Job ID = 9160010 sra ファイルのダウンロード中... Completed: 1007226K bytes transferred in 16 seconds (487703K 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 10634138 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2402735/SRR5085180.sra Written 10634138 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: 00:11:14 10634138 reads; of these: 10634138 (100.00%) were paired; of these: 860738 (8.09%) aligned concordantly 0 times 6976379 (65.60%) aligned concordantly exactly 1 time 2797021 (26.30%) aligned concordantly >1 times ---- 860738 pairs aligned concordantly 0 times; of these: 32210 (3.74%) aligned discordantly 1 time ---- 828528 pairs aligned 0 times concordantly or discordantly; of these: 1657056 mates make up the pairs; of these: 1365523 (82.41%) aligned 0 times 193787 (11.69%) aligned exactly 1 time 97746 (5.90%) aligned >1 times 93.58% overall alignment rate Time searching: 00:11:14 Overall time: 00:11:14 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 12 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] 8960384 / 9798581 = 0.9145 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 01:52:19: # Command line: callpeak -t SRX2402735.bam -f BAM -g 12100000 -n SRX2402735.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2402735.10 # format = BAM # ChIP-seq file = ['SRX2402735.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 01:52:19: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:52:19: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:52:19: # Command line: callpeak -t SRX2402735.bam -f BAM -g 12100000 -n SRX2402735.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2402735.05 # format = BAM # ChIP-seq file = ['SRX2402735.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 01:52:19: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:52:19: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:52:19: # Command line: callpeak -t SRX2402735.bam -f BAM -g 12100000 -n SRX2402735.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2402735.20 # format = BAM # ChIP-seq file = ['SRX2402735.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 01:52:19: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:52:19: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:52:26: 1000000 INFO @ Wed, 28 Jun 2017 01:52:26: 1000000 INFO @ Wed, 28 Jun 2017 01:52:26: 1000000 INFO @ Wed, 28 Jun 2017 01:52:33: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 01:52:33: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 01:52:33: #1 total tags in treatment: 833730 INFO @ Wed, 28 Jun 2017 01:52:33: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:52:33: #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 01:52:33: #1 tags after filtering in treatment: 594154 INFO @ Wed, 28 Jun 2017 01:52:33: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 28 Jun 2017 01:52:33: #1 finished! INFO @ Wed, 28 Jun 2017 01:52:33: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:52:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:52:33: #2 number of paired peaks: 400 WARNING @ Wed, 28 Jun 2017 01:52:33: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Wed, 28 Jun 2017 01:52:33: start model_add_line... INFO @ Wed, 28 Jun 2017 01:52:33: start X-correlation... INFO @ Wed, 28 Jun 2017 01:52:33: end of X-cor INFO @ Wed, 28 Jun 2017 01:52:33: #2 finished! INFO @ Wed, 28 Jun 2017 01:52:33: #2 predicted fragment length is 158 bps INFO @ Wed, 28 Jun 2017 01:52:33: #2 alternative fragment length(s) may be 2,145,158,185,565,589 bps INFO @ Wed, 28 Jun 2017 01:52:33: #2.2 Generate R script for model : SRX2402735.10_model.r INFO @ Wed, 28 Jun 2017 01:52:33: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:52:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:52:34: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 01:52:34: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 01:52:34: #1 total tags in treatment: 833730 INFO @ Wed, 28 Jun 2017 01:52:34: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:52:34: #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 01:52:34: #1 tags after filtering in treatment: 594154 INFO @ Wed, 28 Jun 2017 01:52:34: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 28 Jun 2017 01:52:34: #1 finished! INFO @ Wed, 28 Jun 2017 01:52:34: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:52:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:52:34: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 01:52:34: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 01:52:34: #1 total tags in treatment: 833730 INFO @ Wed, 28 Jun 2017 01:52:34: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:52:34: #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 01:52:34: #1 tags after filtering in treatment: 594154 INFO @ Wed, 28 Jun 2017 01:52:34: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 28 Jun 2017 01:52:34: #1 finished! INFO @ Wed, 28 Jun 2017 01:52:34: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:52:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:52:34: #2 number of paired peaks: 400 WARNING @ Wed, 28 Jun 2017 01:52:34: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Wed, 28 Jun 2017 01:52:34: start model_add_line... INFO @ Wed, 28 Jun 2017 01:52:34: start X-correlation... INFO @ Wed, 28 Jun 2017 01:52:34: end of X-cor INFO @ Wed, 28 Jun 2017 01:52:34: #2 finished! INFO @ Wed, 28 Jun 2017 01:52:34: #2 predicted fragment length is 158 bps INFO @ Wed, 28 Jun 2017 01:52:34: #2 alternative fragment length(s) may be 2,145,158,185,565,589 bps INFO @ Wed, 28 Jun 2017 01:52:34: #2.2 Generate R script for model : SRX2402735.20_model.r INFO @ Wed, 28 Jun 2017 01:52:34: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:52:34: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:52:34: #2 number of paired peaks: 400 WARNING @ Wed, 28 Jun 2017 01:52:34: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Wed, 28 Jun 2017 01:52:34: start model_add_line... INFO @ Wed, 28 Jun 2017 01:52:34: start X-correlation... INFO @ Wed, 28 Jun 2017 01:52:34: end of X-cor INFO @ Wed, 28 Jun 2017 01:52:34: #2 finished! INFO @ Wed, 28 Jun 2017 01:52:34: #2 predicted fragment length is 158 bps INFO @ Wed, 28 Jun 2017 01:52:34: #2 alternative fragment length(s) may be 2,145,158,185,565,589 bps INFO @ Wed, 28 Jun 2017 01:52:34: #2.2 Generate R script for model : SRX2402735.05_model.r INFO @ Wed, 28 Jun 2017 01:52:34: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:52:34: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:52:35: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:52:36: #4 Write output xls file... SRX2402735.10_peaks.xls INFO @ Wed, 28 Jun 2017 01:52:36: #4 Write peak in narrowPeak format file... SRX2402735.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:52:36: #4 Write summits bed file... SRX2402735.10_summits.bed INFO @ Wed, 28 Jun 2017 01:52:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (146 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:52:36: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:52:36: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:52:37: #4 Write output xls file... SRX2402735.05_peaks.xls INFO @ Wed, 28 Jun 2017 01:52:37: #4 Write peak in narrowPeak format file... SRX2402735.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:52:37: #4 Write summits bed file... SRX2402735.05_summits.bed INFO @ Wed, 28 Jun 2017 01:52:37: Done! INFO @ Wed, 28 Jun 2017 01:52:37: #4 Write output xls file... SRX2402735.20_peaks.xls INFO @ Wed, 28 Jun 2017 01:52:37: #4 Write peak in narrowPeak format file... SRX2402735.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:52:37: #4 Write summits bed file... SRX2402735.20_summits.bed INFO @ Wed, 28 Jun 2017 01:52:37: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (389 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (12 chroms): 0 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。