Job ID = 10937362 sra ファイルのダウンロード中... Completed: 96626K bytes transferred in 4 seconds (185770K bits/sec), in 1 file. 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... Read 1872480 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198712/SRR4304442.sra Written 1872480 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198712/SRR4304442.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:00:57 1872480 reads; of these: 1872480 (100.00%) were paired; of these: 1210327 (64.64%) aligned concordantly 0 times 425298 (22.71%) aligned concordantly exactly 1 time 236855 (12.65%) aligned concordantly >1 times ---- 1210327 pairs aligned concordantly 0 times; of these: 16564 (1.37%) aligned discordantly 1 time ---- 1193763 pairs aligned 0 times concordantly or discordantly; of these: 2387526 mates make up the pairs; of these: 2171268 (90.94%) aligned 0 times 127302 (5.33%) aligned exactly 1 time 88956 (3.73%) aligned >1 times 42.02% overall alignment rate Time searching: 00:00:57 Overall time: 00:00:57 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] 14364 / 676090 = 0.0212 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 @ Fri, 10 Aug 2018 01:52:43: # Command line: callpeak -t SRX2198712.bam -f BAM -g 12100000 -n SRX2198712.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2198712.20 # format = BAM # ChIP-seq file = ['SRX2198712.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 @ Fri, 10 Aug 2018 01:52:43: #1 read tag files... INFO @ Fri, 10 Aug 2018 01:52:43: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 01:52:43: # Command line: callpeak -t SRX2198712.bam -f BAM -g 12100000 -n SRX2198712.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2198712.05 # format = BAM # ChIP-seq file = ['SRX2198712.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 @ Fri, 10 Aug 2018 01:52:43: #1 read tag files... INFO @ Fri, 10 Aug 2018 01:52:43: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 01:52:43: # Command line: callpeak -t SRX2198712.bam -f BAM -g 12100000 -n SRX2198712.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2198712.10 # format = BAM # ChIP-seq file = ['SRX2198712.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 @ Fri, 10 Aug 2018 01:52:43: #1 read tag files... INFO @ Fri, 10 Aug 2018 01:52:43: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 01:52:50: 1000000 INFO @ Fri, 10 Aug 2018 01:52:50: 1000000 INFO @ Fri, 10 Aug 2018 01:52:50: 1000000 INFO @ Fri, 10 Aug 2018 01:52:54: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 01:52:54: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 01:52:54: #1 total tags in treatment: 647985 INFO @ Fri, 10 Aug 2018 01:52:54: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 01:52:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 01:52:54: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 01:52:54: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 01:52:54: #1 total tags in treatment: 647985 INFO @ Fri, 10 Aug 2018 01:52:54: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 01:52:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 01:52:54: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 01:52:54: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 01:52:54: #1 total tags in treatment: 647985 INFO @ Fri, 10 Aug 2018 01:52:54: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 01:52:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 01:52:54: #1 tags after filtering in treatment: 458888 INFO @ Fri, 10 Aug 2018 01:52:54: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 10 Aug 2018 01:52:54: #1 finished! INFO @ Fri, 10 Aug 2018 01:52:54: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 01:52:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 01:52:54: #1 tags after filtering in treatment: 458888 INFO @ Fri, 10 Aug 2018 01:52:54: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 10 Aug 2018 01:52:54: #1 finished! INFO @ Fri, 10 Aug 2018 01:52:54: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 