Job ID = 10609011 sra ファイルのダウンロード中... Completed: 272941K bytes transferred in 6 seconds (343043K 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 2815526 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3063098/SRR5901528.sra Written 2815526 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: 00:03:29 2815526 reads; of these: 2815526 (100.00%) were paired; of these: 146895 (5.22%) aligned concordantly 0 times 2405360 (85.43%) aligned concordantly exactly 1 time 263271 (9.35%) aligned concordantly >1 times ---- 146895 pairs aligned concordantly 0 times; of these: 16673 (11.35%) aligned discordantly 1 time ---- 130222 pairs aligned 0 times concordantly or discordantly; of these: 260444 mates make up the pairs; of these: 221824 (85.17%) aligned 0 times 29987 (11.51%) aligned exactly 1 time 8633 (3.31%) aligned >1 times 96.06% overall alignment rate Time searching: 00:03:29 Overall time: 00:03:29 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] 175430 / 2666540 = 0.0658 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 @ Thu, 03 May 2018 23:10:21: # Command line: callpeak -t SRX3063098.bam -f BAM -g 12100000 -n SRX3063098.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3063098.05 # format = BAM # ChIP-seq file = ['SRX3063098.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 @ Thu, 03 May 2018 23:10:21: #1 read tag files... INFO @ Thu, 03 May 2018 23:10:21: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:10:21: # Command line: callpeak -t SRX3063098.bam -f BAM -g 12100000 -n SRX3063098.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3063098.10 # format = BAM # ChIP-seq file = ['SRX3063098.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 @ Thu, 03 May 2018 23:10:21: #1 read tag files... INFO @ Thu, 03 May 2018 23:10:21: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:10:21: # Command line: callpeak -t SRX3063098.bam -f BAM -g 12100000 -n SRX3063098.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3063098.20 # format = BAM # ChIP-seq file = ['SRX3063098.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 @ Thu, 03 May 2018 23:10:21: #1 read tag files... INFO @ Thu, 03 May 2018 23:10:21: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:10:29: 1000000 INFO @ Thu, 03 May 2018 23:10:29: 1000000 INFO @ Thu, 03 May 2018 23:10:30: 1000000 INFO @ Thu, 03 May 2018 23:10:37: 2000000 INFO @ Thu, 03 May 2018 23:10:38: 2000000 INFO @ Thu, 03 May 2018 23:10:38: 2000000 INFO @ Thu, 03 May 2018 23:10:46: 3000000 INFO @ Thu, 03 May 2018 23:10:46: 3000000 INFO @ Thu, 03 May 2018 23:10:47: 3000000 INFO @ Thu, 03 May 2018 23:10:54: 4000000 INFO @ Thu, 03 May 2018 23:10:55: 4000000 INFO @ Thu, 03 May 2018 23:10:55: 4000000 INFO @ Thu, 03 May 2018 23:11:02: 5000000 INFO @ Thu, 03 May 2018 23:11:02: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:11:02: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:11:02: #1 total tags in treatment: 2493566 INFO @ Thu, 03 May 2018 23:11:02: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:11:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:11:02: #1 tags after filtering in treatment: 2199861 INFO @ Thu, 03 May 2018 23:11:02: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 03 May 2018 23:11:02: #1 finished! INFO @ Thu, 03 May 2018 23:11:02: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:11:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:11:03: #2 number of paired peaks: 130 WARNING @ Thu, 03 May 2018 23:11:03: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Thu, 03 May 2018 23:11:03: start model_add_line... INFO @ Thu, 03 May 2018 23:11:03: start X-correlation... INFO @ Thu, 03 May 2018 23:11:03: end of X-cor INFO @ Thu, 03 May 2018 23:11:03: #2 finished! INFO @ Thu, 03 May 2018 23:11:03: #2 predicted fragment length is 136 bps INFO @ Thu, 03 May 2018 23:11:03: #2 alternative fragment length(s) may be 4,136 bps INFO @ Thu, 03 May 2018 23:11:03: #2.2 Generate R script for model : SRX3063098.20_model.r WARNING @ Thu, 03 May 2018 23:11:03: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 23:11:03: #2 You may need to consider one of the other alternative d(s): 4,136 WARNING @ Thu, 03 May 2018 23:11:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 23:11:03: #3 Call peaks... INFO @ Thu, 03 May 2018 23:11:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 23:11:04: 5000000 INFO @ Thu, 03 May 2018 23:11:04: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:11:04: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:11:04: #1 total tags in treatment: 2493566 INFO @ Thu, 03 May 2018 23:11:04: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:11:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:11:04: 5000000 INFO @ Thu, 03 May 2018 23:11:04: #1 tags after filtering in treatment: 2199861 INFO @ Thu, 03 May 2018 23:11:04: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 03 May 2018 23:11:04: #1 finished! INFO @ Thu, 03 May 2018 23:11:04: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:11:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:11:04: #2 number of paired peaks: 130 WARNING @ Thu, 03 May 2018 23:11:04: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Thu, 03 May 2018 23:11:04: start model_add_line... INFO @ Thu, 03 May 2018 23:11:04: start X-correlation... INFO @ Thu, 03 May 2018 23:11:04: end of X-cor INFO @ Thu, 03 May 2018 23:11:04: #2 finished! INFO @ Thu, 03 May 2018 23:11:04: #2 predicted fragment length is 136 bps INFO @ Thu, 03 May 2018 23:11:04: #2 alternative fragment length(s) may be 4,136 bps INFO @ Thu, 03 May 2018 23:11:04: #2.2 Generate R script for model : SRX3063098.05_model.r WARNING @ Thu, 03 May 2018 23:11:04: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 23:11:04: #2 You may need to consider one of the other alternative d(s): 4,136 WARNING @ Thu, 03 May 2018 23:11:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 23:11:04: #3 Call peaks... INFO @ Thu, 03 May 2018 23:11:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 23:11:04: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:11:04: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:11:04: #1 total tags in treatment: 2493566 INFO @ Thu, 03 May 2018 23:11:04: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:11:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:11:04: #1 tags after filtering in treatment: 2199861 INFO @ Thu, 03 May 2018 23:11:04: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 03 May 2018 23:11:04: #1 finished! INFO @ Thu, 03 May 2018 23:11:04: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:11:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:11:05: #2 number of paired peaks: 130 WARNING @ Thu, 03 May 2018 23:11:05: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Thu, 03 May 2018 23:11:05: start model_add_line... INFO @ Thu, 03 May 2018 23:11:05: start X-correlation... INFO @ Thu, 03 May 2018 23:11:05: end of X-cor INFO @ Thu, 03 May 2018 23:11:05: #2 finished! INFO @ Thu, 03 May 2018 23:11:05: #2 predicted fragment length is 136 bps INFO @ Thu, 03 May 2018 23:11:05: #2 alternative fragment length(s) may be 4,136 bps INFO @ Thu, 03 May 2018 23:11:05: #2.2 Generate R script for model : SRX3063098.10_model.r WARNING @ Thu, 03 May 2018 23:11:05: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 23:11:05: #2 You may need to consider one of the other alternative d(s): 4,136 WARNING @ Thu, 03 May 2018 23:11:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 23:11:05: #3 Call peaks... INFO @ Thu, 03 May 2018 23:11:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 23:11:09: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 23:11:11: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 23:11:11: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 23:11:11: #4 Write output xls file... SRX3063098.20_peaks.xls INFO @ Thu, 03 May 2018 23:11:11: #4 Write peak in narrowPeak format file... SRX3063098.20_peaks.narrowPeak INFO @ Thu, 03 May 2018 23:11:11: #4 Write summits bed file... SRX3063098.20_summits.bed INFO @ Thu, 03 May 2018 23:11:11: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (425 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 23:11:13: #4 Write output xls file... SRX3063098.05_peaks.xls INFO @ Thu, 03 May 2018 23:11:13: #4 Write peak in narrowPeak format file... SRX3063098.05_peaks.narrowPeak INFO @ Thu, 03 May 2018 23:11:13: #4 Write summits bed file... SRX3063098.05_summits.bed INFO @ Thu, 03 May 2018 23:11:13: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (1383 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 23:11:13: #4 Write output xls file... SRX3063098.10_peaks.xls INFO @ Thu, 03 May 2018 23:11:13: #4 Write peak in narrowPeak format file... SRX3063098.10_peaks.narrowPeak INFO @ Thu, 03 May 2018 23:11:13: #4 Write summits bed file... SRX3063098.10_summits.bed INFO @ Thu, 03 May 2018 23:11:13: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (855 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。