Job ID = 11193133 sra ファイルのダウンロード中... Completed: 280380K bytes transferred in 9 seconds (236078K 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 7963876 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337725/SRR7467878.sra Written 7963876 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337725/SRR7467878.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: 00:02:48 7963876 reads; of these: 7963876 (100.00%) were paired; of these: 7555195 (94.87%) aligned concordantly 0 times 347585 (4.36%) aligned concordantly exactly 1 time 61096 (0.77%) aligned concordantly >1 times ---- 7555195 pairs aligned concordantly 0 times; of these: 466230 (6.17%) aligned discordantly 1 time ---- 7088965 pairs aligned 0 times concordantly or discordantly; of these: 14177930 mates make up the pairs; of these: 11614713 (81.92%) aligned 0 times 2218830 (15.65%) aligned exactly 1 time 344387 (2.43%) aligned >1 times 27.08% overall alignment rate Time searching: 00:02:48 Overall time: 00:02:48 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] 606745 / 871624 = 0.6961 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 11:03:48: # Command line: callpeak -t SRX4337725.bam -f BAM -g 12100000 -n SRX4337725.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4337725.20 # format = BAM # ChIP-seq file = ['SRX4337725.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 11:03:48: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:03:48: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:03:48: # Command line: callpeak -t SRX4337725.bam -f BAM -g 12100000 -n SRX4337725.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4337725.05 # format = BAM # ChIP-seq file = ['SRX4337725.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 11:03:48: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:03:48: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:03:48: # Command line: callpeak -t SRX4337725.bam -f BAM -g 12100000 -n SRX4337725.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4337725.10 # format = BAM # ChIP-seq file = ['SRX4337725.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 11:03:48: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:03:48: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:03:53: 1000000 INFO @ Sat, 15 Sep 2018 11:03:54: 1000000 INFO @ Sat, 15 Sep 2018 11:03:54: 1000000 INFO @ Sat, 15 Sep 2018 11:03:59: 2000000 INFO @ Sat, 15 Sep 2018 11:04:01: 2000000 INFO @ Sat, 15 Sep 2018 11:04:01: 2000000 INFO @ Sat, 15 Sep 2018 11:04:06: 3000000 INFO @ Sat, 15 Sep 2018 11:04:07: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 11:04:07: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 11:04:07: #1 total tags in treatment: 176635 INFO @ Sat, 15 Sep 2018 11:04:07: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:04:07: #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 11:04:07: #1 tags after filtering in treatment: 162925 INFO @ Sat, 15 Sep 2018 11:04:07: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Sep 2018 11:04:07: #1 finished! INFO @ Sat, 15 Sep 2018 11:04:07: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:04:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:04:07: #2 number of paired peaks: 132 WARNING @ Sat, 15 Sep 2018 11:04:07: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Sat, 15 Sep 2018 11:04:07: start model_add_line... INFO @ Sat, 15 Sep 2018 11:04:07: start X-correlation... INFO @ Sat, 15 Sep 2018 11:04:07: end of X-cor INFO @ Sat, 15 Sep 2018 11:04:07: #2 finished! INFO @ Sat, 15 Sep 2018 11:04:07: #2 predicted fragment length is 202 bps INFO @ Sat, 15 Sep 2018 11:04:07: #2 alternative fragment length(s) may be 4,56,124,146,202,242,282,305,376,407,490,520,592 bps INFO @ Sat, 15 Sep 2018 11:04:07: #2.2 Generate R script for model : SRX4337725.20_model.r INFO @ Sat, 15 Sep 2018 11:04:07: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:04:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:04:07: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:04:07: 3000000 INFO @ Sat, 15 Sep 2018 11:04:07: 3000000 INFO @ Sat, 15 Sep 2018 11:04:08: #4 Write output xls file... SRX4337725.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:04:08: #4 Write peak in narrowPeak format file... SRX4337725.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:04:08: #4 Write summits bed file... SRX4337725.20_summits.bed INFO @ Sat, 15 Sep 2018 11:04:08: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:04:08: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 11:04:08: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 11:04:08: #1 total tags in treatment: 176635 INFO @ Sat, 15 Sep 2018 11:04:08: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:04:08: #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 11:04:08: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 11:04:08: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 11:04:08: #1 total tags in treatment: 176635 INFO @ Sat, 15 Sep 2018 11:04:08: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:04:08: #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 11:04:08: #1 tags after filtering in treatment: 162925 INFO @ Sat, 15 Sep 2018 11:04:08: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Sep 2018 11:04:08: #1 finished! INFO @ Sat, 15 Sep 2018 11:04:08: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:04:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:04:08: #1 tags after filtering in treatment: 162925 INFO @ Sat, 15 Sep 2018 11:04:08: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Sep 2018 11:04:08: #1 finished! INFO @ Sat, 15 Sep 2018 11:04:08: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:04:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:04:08: #2 number of paired peaks: 132 WARNING @ Sat, 15 Sep 2018 11:04:08: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Sat, 15 Sep 2018 11:04:08: start model_add_line... INFO @ Sat, 15 Sep 2018 11:04:08: start X-correlation... INFO @ Sat, 15 Sep 2018 11:04:08: #2 number of paired peaks: 132 WARNING @ Sat, 15 Sep 2018 11:04:08: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Sat, 15 Sep 2018 11:04:08: start model_add_line... INFO @ Sat, 15 Sep 2018 11:04:08: end of X-cor INFO @ Sat, 15 Sep 2018 11:04:08: #2 finished! INFO @ Sat, 15 Sep 2018 11:04:08: #2 predicted fragment length is 202 bps INFO @ Sat, 15 Sep 2018 11:04:08: start X-correlation... INFO @ Sat, 15 Sep 2018 11:04:08: #2 alternative fragment length(s) may be 4,56,124,146,202,242,282,305,376,407,490,520,592 bps INFO @ Sat, 15 Sep 2018 11:04:08: #2.2 Generate R script for model : SRX4337725.05_model.r INFO @ Sat, 15 Sep 2018 11:04:08: end of X-cor INFO @ Sat, 15 Sep 2018 11:04:08: #2 finished! INFO @ Sat, 15 Sep 2018 11:04:08: #2 predicted fragment length is 202 bps INFO @ Sat, 15 Sep 2018 11:04:08: #2 alternative fragment length(s) may be 4,56,124,146,202,242,282,305,376,407,490,520,592 bps INFO @ Sat, 15 Sep 2018 11:04:08: #2.2 Generate R script for model : SRX4337725.10_model.r INFO @ Sat, 15 Sep 2018 11:04:08: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:04:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:04:08: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:04:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:04:09: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:04:09: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:04:09: #4 Write output xls file... SRX4337725.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:04:09: #4 Write peak in narrowPeak format file... SRX4337725.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:04:09: #4 Write summits bed file... SRX4337725.10_summits.bed INFO @ Sat, 15 Sep 2018 11:04:09: Done! INFO @ Sat, 15 Sep 2018 11:04:09: #4 Write output xls file... SRX4337725.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:04:09: #4 Write peak in narrowPeak format file... SRX4337725.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:04:09: #4 Write summits bed file... SRX4337725.05_summits.bed INFO @ Sat, 15 Sep 2018 11:04:09: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (5 records, 4 fields): 1 millis CompletedMACS2peakCalling pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (24 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。