Job ID = 9162517 sra ファイルのダウンロード中... Completed: 1035906K bytes transferred in 9 seconds (859038K 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 17384608 spots for /home/okishinya/chipatlas/results/sacCer3/SRX360914/SRR1003636.sra Written 17384608 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: 00:14:45 17384608 reads; of these: 17384608 (100.00%) were paired; of these: 1343820 (7.73%) aligned concordantly 0 times 13959036 (80.30%) aligned concordantly exactly 1 time 2081752 (11.97%) aligned concordantly >1 times ---- 1343820 pairs aligned concordantly 0 times; of these: 71329 (5.31%) aligned discordantly 1 time ---- 1272491 pairs aligned 0 times concordantly or discordantly; of these: 2544982 mates make up the pairs; of these: 1677139 (65.90%) aligned 0 times 774716 (30.44%) aligned exactly 1 time 93127 (3.66%) aligned >1 times 95.18% overall alignment rate Time searching: 00:14:45 Overall time: 00:14:45 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 16 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] 11770043 / 16107033 = 0.7307 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 08:23:58: # Command line: callpeak -t SRX360914.bam -f BAM -g 12100000 -n SRX360914.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX360914.10 # format = BAM # ChIP-seq file = ['SRX360914.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 08:23:58: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:23:58: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:23:58: # Command line: callpeak -t SRX360914.bam -f BAM -g 12100000 -n SRX360914.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX360914.05 # format = BAM # ChIP-seq file = ['SRX360914.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 08:23:58: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:23:58: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:23:58: # Command line: callpeak -t SRX360914.bam -f BAM -g 12100000 -n SRX360914.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX360914.20 # format = BAM # ChIP-seq file = ['SRX360914.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 08:23:58: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:23:58: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:24:06: 1000000 INFO @ Wed, 28 Jun 2017 08:24:06: 1000000 INFO @ Wed, 28 Jun 2017 08:24:06: 1000000 INFO @ Wed, 28 Jun 2017 08:24:14: 2000000 INFO @ Wed, 28 Jun 2017 08:24:14: 2000000 INFO @ Wed, 28 Jun 2017 08:24:14: 2000000 INFO @ Wed, 28 Jun 2017 08:24:22: 3000000 INFO @ Wed, 28 Jun 2017 08:24:22: 3000000 INFO @ Wed, 28 Jun 2017 08:24:22: 3000000 INFO @ Wed, 28 Jun 2017 08:24:30: 4000000 INFO @ Wed, 28 Jun 2017 08:24:30: 4000000 INFO @ Wed, 28 Jun 2017 08:24:30: 4000000 INFO @ Wed, 28 Jun 2017 08:24:38: 5000000 INFO @ Wed, 28 Jun 2017 08:24:38: 5000000 INFO @ Wed, 28 Jun 2017 08:24:38: 5000000 INFO @ Wed, 28 Jun 2017 08:24:47: 6000000 INFO @ Wed, 28 Jun 2017 08:24:47: 6000000 INFO @ Wed, 28 Jun 2017 08:24:47: 6000000 INFO @ Wed, 28 Jun 2017 08:24:55: 7000000 INFO @ Wed, 28 Jun 2017 08:24:55: 7000000 INFO @ Wed, 28 Jun 2017 08:24:55: 7000000 INFO @ Wed, 28 Jun 2017 08:25:04: 8000000 INFO @ Wed, 28 Jun 2017 08:25:04: 8000000 INFO @ Wed, 28 Jun 2017 08:25:04: 8000000 INFO @ Wed, 28 Jun 2017 08:25:11: 9000000 INFO @ Wed, 28 Jun 2017 08:25:11: 9000000 INFO @ Wed, 28 Jun 2017 08:25:11: 9000000 INFO @ Wed, 28 Jun 2017 08:25:14: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 08:25:14: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 08:25:14: #1 total tags in treatment: 4284804 INFO @ Wed, 28 Jun 2017 08:25:14: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:25:14: #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 08:25:14: #1 tags after filtering in treatment: 3200552 INFO @ Wed, 28 Jun 2017 08:25:14: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 28 Jun 2017 08:25:14: #1 finished! INFO @ Wed, 28 Jun 2017 08:25:14: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:25:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:25:15: #2 number of paired peaks: 126 WARNING @ Wed, 28 Jun 2017 08:25:15: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Wed, 28 Jun 2017 08:25:15: start model_add_line... INFO @ Wed, 28 Jun 2017 08:25:15: start X-correlation... INFO @ Wed, 28 Jun 2017 08:25:15: end of X-cor INFO @ Wed, 28 Jun 2017 08:25:15: #2 finished! INFO @ Wed, 28 Jun 2017 08:25:15: #2 predicted fragment length is 113 bps INFO @ Wed, 