Job ID = 9161996 sra ファイルのダウンロード中... Completed: 1454393K bytes transferred in 16 seconds (727745K 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 24924859 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423728/SRR2931017.sra Written 24924859 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: 00:16:03 24924859 reads; of these: 24924859 (100.00%) were paired; of these: 6703652 (26.90%) aligned concordantly 0 times 16016023 (64.26%) aligned concordantly exactly 1 time 2205184 (8.85%) aligned concordantly >1 times ---- 6703652 pairs aligned concordantly 0 times; of these: 28236 (0.42%) aligned discordantly 1 time ---- 6675416 pairs aligned 0 times concordantly or discordantly; of these: 13350832 mates make up the pairs; of these: 12821862 (96.04%) aligned 0 times 452841 (3.39%) aligned exactly 1 time 76129 (0.57%) aligned >1 times 74.28% overall alignment rate Time searching: 00:16:03 Overall time: 00:16:03 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] 16070739 / 18228433 = 0.8816 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 05:35:35: # Command line: callpeak -t SRX1423728.bam -f BAM -g 12100000 -n SRX1423728.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423728.05 # format = BAM # ChIP-seq file = ['SRX1423728.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 05:35:35: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:35:35: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:35:35: # Command line: callpeak -t SRX1423728.bam -f BAM -g 12100000 -n SRX1423728.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423728.20 # format = BAM # ChIP-seq file = ['SRX1423728.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 05:35:35: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:35:35: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:35:35: # Command line: callpeak -t SRX1423728.bam -f BAM -g 12100000 -n SRX1423728.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423728.10 # format = BAM # ChIP-seq file = ['SRX1423728.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 05:35:35: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:35:35: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:35:41: 1000000 INFO @ Wed, 28 Jun 2017 05:35:41: 1000000 INFO @ Wed, 28 Jun 2017 05:35:41: 1000000 INFO @ Wed, 28 Jun 2017 05:35:47: 2000000 INFO @ Wed, 28 Jun 2017 05:35:47: 2000000 INFO @ Wed, 28 Jun 2017 05:35:47: 2000000 INFO @ Wed, 28 Jun 2017 05:35:52: 3000000 INFO @ Wed, 28 Jun 2017 05:35:54: 3000000 INFO @ Wed, 28 Jun 2017 05:35:54: 3000000 INFO @ Wed, 28 Jun 2017 05:35:58: 4000000 INFO @ Wed, 28 Jun 2017 05:36:00: 4000000 INFO @ Wed, 28 Jun 2017 05:36:00: 4000000 INFO @ Wed, 28 Jun 2017 05:36:03: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:36:03: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:36:03: #1 total tags in treatment: 2154878 INFO @ Wed, 28 Jun 2017 05:36:03: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:36:03: #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 05:36:03: #1 tags after filtering in treatment: 1844777 INFO @ Wed, 28 Jun 2017 05:36:03: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 28 Jun 2017 05:36:03: #1 finished! INFO @ Wed, 28 Jun 2017 05:36:03: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:36:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:36:03: #2 number of paired peaks: 102 WARNING @ Wed, 28 Jun 2017 05:36:03: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Wed, 28 Jun 2017 05:36:03: start model_add_line... INFO @ Wed, 28 Jun 2017 05:36:03: start X-correlation... INFO @ Wed, 28 Jun 2017 05:36:03: end of X-cor INFO @ Wed, 28 Jun 2017 05:36:03: #2 finished! INFO @ Wed, 28 Jun 2017 05:36:03: #2 predicted fragment length is 158 bps INFO @ Wed, 28 Jun 2017 05:36:03: #2 alternative fragment length(s) may be 2,93,124,158,183,198,232,268 bps INFO @ Wed, 28 Jun 2017 05:36:03: #2.2 Generate R script for model : SRX1423728.05_model.r INFO @ Wed, 28 Jun 2017 05:36:03: #3 Call peaks... INFO @ Wed, 28 Jun 2017 05:36:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 