Job ID = 11192926 sra ファイルのダウンロード中... Completed: 359437K bytes transferred in 11 seconds (261018K 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 9842582 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3242041/SRR6129621.sra Written 9842582 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3242041/SRR6129621.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: 00:02:22 9842582 reads; of these: 9842582 (100.00%) were paired; of these: 9355962 (95.06%) aligned concordantly 0 times 370279 (3.76%) aligned concordantly exactly 1 time 116341 (1.18%) aligned concordantly >1 times ---- 9355962 pairs aligned concordantly 0 times; of these: 227290 (2.43%) aligned discordantly 1 time ---- 9128672 pairs aligned 0 times concordantly or discordantly; of these: 18257344 mates make up the pairs; of these: 16688895 (91.41%) aligned 0 times 1252467 (6.86%) aligned exactly 1 time 315982 (1.73%) aligned >1 times 15.22% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 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] 249342 / 707943 = 0.3522 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 10:35:01: # Command line: callpeak -t SRX3242041.bam -f BAM -g 12100000 -n SRX3242041.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3242041.20 # format = BAM # ChIP-seq file = ['SRX3242041.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 10:35:01: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:35:01: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:35:01: # Command line: callpeak -t SRX3242041.bam -f BAM -g 12100000 -n SRX3242041.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3242041.05 # format = BAM # ChIP-seq file = ['SRX3242041.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 10:35:01: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:35:01: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:35:01: # Command line: callpeak -t SRX3242041.bam -f BAM -g 12100000 -n SRX3242041.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3242041.10 # format = BAM # ChIP-seq file = ['SRX3242041.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 10:35:01: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:35:01: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:35:06: 1000000 INFO @ Sat, 15 Sep 2018 10:35:06: 1000000 INFO @ Sat, 15 Sep 2018 10:35:06: 1000000 INFO @ Sat, 15 Sep 2018 10:35:12: 2000000 INFO @ Sat, 15 Sep 2018 10:35:12: 2000000 INFO @ Sat, 15 Sep 2018 10:35:12: 2000000 INFO @ Sat, 15 Sep 2018 10:35:14: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:35:14: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:35:14: #1 total tags in treatment: 355431 INFO @ Sat, 15 Sep 2018 10:35:14: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:35:14: #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 10:35:14: #1 tags after filtering in treatment: 309816 INFO @ Sat, 15 Sep 2018 10:35:14: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Sep 2018 10:35:14: #1 finished! INFO @ Sat, 15 Sep 2018 10:35:14: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:35:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:35:14: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:35:14: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:35:14: #1 total tags in treatment: 355431 INFO @ Sat, 15 Sep 2018 10:35:14: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:35:14: #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 10:35:14: #1 tags after filtering in treatment: 309816 INFO @ Sat, 15 Sep 2018 10:35:14: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Sep 2018 10:35:14: #1 finished! INFO @ Sat, 15 Sep 2018 10:35:14: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:35:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:35:14: #2 number of paired peaks: 134 WARNING @ Sat, 15 Sep 2018 10:35:14: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Sat, 15 Sep 2018 10:35:14: start model_add_line... INFO @ Sat, 15 Sep 2018 10:35:14: start X-correlation... INFO @ Sat, 15 Sep 2018 10:35:14: end of X-cor INFO @ Sat, 15 Sep 2018 10:35:14: #2 finished! INFO @ Sat, 15 Sep 2018 10:35:14: #2 predicted fragment length is 158 bps INFO @ Sat, 15 Sep 2018 10:35:14: #2 alternative fragment length(s) may be 158,185,556 bps INFO @ Sat, 15 Sep 2018 10:35:14: #2.2 Generate R script for model : SRX3242041.20_model.r INFO @ Sat, 15 Sep 2018 10:35:14: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:35:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:35:14: #2 number of paired peaks: 134 WARNING @ Sat, 15 Sep 2018 10:35:14: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Sat, 15 Sep 2018 10:35:14: start model_add_line... INFO @ Sat, 15 Sep 2018 10:35:14: start X-correlation... INFO @ Sat, 15 Sep 2018 10:35:14: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 10:35:14: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 10:35:14: #1 total tags in treatment: 355431 INFO @ Sat, 15 Sep 2018 10:35:14: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:35:14: #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 10:35:14: end of X-cor INFO @ Sat, 15 Sep 2018 10:35:14: #2 finished! INFO @ Sat, 15 Sep 2018 10:35:14: #2 predicted fragment length is 158 bps INFO @ Sat, 15 Sep 2018 10:35:14: #2 alternative fragment length(s) may be 158,185,556 bps INFO @ Sat, 15 Sep 2018 10:35:14: #2.2 Generate R script for model : SRX3242041.10_model.r INFO @ Sat, 15 Sep 2018 10:35:14: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:35:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:35:14: #1 tags after filtering in treatment: 309816 INFO @ Sat, 15 Sep 2018 10:35:14: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Sep 2018 10:35:14: #1 finished! INFO @ Sat, 15 Sep 2018 10:35:14: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:35:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:35:14: #2 number of paired peaks: 134 WARNING @ Sat, 15 Sep 2018 10:35:14: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Sat, 15 Sep 2018 10:35:14: start model_add_line... INFO @ Sat, 15 Sep 2018 10:35:14: start X-correlation... INFO @ Sat, 15 Sep 2018 10:35:14: end of X-cor INFO @ Sat, 15 Sep 2018 10:35:14: #2 finished! INFO @ Sat, 15 Sep 2018 10:35:14: #2 predicted fragment length is 158 bps INFO @ Sat, 15 Sep 2018 10:35:14: #2 alternative fragment length(s) may be 158,185,556 bps INFO @ Sat, 15 Sep 2018 10:35:14: #2.2 Generate R script for model : SRX3242041.05_model.r INFO @ Sat, 15 Sep 2018 10:35:14: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:35:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:35:15: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:35:15: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:35:16: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:35:16: #4 Write output xls file... SRX3242041.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:35:16: #4 Write peak in narrowPeak format file... SRX3242041.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:35:16: #4 Write summits bed file... SRX3242041.20_summits.bed INFO @ Sat, 15 Sep 2018 10:35:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (40 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:35:16: #4 Write output xls file... SRX3242041.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:35:16: #4 Write peak in narrowPeak format file... SRX3242041.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:35:16: #4 Write summits bed file... SRX3242041.10_summits.bed INFO @ Sat, 15 Sep 2018 10:35:16: Done! INFO @ Sat, 15 Sep 2018 10:35:16: #4 Write output xls file... SRX3242041.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:35:16: #4 Write peak in narrowPeak format file... SRX3242041.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:35:16: #4 Write summits bed file... SRX3242041.05_summits.bed INFO @ Sat, 15 Sep 2018 10:35:16: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (63 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (115 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。