28 Jun 2017 08:25:15: #2 alternative fragment length(s) may be 4,113,128 bps INFO @ Wed, 28 Jun 2017 08:25:15: #2.2 Generate R script for model : SRX360914.10_model.r INFO @ Wed, 28 Jun 2017 08:25:15: #3 Call peaks... INFO @ Wed, 28 Jun 2017 08:25:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 08:25:15: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 08:25:15: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 08:25:15: #1 total tags in treatment: 4284804 INFO @ Wed, 28 Jun 2017 08:25:15: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:25:15: #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 08:25:15: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 08:25:15: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 08:25:15: #1 total tags in treatment: 4284804 INFO @ Wed, 28 Jun 2017 08:25:15: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:25:15: #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 08:25:15: #1 tags after filtering in treatment: 3200552 INFO @ Wed, 28 Jun 2017 08:25:15: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 28 Jun 2017 08:25:15: #1 finished! INFO @ Wed, 28 Jun 2017 08:25:15: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:25:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:25:15: #1 tags after filtering in treatment: 3200552 INFO @ Wed, 28 Jun 2017 08:25:15: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 28 Jun 2017 08:25:15: #1 finished! INFO @ Wed, 28 Jun 2017 08:25:15: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:25:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:25:16: #2 number of paired peaks: 126 WARNING @ Wed, 28 Jun 2017 08:25:16: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Wed, 28 Jun 2017 08:25:16: start model_add_line... INFO @ Wed, 28 Jun 2017 08:25:16: #2 number of paired peaks: 126 WARNING @ Wed, 28 Jun 2017 08:25:16: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Wed, 28 Jun 2017 08:25:16: start model_add_line... INFO @ Wed, 28 Jun 2017 08:25:16: start X-correlation... INFO @ Wed, 28 Jun 2017 08:25:16: end of X-cor INFO @ Wed, 28 Jun 2017 08:25:16: #2 finished! INFO @ Wed, 28 Jun 2017 08:25:16: #2 predicted fragment length is 113 bps INFO @ Wed, 28 Jun 2017 08:25:16: #2 alternative fragment length(s) may be 4,113,128 bps INFO @ Wed, 28 Jun 2017 08:25:16: #2.2 Generate R script for model : SRX360914.05_model.r INFO @ Wed, 28 Jun 2017 08:25:16: #3 Call peaks... INFO @ Wed, 28 Jun 2017 08:25:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 08:25:16: start X-correlation... INFO @ Wed, 28 Jun 2017 08:25:16: end of X-cor INFO @ Wed, 28 Jun 2017 08:25:16: #2 finished! INFO @ Wed, 28 Jun 2017 08:25:16: #2 predicted fragment length is 113 bps INFO @ Wed, 28 Jun 2017 08:25:16: #2 alternative fragment length(s) may be 4,113,128 bps INFO @ Wed, 28 Jun 2017 08:25:16: #2.2 Generate R script for model : SRX360914.20_model.r INFO @ Wed, 28 Jun 2017 08:25:16: #3 Call peaks... INFO @ Wed, 28 Jun 2017 08:25:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 08:25:24: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 08:25:24: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 08:25:25: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 08:25:27: #4 Write output xls file... SRX360914.10_peaks.xls INFO @ Wed, 28 Jun 2017 08:25:27: #4 Write peak in narrowPeak format file... SRX360914.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 08:25:27: #4 Write summits bed file... SRX360914.10_summits.bed INFO @ Wed, 28 Jun 2017 08:25:27: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1027 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 08:25:28: #4 Write output xls file... SRX360914.05_peaks.xls INFO @ Wed, 28 Jun 2017 08:25:28: #4 Write peak in narrowPeak format file... SRX360914.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 08:25:28: #4 Write summits bed file... SRX360914.05_summits.bed INFO @ Wed, 28 Jun 2017 08:25:28: Done! INFO @ Wed, 28 Jun 2017 08:25:28: #4 Write output xls file... SRX360914.20_peaks.xls INFO @ Wed, 28 Jun 2017 08:25:28: #4 Write peak in narrowPeak format file... SRX360914.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 08:25:28: #4 Write summits bed file... SRX360914.20_summits.bed INFO @ Wed, 28 Jun 2017 08:25:28: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1704 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (547 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。