05:36:05: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:36:05: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:36:05: #1 total tags in treatment: 2154878 INFO @ Wed, 28 Jun 2017 05:36:05: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:36:05: #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 05:36:05: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:36:05: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:36:05: #1 total tags in treatment: 2154878 INFO @ Wed, 28 Jun 2017 05:36:05: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:36:05: #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 05:36:05: #1 tags after filtering in treatment: 1844777 INFO @ Wed, 28 Jun 2017 05:36:05: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 28 Jun 2017 05:36:05: #1 finished! INFO @ Wed, 28 Jun 2017 05:36:05: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:36:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:36:05: #1 tags after filtering in treatment: 1844777 INFO @ Wed, 28 Jun 2017 05:36:05: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 28 Jun 2017 05:36:05: #1 finished! INFO @ Wed, 28 Jun 2017 05:36:05: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:36:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:36:05: #2 number of paired peaks: 102 WARNING @ Wed, 28 Jun 2017 05:36:05: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Wed, 28 Jun 2017 05:36:05: start model_add_line... INFO @ Wed, 28 Jun 2017 05:36:05: #2 number of paired peaks: 102 WARNING @ Wed, 28 Jun 2017 05:36:05: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Wed, 28 Jun 2017 05:36:05: start model_add_line... INFO @ Wed, 28 Jun 2017 05:36:05: start X-correlation... INFO @ Wed, 28 Jun 2017 05:36:05: end of X-cor INFO @ Wed, 28 Jun 2017 05:36:05: #2 finished! INFO @ Wed, 28 Jun 2017 05:36:05: #2 predicted fragment length is 158 bps INFO @ Wed, 28 Jun 2017 05:36:05: #2 alternative fragment length(s) may be 2,93,124,158,183,198,232,268 bps INFO @ Wed, 28 Jun 2017 05:36:05: #2.2 Generate R script for model : SRX1423728.10_model.r INFO @ Wed, 28 Jun 2017 05:36:05: #3 Call peaks... INFO @ Wed, 28 Jun 2017 05:36:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 05:36:05: start X-correlation... INFO @ Wed, 28 Jun 2017 05:36:05: end of X-cor INFO @ Wed, 28 Jun 2017 05:36:05: #2 finished! INFO @ Wed, 28 Jun 2017 05:36:05: #2 predicted fragment length is 158 bps INFO @ Wed, 28 Jun 2017 05:36:05: #2 alternative fragment length(s) may be 2,93,124,158,183,198,232,268 bps INFO @ Wed, 28 Jun 2017 05:36:05: #2.2 Generate R script for model : SRX1423728.20_model.r INFO @ Wed, 28 Jun 2017 05:36:05: #3 Call peaks... INFO @ Wed, 28 Jun 2017 05:36:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 05:36:09: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 05:36:11: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 05:36:11: #4 Write output xls file... SRX1423728.05_peaks.xls INFO @ Wed, 28 Jun 2017 05:36:11: #4 Write peak in narrowPeak format file... SRX1423728.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 05:36:11: #4 Write summits bed file... SRX1423728.05_summits.bed INFO @ Wed, 28 Jun 2017 05:36:11: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (861 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 05:36:11: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 05:36:13: #4 Write output xls file... SRX1423728.20_peaks.xls INFO @ Wed, 28 Jun 2017 05:36:13: #4 Write peak in narrowPeak format file... SRX1423728.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 05:36:13: #4 Write summits bed file... SRX1423728.20_summits.bed INFO @ Wed, 28 Jun 2017 05:36:13: 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 05:36:13: #4 Write output xls file... SRX1423728.10_peaks.xls INFO @ Wed, 28 Jun 2017 05:36:13: #4 Write peak in narrowPeak format file... SRX1423728.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 05:36:13: #4 Write summits bed file... SRX1423728.10_summits.bed INFO @ Wed, 28 Jun 2017 05:36:13: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (400 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。