 Write peak in narrowPeak format file... SRX1872722.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 07:25:47: #4 Write summits bed file... SRX1872722.20_summits.bed INFO @ Wed, 28 Jun 2017 07:25:47: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (7 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 07:25:48: #4 Write output xls file... SRX1872722.05_peaks.xls INFO @ Wed, 28 Jun 2017 07:25:48: #4 Write peak in narrowPeak format file... SRX1872722.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 07:25:48: #4 Write summits bed file... SRX1872722.05_summits.bed INFO @ Wed, 28 Jun 2017 07:25:48: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (25 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。