Job ID = 11245047 sra ファイルのダウンロード中... Completed: 128857K bytes transferred in 6 seconds (157917K 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 4069493 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554759/SRR7696432.sra Written 4069493 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554759/SRR7696432.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: 00:02:07 4069493 reads; of these: 4069493 (100.00%) were paired; of these: 2320752 (57.03%) aligned concordantly 0 times 1257820 (30.91%) aligned concordantly exactly 1 time 490921 (12.06%) aligned concordantly >1 times ---- 2320752 pairs aligned concordantly 0 times; of these: 5240 (0.23%) aligned discordantly 1 time ---- 2315512 pairs aligned 0 times concordantly or discordantly; of these: 4631024 mates make up the pairs; of these: 3527323 (76.17%) aligned 0 times 806712 (17.42%) aligned exactly 1 time 296989 (6.41%) aligned >1 times 56.66% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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] 238707 / 1753608 = 0.1361 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 @ Tue, 09 Oct 2018 23:16:28: # Command line: callpeak -t SRX4554759.bam -f BAM -g 12100000 -n SRX4554759.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554759.10 # format = BAM # ChIP-seq file = ['SRX4554759.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 @ Tue, 09 Oct 2018 23:16:28: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:16:28: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:16:28: # Command line: callpeak -t SRX4554759.bam -f BAM -g 12100000 -n SRX4554759.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554759.20 # format = BAM # ChIP-seq file = ['SRX4554759.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 @ Tue, 09 Oct 2018 23:16:28: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:16:28: # Command line: callpeak -t SRX4554759.bam -f BAM -g 12100000 -n SRX4554759.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554759.05 # format = BAM # ChIP-seq file = ['SRX4554759.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 @ Tue, 09 Oct 2018 23:16:28: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:16:28: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:16:28: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:16:33: 1000000 INFO @ Tue, 09 Oct 2018 23:16:33: 1000000 INFO @ Tue, 09 Oct 2018 23:16:33: 1000000 INFO @ Tue, 09 Oct 2018 23:16:38: 2000000 INFO @ Tue, 09 Oct 2018 23:16:38: 2000000 INFO @ Tue, 09 Oct 2018 23:16:38: 2000000 INFO @ Tue, 09 Oct 2018 23:16:43: 3000000 INFO @ Tue, 09 Oct 2018 23:16:43: 3000000 INFO @ Tue, 09 Oct 2018 23:16:43: 3000000 INFO @ Tue, 09 Oct 2018 23:16:48: 4000000 INFO @ Tue, 09 Oct 2018 23:16:48: 4000000 INFO @ Tue, 09 Oct 2018 23:16:48: 4000000 INFO @ Tue, 09 Oct 2018 23:16:48: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:16:48: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:16:48: #1 total tags in treatment: 1510070 INFO @ Tue, 09 Oct 2018 23:16:48: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:16:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:16:48: #1 tags after filtering in treatment: 918532 INFO @ Tue, 09 Oct 2018 23:16:48: #1 Redundant rate of treatment: 0.39 INFO @ Tue, 09 Oct 2018 23:16:48: #1 finished! INFO @ Tue, 09 Oct 2018 23:16:48: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:16:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:16:48: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:16:48: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:16:48: #1 total tags in treatment: 1510070 INFO @ Tue, 09 Oct 2018 23:16:48: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:16:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:16:48: #1 tags after filtering in treatment: 918532 INFO @ Tue, 09 Oct 2018 23:16:48: #1 Redundant rate of treatment: 0.39 INFO @ Tue, 09 Oct 2018 23:16:48: #1 finished! INFO @ Tue, 09 Oct 2018 23:16:48: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:16:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:16:48: #2 number of paired peaks: 369 WARNING @ Tue, 09 Oct 2018 23:16:48: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Tue, 09 Oct 2018 23:16:48: start model_add_line... INFO @ Tue, 09 Oct 2018 23:16:49: start X-correlation... INFO @ Tue, 09 Oct 2018 23:16:49: end of X-cor INFO @ Tue, 09 Oct 2018 23:16:49: #2 finished! INFO @ Tue, 09 Oct 2018 23:16:49: #2 predicted fragment length is 210 bps INFO @ Tue, 09 Oct 2018 23:16:49: #2 alternative fragment length(s) may be 1,188,210,217,241,255,285,522 bps INFO @ Tue, 09 Oct 2018 23:16:49: #2.2 Generate R script for model : SRX4554759.05_model.r INFO @ Tue, 09 Oct 2018 23:16:49: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:16:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:16:49: #2 number of paired peaks: 369 WARNING @ Tue, 09 Oct 2018 23:16:49: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Tue, 09 Oct 2018 23:16:49: start model_add_line... INFO @ Tue, 09 Oct 2018 23:16:49: start X-correlation... INFO @ Tue, 09 Oct 2018 23:16:49: end of X-cor INFO @ Tue, 09 Oct 2018 23:16:49: #2 finished! INFO @ Tue, 09 Oct 2018 23:16:49: #2 predicted fragment length is 210 bps INFO @ Tue, 09 Oct 2018 23:16:49: #2 alternative fragment length(s) may be 1,188,210,217,241,255,285,522 bps INFO @ Tue, 09 Oct 2018 23:16:49: #2.2 Generate R script for model : SRX4554759.10_model.r INFO @ Tue, 09 Oct 2018 23:16:49: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:16:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:16:49: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:16:49: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:16:49: #1 total tags in treatment: 1510070 INFO @ Tue, 09 Oct 2018 23:16:49: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:16:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:16:49: #1 tags after filtering in treatment: 918532 INFO @ Tue, 09 Oct 2018 23:16:49: #1 Redundant rate of treatment: 0.39 INFO @ Tue, 09 Oct 2018 23:16:49: #1 finished! INFO @ Tue, 09 Oct 2018 23:16:49: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:16:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:16:49: #2 number of paired peaks: 369 WARNING @ Tue, 09 Oct 2018 23:16:49: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Tue, 09 Oct 2018 23:16:49: start model_add_line... INFO @ Tue, 09 Oct 2018 23:16:49: start X-correlation... INFO @ Tue, 09 Oct 2018 23:16:49: end of X-cor INFO @ Tue, 09 Oct 2018 23:16:49: #2 finished! INFO @ Tue, 09 Oct 2018 23:16:49: #2 predicted fragment length is 210 bps INFO @ Tue, 09 Oct 2018 23:16:49: #2 alternative fragment length(s) may be 1,188,210,217,241,255,285,522 bps INFO @ Tue, 09 Oct 2018 23:16:49: #2.2 Generate R script for model : SRX4554759.20_model.r INFO @ Tue, 09 Oct 2018 23:16:49: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:16:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:16:53: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:16:53: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:16:54: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:16:54: #4 Write output xls file... SRX4554759.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:16:54: #4 Write peak in narrowPeak format file... SRX4554759.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:16:54: #4 Write summits bed file... SRX4554759.05_summits.bed INFO @ Tue, 09 Oct 2018 23:16:54: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (235 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:16:54: #4 Write output xls file... SRX4554759.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:16:54: #4 Write peak in narrowPeak format file... SRX4554759.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:16:54: #4 Write summits bed file... SRX4554759.10_summits.bed INFO @ Tue, 09 Oct 2018 23:16:54: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (69 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:16:55: #4 Write output xls file... SRX4554759.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:16:55: #4 Write peak in narrowPeak format file... SRX4554759.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:16:55: #4 Write summits bed file... SRX4554759.20_summits.bed INFO @ Tue, 09 Oct 2018 23:16:55: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (17 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。