Job ID = 10254409 sra ファイルのダウンロード中... Completed: 1132467K bytes transferred in 13 seconds (691667K 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... Written 24684449 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2658703/SRR5363219.sra Written 24684449 spots total 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: 00:15:36 24684449 reads; of these: 24684449 (100.00%) were paired; of these: 6223078 (25.21%) aligned concordantly 0 times 14683664 (59.49%) aligned concordantly exactly 1 time 3777707 (15.30%) aligned concordantly >1 times ---- 6223078 pairs aligned concordantly 0 times; of these: 418257 (6.72%) aligned discordantly 1 time ---- 5804821 pairs aligned 0 times concordantly or discordantly; of these: 11609642 mates make up the pairs; of these: 11040959 (95.10%) aligned 0 times 245759 (2.12%) aligned exactly 1 time 322924 (2.78%) aligned >1 times 77.64% overall alignment rate Time searching: 00:15:36 Overall time: 00:15:36 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_sort_core] merging from 16 files... [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] 16127124 / 18858081 = 0.8552 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 @ Wed, 06 Dec 2017 18:11:10: # Command line: callpeak -t SRX2658703.bam -f BAM -g 12100000 -n SRX2658703.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2658703.10 # format = BAM # ChIP-seq file = ['SRX2658703.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 @ Wed, 06 Dec 2017 18:11:10: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:11:10: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:11:10: # Command line: callpeak -t SRX2658703.bam -f BAM -g 12100000 -n SRX2658703.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2658703.20 # format = BAM # ChIP-seq file = ['SRX2658703.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 @ Wed, 06 Dec 2017 18:11:10: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:11:10: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:11:10: # Command line: callpeak -t SRX2658703.bam -f BAM -g 12100000 -n SRX2658703.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2658703.05 # format = BAM # ChIP-seq file = ['SRX2658703.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 @ Wed, 06 Dec 2017 18:11:10: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:11:10: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:11:16: 1000000 INFO @ Wed, 06 Dec 2017 18:11:16: 1000000 INFO @ Wed, 06 Dec 2017 18:11:16: 1000000 INFO @ Wed, 06 Dec 2017 18:11:21: 2000000 INFO @ Wed, 06 Dec 2017 18:11:22: 2000000 INFO @ Wed, 06 Dec 2017 18:11:22: 2000000 INFO @ Wed, 06 Dec 2017 18:11:27: 3000000 INFO @ Wed, 06 Dec 2017 18:11:28: 3000000 INFO @ Wed, 06 Dec 2017 18:11:28: 3000000 INFO @ Wed, 06 Dec 2017 18:11:33: 4000000 INFO @ Wed, 06 Dec 2017 18:11:33: 4000000 INFO @ Wed, 06 Dec 2017 18:11:33: 4000000 INFO @ Wed, 06 Dec 2017 18:11:38: 5000000 INFO @ Wed, 06 Dec 2017 18:11:39: 5000000 INFO @ Wed, 06 Dec 2017 18:11:39: 5000000 INFO @ Wed, 06 Dec 2017 18:11:44: 6000000 INFO @ Wed, 06 Dec 2017 18:11:44: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 18:11:44: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 18:11:44: #1 total tags in treatment: 2630085 INFO @ Wed, 06 Dec 2017 18:11:44: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:11:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:11:44: #1 tags after filtering in treatment: 1725222 INFO @ Wed, 06 Dec 2017 18:11:44: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 06 Dec 2017 18:11:44: #1 finished! INFO @ Wed, 06 Dec 2017 18:11:44: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:11:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:11:44: #2 number of paired peaks: 183 WARNING @ Wed, 06 Dec 2017 18:11:44: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Wed, 06 Dec 2017 18:11:44: start model_add_line... INFO @ Wed, 06 Dec 2017 18:11:44: start X-correlation... INFO @ Wed, 06 Dec 2017 18:11:44: end of X-cor INFO @ Wed, 06 Dec 2017 18:11:44: #2 finished! INFO @ Wed, 06 Dec 2017 18:11:44: #2 predicted fragment length is 207 bps INFO @ Wed, 06 Dec 2017 18:11:44: #2 alternative fragment length(s) may be 4,207 bps INFO @ Wed, 06 Dec 2017 18:11:44: #2.2 Generate R script for model : SRX2658703.10_model.r INFO @ Wed, 06 Dec 2017 18:11:44: 6000000 INFO @ Wed, 06 Dec 2017 18:11:44: #3 Call peaks... INFO @ Wed, 06 Dec 2017 18:11:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 06 Dec 2017 18:11:45: 6000000 INFO @ Wed, 06 Dec 2017 18:11:45: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 18:11:45: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 18:11:45: #1 total tags in treatment: 2630085 INFO @ Wed, 06 Dec 2017 18:11:45: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:11:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:11:45: #1 tags after filtering in treatment: 1725222 INFO @ Wed, 06 Dec 2017 18:11:45: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 06 Dec 2017 18:11:45: #1 finished! INFO @ Wed, 06 Dec 2017 18:11:45: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:11:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:11:45: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 18:11:45: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 18:11:45: #1 total tags in treatment: 2630085 INFO @ Wed, 06 Dec 2017 18:11:45: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:11:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:11:45: #1 tags after filtering in treatment: 1725222 INFO @ Wed, 06 Dec 2017 18:11:45: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 06 Dec 2017 18:11:45: #1 finished! INFO @ Wed, 06 Dec 2017 18:11:45: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:11:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:11:45: #2 number of paired peaks: 183 WARNING @ Wed, 06 Dec 2017 18:11:45: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Wed, 06 Dec 2017 18:11:45: start model_add_line... INFO @ Wed, 06 Dec 2017 18:11:45: start X-correlation... INFO @ Wed, 06 Dec 2017 18:11:45: end of X-cor INFO @ Wed, 06 Dec 2017 18:11:45: #2 finished! INFO @ Wed, 06 Dec 2017 18:11:45: #2 predicted fragment length is 207 bps INFO @ Wed, 06 Dec 2017 18:11:45: #2 alternative fragment length(s) may be 4,207 bps INFO @ Wed, 06 Dec 2017 18:11:45: #2.2 Generate R script for model : SRX2658703.05_model.r INFO @ Wed, 06 Dec 2017 18:11:45: #3 Call peaks... INFO @ Wed, 06 Dec 2017 18:11:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 06 Dec 2017 18:11:45: #2 number of paired peaks: 183 WARNING @ Wed, 06 Dec 2017 18:11:45: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Wed, 06 Dec 2017 18:11:45: start model_add_line... INFO @ Wed, 06 Dec 2017 18:11:45: start X-correlation... INFO @ Wed, 06 Dec 2017 18:11:45: end of X-cor INFO @ Wed, 06 Dec 2017 18:11:45: #2 finished! INFO @ Wed, 06 Dec 2017 18:11:45: #2 predicted fragment length is 207 bps INFO @ Wed, 06 Dec 2017 18:11:45: #2 alternative fragment length(s) may be 4,207 bps INFO @ Wed, 06 Dec 2017 18:11:45: #2.2 Generate R script for model : SRX2658703.20_model.r INFO @ Wed, 06 Dec 2017 18:11:45: #3 Call peaks... INFO @ Wed, 06 Dec 2017 18:11:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 06 Dec 2017 18:11:52: #3 Call peaks for each chromosome... INFO @ Wed, 06 Dec 2017 18:11:52: #3 Call peaks for each chromosome... INFO @ Wed, 06 Dec 2017 18:11:52: #3 Call peaks for each chromosome... INFO @ Wed, 06 Dec 2017 18:11:54: #4 Write output xls file... SRX2658703.10_peaks.xls INFO @ Wed, 06 Dec 2017 18:11:54: #4 Write peak in narrowPeak format file... SRX2658703.10_peaks.narrowPeak INFO @ Wed, 06 Dec 2017 18:11:54: #4 Write summits bed file... SRX2658703.10_summits.bed INFO @ Wed, 06 Dec 2017 18:11:54: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (823 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 06 Dec 2017 18:11:54: #4 Write output xls file... SRX2658703.05_peaks.xls INFO @ Wed, 06 Dec 2017 18:11:54: #4 Write peak in narrowPeak format file... SRX2658703.05_peaks.narrowPeak INFO @ Wed, 06 Dec 2017 18:11:54: #4 Write summits bed file... SRX2658703.05_summits.bed INFO @ Wed, 06 Dec 2017 18:11:54: Done! INFO @ Wed, 06 Dec 2017 18:11:54: #4 Write output xls file... SRX2658703.20_peaks.xls INFO @ Wed, 06 Dec 2017 18:11:54: #4 Write peak in narrowPeak format file... SRX2658703.20_peaks.narrowPeak INFO @ Wed, 06 Dec 2017 18:11:54: #4 Write summits bed file... SRX2658703.20_summits.bed pass1 - making usageList (17 chroms): 0 millis INFO @ Wed, 06 Dec 2017 18:11:54: Done! pass2 - checking and writing primary data (1209 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (485 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。