Job ID = 11245054 sra ファイルのダウンロード中... Completed: 188772K bytes transferred in 6 seconds (241567K 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 5983381 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554766/SRR7696438.sra Written 5983381 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554766/SRR7696438.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: 00:02:51 5983381 reads; of these: 5983381 (100.00%) were paired; of these: 3833367 (64.07%) aligned concordantly 0 times 1531266 (25.59%) aligned concordantly exactly 1 time 618748 (10.34%) aligned concordantly >1 times ---- 3833367 pairs aligned concordantly 0 times; of these: 8947 (0.23%) aligned discordantly 1 time ---- 3824420 pairs aligned 0 times concordantly or discordantly; of these: 7648840 mates make up the pairs; of these: 6138252 (80.25%) aligned 0 times 1083551 (14.17%) aligned exactly 1 time 427037 (5.58%) aligned >1 times 48.71% overall alignment rate Time searching: 00:02:51 Overall time: 00:02:51 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] 296499 / 2158463 = 0.1374 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 @ Tue, 09 Oct 2018 23:18:29: # Command line: callpeak -t SRX4554766.bam -f BAM -g 12100000 -n SRX4554766.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554766.10 # format = BAM # ChIP-seq file = ['SRX4554766.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 @ Tue, 09 Oct 2018 23:18:29: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:18:29: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:18:29: # Command line: callpeak -t SRX4554766.bam -f BAM -g 12100000 -n SRX4554766.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554766.20 # format = BAM # ChIP-seq file = ['SRX4554766.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 @ Tue, 09 Oct 2018 23:18:29: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:18:29: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:18:29: # Command line: callpeak -t SRX4554766.bam -f BAM -g 12100000 -n SRX4554766.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554766.05 # format = BAM # ChIP-seq file = ['SRX4554766.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 @ Tue, 09 Oct 2018 23:18:29: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:18:29: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:18:36: 1000000 INFO @ Tue, 09 Oct 2018 23:18:36: 1000000 INFO @ Tue, 09 Oct 2018 23:18:36: 1000000 INFO @ Tue, 09 Oct 2018 23:18:42: 2000000 INFO @ Tue, 09 Oct 2018 23:18:42: 2000000 INFO @ Tue, 09 Oct 2018 23:18:42: 2000000 INFO @ Tue, 09 Oct 2018 23:18:48: 3000000 INFO @ Tue, 09 Oct 2018 23:18:49: 3000000 INFO @ Tue, 09 Oct 2018 23:18:49: 3000000 INFO @ Tue, 09 Oct 2018 23:18:55: 4000000 INFO @ Tue, 09 Oct 2018 23:18:55: 4000000 INFO @ Tue, 09 Oct 2018 23:18:55: 4000000 INFO @ Tue, 09 Oct 2018 23:19:01: 5000000 INFO @ Tue, 09 Oct 2018 23:19:02: 5000000 INFO @ Tue, 09 Oct 2018 23:19:02: 5000000 INFO @ Tue, 09 Oct 2018 23:19:02: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:19:02: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:19:02: #1 total tags in treatment: 1853573 INFO @ Tue, 09 Oct 2018 23:19:02: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:19:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:19:02: #1 tags after filtering in treatment: 1098792 INFO @ Tue, 09 Oct 2018 23:19:02: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 09 Oct 2018 23:19:02: #1 finished! INFO @ Tue, 09 Oct 2018 23:19:02: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:19:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:19:02: #2 number of paired peaks: 413 WARNING @ Tue, 09 Oct 2018 23:19:02: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Tue, 09 Oct 2018 23:19:02: start model_add_line... INFO @ Tue, 09 Oct 2018 23:19:03: start X-correlation... INFO @ Tue, 09 Oct 2018 23:19:03: end of X-cor INFO @ Tue, 09 Oct 2018 23:19:03: #2 finished! INFO @ Tue, 09 Oct 2018 23:19:03: #2 predicted fragment length is 259 bps INFO @ Tue, 09 Oct 2018 23:19:03: #2 alternative fragment length(s) may be 0,185,222,259,429,485,530,572 bps INFO @ Tue, 09 Oct 2018 23:19:03: #2.2 Generate R script for model : SRX4554766.05_model.r INFO @ Tue, 09 Oct 2018 