Job ID = 11193204 sra ファイルのダウンロード中... Completed: 403852K bytes transferred in 6 seconds (476745K 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 9216998 spots for /home/okishinya/chipatlas/results/sacCer3/SRX876292/SRR1802395.sra Written 9216998 spots for /home/okishinya/chipatlas/results/sacCer3/SRX876292/SRR1802395.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: 00:03:42 9216998 reads; of these: 9216998 (100.00%) were paired; of these: 5298034 (57.48%) aligned concordantly 0 times 3316535 (35.98%) aligned concordantly exactly 1 time 602429 (6.54%) aligned concordantly >1 times ---- 5298034 pairs aligned concordantly 0 times; of these: 82935 (1.57%) aligned discordantly 1 time ---- 5215099 pairs aligned 0 times concordantly or discordantly; of these: 10430198 mates make up the pairs; of these: 10218335 (97.97%) aligned 0 times 146729 (1.41%) aligned exactly 1 time 65134 (0.62%) aligned >1 times 44.57% overall alignment rate Time searching: 00:03:42 Overall time: 00:03:42 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] 3501428 / 3977993 = 0.8802 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 @ Sat, 15 Sep 2018 11:13:24: # Command line: callpeak -t SRX876292.bam -f BAM -g 12100000 -n SRX876292.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX876292.05 # format = BAM # ChIP-seq file = ['SRX876292.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 @ Sat, 15 Sep 2018 11:13:24: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:13:24: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:13:24: # Command line: callpeak -t SRX876292.bam -f BAM -g 12100000 -n SRX876292.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX876292.10 # format = BAM # ChIP-seq file = ['SRX876292.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 @ Sat, 15 Sep 2018 11:13:24: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:13:24: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:13:24: # Command line: callpeak -t SRX876292.bam -f BAM -g 12100000 -n SRX876292.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX876292.20 # format = BAM # ChIP-seq file = ['SRX876292.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 @ Sat, 15 Sep 2018 11:13:24: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:13:24: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:13:32: 1000000 INFO @ Sat, 15 Sep 2018 11:13:32: 1000000 INFO @ Sat, 15 Sep 2018 11:13:32: 1000000 INFO @ Sat, 15 Sep 2018 11:13:34: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:13:34: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:13:34: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:13:34: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:13:34: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:13:34: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:13:34: #1 total tags in treatment: 483972 INFO @ Sat, 15 Sep 2018 11:13:34: #1 total tags in treatment: 483972 INFO @ Sat, 15 Sep 2018 11:13:34: #1 total tags in treatment: 483972 INFO @ Sat, 15 Sep 2018 11:13:34: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:13:34: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:13:34: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:13:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:13:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:13:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:13:34: #1 tags after filtering in treatment: 404205 INFO @ Sat, 15 Sep 2018 11:13:34: #1 tags after filtering in treatment: 404205 INFO @ Sat, 15 Sep 2018 11:13:34: #1 tags after filtering in treatment: 404205 INFO @ Sat, 15 Sep 2018 11:13:34: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 15 Sep 2018 11:13:34: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 15 Sep 2018 11:13:34: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 15 Sep 2018 11:13:34: #1 finished! INFO @ Sat, 15 Sep 2018 11:13:34: #1 finished! INFO @ Sat, 15 Sep 2018 11:13:34: #1 finished! INFO @ Sat, 15 Sep 2018 11:13:34: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:13:34: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:13:34: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:13:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:13:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:13:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:13:34: #2 number of paired peaks: 356 INFO @ Sat, 15 Sep 2018 