Job ID = 11244906 sra ファイルのダウンロード中... Completed: 254166K bytes transferred in 11 seconds (186390K 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 7817383 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554653/SRR7696327.sra Written 7817383 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554653/SRR7696327.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: 00:03:34 7817383 reads; of these: 7817383 (100.00%) were paired; of these: 4013701 (51.34%) aligned concordantly 0 times 3289342 (42.08%) aligned concordantly exactly 1 time 514340 (6.58%) aligned concordantly >1 times ---- 4013701 pairs aligned concordantly 0 times; of these: 114302 (2.85%) aligned discordantly 1 time ---- 3899399 pairs aligned 0 times concordantly or discordantly; of these: 7798798 mates make up the pairs; of these: 7636386 (97.92%) aligned 0 times 104191 (1.34%) aligned exactly 1 time 58221 (0.75%) aligned >1 times 51.16% overall alignment rate Time searching: 00:03:34 Overall time: 00:03:34 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] 94407 / 3895091 = 0.0242 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 22:50:03: # Command line: callpeak -t SRX4554653.bam -f BAM -g 12100000 -n SRX4554653.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554653.10 # format = BAM # ChIP-seq file = ['SRX4554653.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 22:50:03: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:50:03: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:50:03: # Command line: callpeak -t SRX4554653.bam -f BAM -g 12100000 -n SRX4554653.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554653.20 # format = BAM # ChIP-seq file = ['SRX4554653.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 22:50:03: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:50:03: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:50:03: # Command line: callpeak -t SRX4554653.bam -f BAM -g 12100000 -n SRX4554653.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554653.05 # format = BAM # ChIP-seq file = ['SRX4554653.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 22:50:03: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:50:03: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:50:09: 1000000 INFO @ Tue, 09 Oct 2018 22:50:09: 1000000 INFO @ Tue, 09 Oct 2018 22:50:09: 1000000 INFO @ Tue, 09 Oct 2018 22:50:14: 2000000 INFO @ Tue, 09 Oct 2018 22:50:16: 2000000 INFO @ Tue, 09 Oct 2018 22:50:16: 2000000 INFO @ Tue, 09 Oct 2018 22:50:20: 3000000 INFO @ Tue, 09 Oct 2018 22:50:22: 3000000 INFO @ Tue, 09 Oct 2018 22:50:22: 3000000 INFO @ Tue, 09 Oct 2018 22:50:25: 4000000 INFO @ Tue, 09 Oct 2018 22:50:28: 4000000 INFO @ Tue, 09 Oct 2018 22:50:28: 4000000 INFO @ Tue, 09 Oct 2018 22:50:31: 5000000 INFO @ Tue, 09 Oct 2018 22:50:34: 5000000 INFO @ Tue, 09 Oct 2018 22:50:34: 5000000 INFO @ Tue, 09 Oct 2018 22:50:36: 6000000 INFO @ Tue, 09 Oct 2018 22:50:40: 6000000 INFO @ Tue, 09 Oct 2018 22:50:40: 6000000 INFO @ Tue, 09 Oct 2018 22:50:42: 7000000 INFO @ Tue, 09 Oct 2018 22:50:46: 7000000 INFO @ Tue, 09 Oct 2018 22:50:46: 7000000 INFO @ Tue, 09 Oct 2018 22:50:47: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:50:47: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:50:47: #1 total tags in treatment: 3712705 INFO @ Tue, 09 Oct 2018 22:50:47: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:50:47: #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 22:50:47: #1 tags after filtering in treatment: 1883906 INFO @ Tue, 09 Oct 2018 22:50:47: #1 Redundant rate of treatment: 0.49 INFO @ Tue, 09 Oct 2018 22:50:47: #1 finished! INFO @ Tue, 09 Oct 2018 22:50:47: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:50:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:50:47: #2 number of paired peaks: 1245 INFO @ Tue, 09 Oct 2018 22:50:47: start model_add_line... INFO @ Tue, 09 Oct 2018 22:50:47: start X-correlation... INFO @ Tue, 09 Oct 2018 22:50:47: end of X-cor INFO @ Tue, 09 Oct 2018 22:50:47: #2 finished! INFO @ Tue, 09 Oct 2018 22:50:47: #2 predicted fragment length is 175 bps INFO @ Tue, 09 Oct 2018 22:50:47: #2 alternative fragment length(s) may be 0,160,175,214 bps INFO @ Tue, 09 Oct 2018 22:50:47: #2.2 Generate R script for model : SRX4554653.10_model.r INFO @ Tue, 09 Oct 2018 22:50:47: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:50:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:50:51: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:50:51: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:50:51: #1 total tags in treatment: 3712705 INFO @ Tue, 09 Oct 2018 22:50:51: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:50:51: #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 22:50:51: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:50:51: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:50:51: #1 total tags in treatment: 3712705 INFO @ Tue, 09 Oct 2018 22:50:51: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:50:51: #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 22:50:51: #1 tags after filtering in treatment: 1883906 INFO @ Tue, 09 Oct 2018 22:50:51: #1 tags after filtering in treatment: 1883906 INFO @ Tue, 09 Oct 2018 22:50:51: #1 Redundant rate of treatment: 0.49 INFO @ Tue, 09 Oct 2018 22:50:51: #1 Redundant rate of treatment: 0.49 INFO @ Tue, 09 Oct 2018 22:50:51: #1 finished! INFO @ Tue, 09 Oct 2018 22:50:51: #1 finished! INFO @ Tue, 09 Oct 2018 22:50:51: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:50:51: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:50:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:50:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:50:52: #2 number of paired peaks: 1245 INFO @ Tue, 09 Oct 2018 22:50:52: start model_add_line... INFO @ Tue, 09 Oct 2018 22:50:52: #2 number of paired peaks: 1245 INFO @ Tue, 09 Oct 2018 22:50:52: start model_add_line... INFO @ Tue, 09 Oct 2018 22:50:52: start X-correlation... INFO @ Tue, 09 Oct 2018 22:50:52: start X-correlation... INFO @ Tue, 09 Oct 2018 22:50:52: end of X-cor INFO @ Tue, 09 Oct 2018 22:50:52: end of X-cor INFO @ Tue, 09 Oct 2018 22:50:52: #2 finished! INFO @ Tue, 09 Oct 2018 22:50:52: #2 finished! INFO @ Tue, 09 Oct 2018 22:50:52: #2 predicted fragment length is 175 bps INFO @ Tue, 09 Oct 2018 22:50:52: #2 predicted fragment length is 175 bps INFO @ Tue, 09 Oct 2018 22:50:52: #2 alternative fragment length(s) may be 0,160,175,214 bps INFO @ Tue, 09 Oct 2018 22:50:52: #2 alternative fragment length(s) may be 0,160,175,214 bps INFO @ Tue, 09 Oct 2018 22:50:52: #2.2 Generate R script for model : SRX4554653.05_model.r INFO @ Tue, 09 Oct 2018 22:50:52: #2.2 Generate R script for model : SRX4554653.20_model.r INFO @ Tue, 09 Oct 2018 22:50:52: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:50:52: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:50:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:50:52: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 09 Oct 2018 22:51:00: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:51:02: #4 Write output xls file... SRX4554653.10_peaks.xls INFO @ Tue, 09 Oct 2018 22:51:02: #4 Write peak in narrowPeak format file... SRX4554653.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:51:02: #4 Write summits bed file... SRX4554653.10_summits.bed INFO @ Tue, 09 Oct 2018 22:51:02: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (503 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 09 Oct 2018 22:51:05: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:51:05: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:51:07: #4 Write output xls file... SRX4554653.05_peaks.xls INFO @ Tue, 09 Oct 2018 22:51:07: #4 Write peak in narrowPeak format file... SRX4554653.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:51:07: #4 Write summits bed file... SRX4554653.05_summits.bed INFO @ Tue, 09 Oct 2018 22:51:07: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (609 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 22:51:07: #4 Write output xls file... SRX4554653.20_peaks.xls INFO @ Tue, 09 Oct 2018 22:51:07: #4 Write peak in narrowPeak format file... SRX4554653.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:51:07: #4 Write summits bed file... SRX4554653.20_summits.bed INFO @ Tue, 09 Oct 2018 22:51:07: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (264 records, 4 fields): 3 millis CompletedMACS2peakCalling