23:19:03: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:19:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:19:03: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:19:03: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:19:03: #1 total tags in treatment: 1853573 INFO @ Tue, 09 Oct 2018 23:19:03: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:19:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:19:03: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:19:03: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:19:03: #1 total tags in treatment: 1853573 INFO @ Tue, 09 Oct 2018 23:19:03: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:19:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:19:03: #1 tags after filtering in treatment: 1098792 INFO @ Tue, 09 Oct 2018 23:19:03: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 09 Oct 2018 23:19:03: #1 finished! INFO @ Tue, 09 Oct 2018 23:19:03: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:19:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:19:03: #1 tags after filtering in treatment: 1098792 INFO @ Tue, 09 Oct 2018 23:19:03: #1 Redundant rate of treatment: 0.41 INFO @ Tue, 09 Oct 2018 23:19:03: #1 finished! INFO @ Tue, 09 Oct 2018 23:19:03: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:19:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:19:03: #2 number of paired peaks: 413 WARNING @ Tue, 09 Oct 2018 23:19:03: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Tue, 09 Oct 2018 23:19:03: start model_add_line... INFO @ Tue, 09 Oct 2018 23:19:03: #2 number of paired peaks: 413 WARNING @ Tue, 09 Oct 2018 23:19:03: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Tue, 09 Oct 2018 23:19:03: start X-correlation... INFO @ Tue, 09 Oct 2018 23:19:03: start model_add_line... INFO @ Tue, 09 Oct 2018 23:19:03: end of X-cor INFO @ Tue, 09 Oct 2018 23:19:03: #2 finished! INFO @ Tue, 09 Oct 2018 23:19:03: #2 predicted fragment length is 259 bps INFO @ Tue, 09 Oct 2018 23:19:03: #2 alternative fragment length(s) may be 0,185,222,259,429,485,530,572 bps INFO @ Tue, 09 Oct 2018 23:19:03: #2.2 Generate R script for model : SRX4554766.10_model.r INFO @ Tue, 09 Oct 2018 23:19:03: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:19:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:19:03: start X-correlation... INFO @ Tue, 09 Oct 2018 23:19:03: end of X-cor INFO @ Tue, 09 Oct 2018 23:19:03: #2 finished! INFO @ Tue, 09 Oct 2018 23:19:03: #2 predicted fragment length is 259 bps INFO @ Tue, 09 Oct 2018 23:19:03: #2 alternative fragment length(s) may be 0,185,222,259,429,485,530,572 bps INFO @ Tue, 09 Oct 2018 23:19:03: #2.2 Generate R script for model : SRX4554766.20_model.r INFO @ Tue, 09 Oct 2018 23:19:03: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:19:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:19:09: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:19:10: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:19:10: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:19:10: #4 Write output xls file... SRX4554766.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:19:10: #4 Write peak in narrowPeak format file... SRX4554766.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:19:10: #4 Write summits bed file... SRX4554766.05_summits.bed INFO @ Tue, 09 Oct 2018 23:19:10: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (251 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:19:11: #4 Write output xls file... SRX4554766.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:19:11: #4 Write peak in narrowPeak format file... SRX4554766.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:19:11: #4 Write summits bed file... SRX4554766.20_summits.bed INFO @ Tue, 09 Oct 2018 23:19:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:19:11: #4 Write output xls file... SRX4554766.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:19:11: #4 Write peak in narrowPeak format file... SRX4554766.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:19:11: #4 Write summits bed file... SRX4554766.10_summits.bed INFO @ Tue, 09 Oct 2018 23:19:11: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (89 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。