Job ID = 11193223 sra ファイルのダウンロード中... Completed: 280459K bytes transferred in 6 seconds (371019K 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 6495548 spots for /home/okishinya/chipatlas/results/sacCer3/SRX977509/SRR1951355.sra Written 6495548 spots for /home/okishinya/chipatlas/results/sacCer3/SRX977509/SRR1951355.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: 00:03:13 6495548 reads; of these: 6495548 (100.00%) were paired; of these: 2485267 (38.26%) aligned concordantly 0 times 2207899 (33.99%) aligned concordantly exactly 1 time 1802382 (27.75%) aligned concordantly >1 times ---- 2485267 pairs aligned concordantly 0 times; of these: 95540 (3.84%) aligned discordantly 1 time ---- 2389727 pairs aligned 0 times concordantly or discordantly; of these: 4779454 mates make up the pairs; of these: 4471537 (93.56%) aligned 0 times 112938 (2.36%) aligned exactly 1 time 194979 (4.08%) aligned >1 times 65.58% overall alignment rate Time searching: 00:03:13 Overall time: 00:03:13 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] 3249134 / 4073805 = 0.7976 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 11:17:22: # Command line: callpeak -t SRX977509.bam -f BAM -g 12100000 -n SRX977509.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX977509.05 # format = BAM # ChIP-seq file = ['SRX977509.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 11:17:22: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:17:22: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:17:22: # Command line: callpeak -t SRX977509.bam -f BAM -g 12100000 -n SRX977509.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX977509.20 # format = BAM # ChIP-seq file = ['SRX977509.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 11:17:22: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:17:22: # Command line: callpeak -t SRX977509.bam -f BAM -g 12100000 -n SRX977509.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX977509.10 # format = BAM # ChIP-seq file = ['SRX977509.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 11:17:22: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:17:22: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:17:22: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:17:27: 1000000 INFO @ Sat, 15 Sep 2018 11:17:29: 1000000 INFO @ Sat, 15 Sep 2018 11:17:29: 1000000 INFO @ Sat, 15 Sep 2018 11:17:33: 2000000 INFO @ Sat, 15 Sep 2018 11:17:33: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:17:33: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:17:33: #1 total tags in treatment: 833771 INFO @ Sat, 15 Sep 2018 11:17:33: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:17:33: #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 11:17:33: #1 tags after filtering in treatment: 358586 INFO @ Sat, 15 Sep 2018 11:17:33: #1 Redundant rate of treatment: 0.57 INFO @ Sat, 15 Sep 2018 11:17:33: #1 finished! INFO @ Sat, 15 Sep 2018 11:17:33: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:17:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:17:33: #2 number of paired peaks: 269 WARNING @ Sat, 15 Sep 2018 11:17:33: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Sat, 15 Sep 2018 11:17:33: start model_add_line... INFO @ Sat, 15 Sep 2018 11:17:33: start X-correlation... INFO @ Sat, 15 Sep 2018 11:17:33: end of X-cor INFO @ Sat, 15 Sep 2018 11:17:33: #2 finished! INFO @ Sat, 15 Sep 2018 11:17:33: #2 predicted fragment length is 49 bps INFO @ Sat, 15 Sep 2018 11:17:33: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 15 Sep 2018 11:17:33: #2.2 Generate R script for model : SRX977509.05_model.r WARNING @ Sat, 15 Sep 2018 11:17:33: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 11:17:33: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 15 Sep 2018 11:17:33: #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 11:17:33: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:17:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:17:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:17:35: #4 Write output xls file... SRX977509.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:17:35: #4 Write peak in narrowPeak format file... SRX977509.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:17:35: #4 Write summits bed file... SRX977509.05_summits.bed INFO @ Sat, 15 Sep 2018 11:17:35: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (228 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:17:36: 2000000 INFO @ Sat, 15 Sep 2018 11:17:36: 2000000 INFO @ Sat, 15 Sep 2018 11:17:36: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:17:36: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:17:36: #1 total tags in treatment: 833771 INFO @ Sat, 15 Sep 2018 11:17:36: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:17:36: #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 11:17:36: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:17:36: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:17:36: #1 total tags in treatment: 833771 INFO @ Sat, 15 Sep 2018 11:17:36: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:17:36: #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 11:17:36: #1 tags after filtering in treatment: 358586 INFO @ Sat, 15 Sep 2018 11:17:36: #1 Redundant rate of treatment: 0.57 INFO @ Sat, 15 Sep 2018 11:17:36: #1 finished! INFO @ Sat, 15 Sep 2018 11:17:36: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:17:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:17:36: #1 tags after filtering in treatment: 358586 INFO @ Sat, 15 Sep 2018 11:17:36: #1 Redundant rate of treatment: 0.57 INFO @ Sat, 15 Sep 2018 11:17:36: #1 finished! INFO @ Sat, 15 Sep 2018 11:17:36: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:17:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:17:36: #2 number of paired peaks: 269 WARNING @ Sat, 15 Sep 2018 11:17:36: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Sat, 15 Sep 2018 11:17:36: start model_add_line... INFO @ Sat, 15 Sep 2018 11:17:36: #2 number of paired peaks: 269 WARNING @ Sat, 15 Sep 2018 11:17:36: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Sat, 15 Sep 2018 11:17:36: start model_add_line... INFO @ Sat, 15 Sep 2018 11:17:36: start X-correlation... INFO @ Sat, 15 Sep 2018 11:17:36: start X-correlation... INFO @ Sat, 15 Sep 2018 11:17:36: end of X-cor INFO @ Sat, 15 Sep 2018 11:17:36: #2 finished! INFO @ Sat, 15 Sep 2018 11:17:36: #2 predicted fragment length is 49 bps INFO @ Sat, 15 Sep 2018 11:17:36: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 15 Sep 2018 11:17:36: #2.2 Generate R script for model : SRX977509.20_model.r INFO @ Sat, 15 Sep 2018 11:17:36: end of X-cor INFO @ Sat, 15 Sep 2018 11:17:36: #2 finished! INFO @ Sat, 15 Sep 2018 11:17:36: #2 predicted fragment length is 49 bps INFO @ Sat, 15 Sep 2018 11:17:36: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 15 Sep 2018 11:17:36: #2.2 Generate R script for model : SRX977509.10_model.r WARNING @ Sat, 15 Sep 2018 11:17:36: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 11:17:36: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 15 Sep 2018 11:17:36: #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 11:17:36: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:17:36: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 15 Sep 2018 11:17:36: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 11:17:36: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 15 Sep 2018 11:17:36: #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 11:17:36: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:17:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:17:37: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:17:37: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:17:37: #4 Write output xls file... SRX977509.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:17:37: #4 Write peak in narrowPeak format file... SRX977509.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:17:37: #4 Write summits bed file... SRX977509.20_summits.bed INFO @ Sat, 15 Sep 2018 11:17:37: Done! pass1 - making usageList (15 chroms): 1 millis INFO @ Sat, 15 Sep 2018 11:17:37: #4 Write output xls file... SRX977509.10_peaks.xls pass2 - checking and writing primary data (119 records, 4 fields): 2 millis INFO @ Sat, 15 Sep 2018 11:17:37: #4 Write peak in narrowPeak format file... SRX977509.10_peaks.narrowPeak CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:17:37: #4 Write summits bed file... SRX977509.10_summits.bed INFO @ Sat, 15 Sep 2018 11:17:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (154 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。