Job ID = 11192916 sra ファイルのダウンロード中... Completed: 340629K bytes transferred in 6 seconds (422562K 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 8893976 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3242031/SRR6129631.sra Written 8893976 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3242031/SRR6129631.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: 00:01:52 8893976 reads; of these: 8893976 (100.00%) were paired; of these: 8639500 (97.14%) aligned concordantly 0 times 213320 (2.40%) aligned concordantly exactly 1 time 41156 (0.46%) aligned concordantly >1 times ---- 8639500 pairs aligned concordantly 0 times; of these: 101686 (1.18%) aligned discordantly 1 time ---- 8537814 pairs aligned 0 times concordantly or discordantly; of these: 17075628 mates make up the pairs; of these: 16030344 (93.88%) aligned 0 times 896450 (5.25%) aligned exactly 1 time 148834 (0.87%) aligned >1 times 9.88% overall alignment rate Time searching: 00:01:53 Overall time: 00:01:53 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] 150313 / 352053 = 0.4270 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 10:27:49: # Command line: callpeak -t SRX3242031.bam -f BAM -g 12100000 -n SRX3242031.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3242031.05 # format = BAM # ChIP-seq file = ['SRX3242031.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 10:27:49: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:27:49: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:27:49: # Command line: callpeak -t SRX3242031.bam -f BAM -g 12100000 -n SRX3242031.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3242031.10 # format = BAM # ChIP-seq file = ['SRX3242031.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 10:27:49: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:27:49: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:27:49: # Command line: callpeak -t SRX3242031.bam -f BAM -g 12100000 -n SRX3242031.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3242031.20 # format = BAM # ChIP-seq file = ['SRX3242031.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 10:27:49: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:27:49: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:27:55: 1000000 INFO @ Sat, 15 Sep 2018 10:27:55: 1000000 INFO @ Sat, 15 Sep 2018 10:27:55: 1000000 INFO @ Sat, 15 Sep 2018 10:27:58: #1 tag size is determined as 45 bps INFO @ Sat, 15 Sep 2018 10:27:58: #1 tag size = 45 INFO @ Sat, 15 Sep 2018 10:27:58: #1 total tags in treatment: 171140 INFO @ Sat, 15 Sep 2018 10:27:58: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:27:58: #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 10:27:58: #1 tags after filtering in treatment: 162307 INFO @ Sat, 15 Sep 2018 10:27:58: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 15 Sep 2018 10:27:58: #1 finished! INFO @ Sat, 15 Sep 2018 10:27:58: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:27:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:27:58: #2 number of paired peaks: 102 WARNING @ Sat, 15 Sep 2018 10:27:58: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Sat, 15 Sep 2018 10:27:58: start model_add_line... INFO @ Sat, 15 Sep 2018 10:27:58: start X-correlation... INFO @ Sat, 15 Sep 2018 10:27:58: end of X-cor INFO @ Sat, 15 Sep 2018 10:27:58: #2 finished! INFO @ Sat, 15 Sep 2018 10:27:58: #2 predicted fragment length is 159 bps INFO @ Sat, 15 Sep 2018 10:27:58: #2 alternative fragment length(s) may be 4,8,108,159,182,206,237,251,280,304,320,381,395,417,470,519,545,565 bps INFO @ Sat, 15 Sep 2018 10:27:58: #2.2 Generate R script for model : SRX3242031.20_model.r INFO @ Sat, 15 Sep 2018 10:27:58: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:27:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:27:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:27:59: #1 tag size is determined as 45 bps INFO @ Sat, 15 Sep 2018 10:27:59: #1 tag size is determined as 45 bps INFO @ Sat, 15 Sep 2018 10:27:59: #1 tag size = 45 INFO @ Sat, 15 Sep 2018 10:27:59: #1 tag size = 45 INFO @ Sat, 15 Sep 2018 10:27:59: #1 total tags in treatment: 171140 INFO @ Sat, 15 Sep 2018 10:27:59: #1 total tags in treatment: 171140 INFO @ Sat, 15 Sep 2018 10:27:59: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:27:59: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:27:59: #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 10:27:59: #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 10:27:59: #1 tags after filtering in treatment: 162307 INFO @ Sat, 15 Sep 2018 10:27:59: #1 tags after filtering in treatment: 162307 INFO @ Sat, 15 Sep 2018 10:27:59: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 15 Sep 2018 10:27:59: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 15 Sep 2018 10:27:59: #1 finished! INFO @ Sat, 15 Sep 2018 10:27:59: #1 finished! INFO @ Sat, 15 Sep 2018 10:27:59: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:27:59: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:27:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:27:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:27:59: #2 number of paired peaks: 102 WARNING @ Sat, 15 Sep 2018 10:27:59: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Sat, 15 Sep 2018 10:27:59: start model_add_line... INFO @ Sat, 15 Sep 2018 10:27:59: #2 number of paired peaks: 102 WARNING @ Sat, 15 Sep 2018 10:27:59: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Sat, 15 Sep 2018 10:27:59: start model_add_line... INFO @ Sat, 15 Sep 2018 10:27:59: start X-correlation... INFO @ Sat, 15 Sep 2018 10:27:59: start X-correlation... INFO @ Sat, 15 Sep 2018 10:27:59: end of X-cor INFO @ Sat, 15 Sep 2018 10:27:59: end of X-cor INFO @ Sat, 15 Sep 2018 10:27:59: #2 finished! INFO @ Sat, 15 Sep 2018 10:27:59: #2 finished! INFO @ Sat, 15 Sep 2018 10:27:59: #2 predicted fragment length is 159 bps INFO @ Sat, 15 Sep 2018 10:27:59: #2 predicted fragment length is 159 bps INFO @ Sat, 15 Sep 2018 10:27:59: #2 alternative fragment length(s) may be 4,8,108,159,182,206,237,251,280,304,320,381,395,417,470,519,545,565 bps INFO @ Sat, 15 Sep 2018 10:27:59: #2 alternative fragment length(s) may be 4,8,108,159,182,206,237,251,280,304,320,381,395,417,470,519,545,565 bps INFO @ Sat, 15 Sep 2018 10:27:59: #2.2 Generate R script for model : SRX3242031.05_model.r INFO @ Sat, 15 Sep 2018 10:27:59: #2.2 Generate R script for model : SRX3242031.10_model.r INFO @ Sat, 15 Sep 2018 10:27:59: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:27:59: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:27:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:27:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:27:59: #4 Write output xls file... SRX3242031.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:27:59: #4 Write peak in narrowPeak format file... SRX3242031.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:27:59: #4 Write summits bed file... SRX3242031.20_summits.bed INFO @ Sat, 15 Sep 2018 10:27:59: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (4 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:27:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:27:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:27:59: #4 Write output xls file... SRX3242031.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:27:59: #4 Write peak in narrowPeak format file... SRX3242031.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:27:59: #4 Write summits bed file... SRX3242031.05_summits.bed INFO @ Sat, 15 Sep 2018 10:27:59: Done! INFO @ Sat, 15 Sep 2018 10:27:59: #4 Write output xls file... SRX3242031.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:27:59: #4 Write peak in narrowPeak format file... SRX3242031.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:27:59: #4 Write summits bed file... SRX3242031.10_summits.bed INFO @ Sat, 15 Sep 2018 10:27:59: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (29 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。