01:52:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 01:52:54: #1 tags after filtering in treatment: 458888 INFO @ Fri, 10 Aug 2018 01:52:54: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 10 Aug 2018 01:52:54: #1 finished! INFO @ Fri, 10 Aug 2018 01:52:54: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 01:52:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 01:52:54: #2 number of paired peaks: 193 WARNING @ Fri, 10 Aug 2018 01:52:54: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Fri, 10 Aug 2018 01:52:54: start model_add_line... INFO @ Fri, 10 Aug 2018 01:52:54: start X-correlation... INFO @ Fri, 10 Aug 2018 01:52:54: #2 number of paired peaks: 193 WARNING @ Fri, 10 Aug 2018 01:52:54: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Fri, 10 Aug 2018 01:52:54: start model_add_line... INFO @ Fri, 10 Aug 2018 01:52:54: end of X-cor INFO @ Fri, 10 Aug 2018 01:52:54: #2 finished! INFO @ Fri, 10 Aug 2018 01:52:54: #2 predicted fragment length is 158 bps INFO @ Fri, 10 Aug 2018 01:52:54: #2 alternative fragment length(s) may be 4,110,133,154,158,212,477,508,557,583 bps INFO @ Fri, 10 Aug 2018 01:52:54: #2.2 Generate R script for model : SRX2198712.05_model.r INFO @ Fri, 10 Aug 2018 01:52:54: #2 number of paired peaks: 193 WARNING @ Fri, 10 Aug 2018 01:52:54: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Fri, 10 Aug 2018 01:52:54: start model_add_line... INFO @ Fri, 10 Aug 2018 01:52:54: start X-correlation... INFO @ Fri, 10 Aug 2018 01:52:54: #3 Call peaks... INFO @ Fri, 10 Aug 2018 01:52:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 01:52:54: start X-correlation... INFO @ Fri, 10 Aug 2018 01:52:54: end of X-cor INFO @ Fri, 10 Aug 2018 01:52:54: #2 finished! INFO @ Fri, 10 Aug 2018 01:52:54: #2 predicted fragment length is 158 bps INFO @ Fri, 10 Aug 2018 01:52:54: #2 alternative fragment length(s) may be 4,110,133,154,158,212,477,508,557,583 bps INFO @ Fri, 10 Aug 2018 01:52:54: #2.2 Generate R script for model : SRX2198712.10_model.r INFO @ Fri, 10 Aug 2018 01:52:54: end of X-cor INFO @ Fri, 10 Aug 2018 01:52:54: #2 finished! INFO @ Fri, 10 Aug 2018 01:52:54: #2 predicted fragment length is 158 bps INFO @ Fri, 10 Aug 2018 01:52:54: #2 alternative fragment length(s) may be 4,110,133,154,158,212,477,508,557,583 bps INFO @ Fri, 10 Aug 2018 01:52:54: #2.2 Generate R script for model : SRX2198712.20_model.r INFO @ Fri, 10 Aug 2018 01:52:54: #3 Call peaks... INFO @ Fri, 10 Aug 2018 01:52:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 01:52:54: #3 Call peaks... INFO @ Fri, 10 Aug 2018 01:52:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 01:52:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 01:52:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 01:52:57: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 01:52:57: #4 Write output xls file... SRX2198712.05_peaks.xls INFO @ Fri, 10 Aug 2018 01:52:57: #4 Write peak in narrowPeak format file... SRX2198712.05_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 01:52:57: #4 Write summits bed file... SRX2198712.05_summits.bed INFO @ Fri, 10 Aug 2018 01:52:57: Done! INFO @ Fri, 10 Aug 2018 01:52:57: #4 Write output xls file... SRX2198712.10_peaks.xls INFO @ Fri, 10 Aug 2018 01:52:57: #4 Write peak in narrowPeak format file... SRX2198712.10_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 01:52:57: #4 Write summits bed file... SRX2198712.10_summits.bed INFO @ Fri, 10 Aug 2018 01:52:57: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (280 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (134 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 01:52:57: #4 Write output xls file... SRX2198712.20_peaks.xls INFO @ Fri, 10 Aug 2018 01:52:57: #4 Write peak in narrowPeak format file... SRX2198712.20_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 01:52:57: #4 Write summits bed file... SRX2198712.20_summits.bed INFO @ Fri, 10 Aug 2018 01:52:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (29 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。