11:13:34: #2 number of paired peaks: 356 WARNING @ Sat, 15 Sep 2018 11:13:34: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! WARNING @ Sat, 15 Sep 2018 11:13:34: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Sat, 15 Sep 2018 11:13:34: start model_add_line... INFO @ Sat, 15 Sep 2018 11:13:34: start model_add_line... INFO @ Sat, 15 Sep 2018 11:13:34: #2 number of paired peaks: 356 WARNING @ Sat, 15 Sep 2018 11:13:34: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Sat, 15 Sep 2018 11:13:34: start model_add_line... INFO @ Sat, 15 Sep 2018 11:13:34: start X-correlation... INFO @ Sat, 15 Sep 2018 11:13:34: start X-correlation... INFO @ Sat, 15 Sep 2018 11:13:34: start X-correlation... INFO @ Sat, 15 Sep 2018 11:13:34: end of X-cor INFO @ Sat, 15 Sep 2018 11:13:34: end of X-cor INFO @ Sat, 15 Sep 2018 11:13:34: #2 finished! INFO @ Sat, 15 Sep 2018 11:13:34: #2 finished! INFO @ Sat, 15 Sep 2018 11:13:34: #2 predicted fragment length is 53 bps INFO @ Sat, 15 Sep 2018 11:13:34: #2 predicted fragment length is 53 bps INFO @ Sat, 15 Sep 2018 11:13:34: #2 alternative fragment length(s) may be 53,63,549 bps INFO @ Sat, 15 Sep 2018 11:13:34: #2 alternative fragment length(s) may be 53,63,549 bps INFO @ Sat, 15 Sep 2018 11:13:34: #2.2 Generate R script for model : SRX876292.10_model.r INFO @ Sat, 15 Sep 2018 11:13:34: #2.2 Generate R script for model : SRX876292.05_model.r INFO @ Sat, 15 Sep 2018 11:13:34: end of X-cor INFO @ Sat, 15 Sep 2018 11:13:34: #2 finished! INFO @ Sat, 15 Sep 2018 11:13:34: #2 predicted fragment length is 53 bps INFO @ Sat, 15 Sep 2018 11:13:34: #2 alternative fragment length(s) may be 53,63,549 bps INFO @ Sat, 15 Sep 2018 11:13:34: #2.2 Generate R script for model : SRX876292.20_model.r WARNING @ Sat, 15 Sep 2018 11:13:34: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 11:13:34: #2 You may need to consider one of the other alternative d(s): 53,63,549 WARNING @ Sat, 15 Sep 2018 11:13:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Sat, 15 Sep 2018 11:13:34: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! INFO @ Sat, 15 Sep 2018 11:13:34: #3 Call peaks... WARNING @ Sat, 15 Sep 2018 11:13:34: #2 You may need to consider one of the other alternative d(s): 53,63,549 WARNING @ Sat, 15 Sep 2018 11:13:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 11:13:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:13:34: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:13:34: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 15 Sep 2018 11:13:34: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 11:13:34: #2 You may need to consider one of the other alternative d(s): 53,63,549 WARNING @ Sat, 15 Sep 2018 11:13:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 11:13:34: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:13:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:13:35: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:13:35: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:13:35: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:13:36: #4 Write output xls file... SRX876292.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:13:36: #4 Write peak in narrowPeak format file... SRX876292.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:13:36: #4 Write summits bed file... SRX876292.20_summits.bed INFO @ Sat, 15 Sep 2018 11:13:36: Done! INFO @ Sat, 15 Sep 2018 11:13:36: #4 Write output xls file... SRX876292.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:13:36: #4 Write peak in narrowPeak format file... SRX876292.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:13:36: #4 Write output xls file... SRX876292.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:13:36: #4 Write summits bed file... SRX876292.10_summits.bed INFO @ Sat, 15 Sep 2018 11:13:36: Done! INFO @ Sat, 15 Sep 2018 11:13:36: #4 Write peak in narrowPeak format file... SRX876292.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:13:36: #4 Write summits bed file... SRX876292.05_summits.bed INFO @ Sat, 15 Sep 2018 11:13:36: Done! pass1 - making usageList (16 chroms): 0 millis pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (197 records, 4 fields): 3 millis pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (527 records, 4 fields): 3 millis pass2 - checking and writing primary data (57 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。