Job ID = 10254414 sra ファイルのダウンロード中... Completed: 1108382K bytes transferred in 15 seconds (600340K 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 24966814 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2658708/SRR5363224.sra Written 24966814 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: 00:16:25 24966814 reads; of these: 24966814 (100.00%) were paired; of these: 4824889 (19.33%) aligned concordantly 0 times 16821350 (67.37%) aligned concordantly exactly 1 time 3320575 (13.30%) aligned concordantly >1 times ---- 4824889 pairs aligned concordantly 0 times; of these: 165420 (3.43%) aligned discordantly 1 time ---- 4659469 pairs aligned 0 times concordantly or discordantly; of these: 9318938 mates make up the pairs; of these: 8922852 (95.75%) aligned 0 times 253861 (2.72%) aligned exactly 1 time 142225 (1.53%) aligned >1 times 82.13% overall alignment rate Time searching: 00:16:25 Overall time: 00:16:25 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 20 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] 14351184 / 20270131 = 0.7080 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 18:14:10: # Command line: callpeak -t SRX2658708.bam -f BAM -g 12100000 -n SRX2658708.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2658708.10 # format = BAM # ChIP-seq file = ['SRX2658708.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 18:14:10: # Command line: callpeak -t SRX2658708.bam -f BAM -g 12100000 -n SRX2658708.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2658708.05 # format = BAM # ChIP-seq file = ['SRX2658708.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 18:14:10: # Command line: callpeak -t SRX2658708.bam -f BAM -g 12100000 -n SRX2658708.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2658708.20 # format = BAM # ChIP-seq file = ['SRX2658708.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 18:14:10: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:14:10: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:14:10: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:14:10: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:14:10: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:14:10: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:14:16: 1000000 INFO @ Wed, 06 Dec 2017 18:14:16: 1000000 INFO @ Wed, 06 Dec 2017 18:14:16: 1000000 INFO @ Wed, 06 Dec 2017 18:14:22: 2000000 INFO @ Wed, 06 Dec 2017 18:14:22: 2000000 INFO @ Wed, 06 Dec 2017 18:14:22: 2000000 INFO @ Wed, 06 Dec 2017 18:14:28: 3000000 INFO @ Wed, 06 Dec 2017 18:14:28: 3000000 INFO @ Wed, 06 Dec 2017 18:14:28: 3000000 INFO @ Wed, 06 Dec 2017 18:14:33: 4000000 INFO @ Wed, 06 Dec 2017 18:14:33: 4000000 INFO @ Wed, 06 Dec 2017 18:14:33: 4000000 INFO @ Wed, 06 Dec 2017 18:14:39: 5000000 INFO @ Wed, 06 Dec 2017 18:14:39: 5000000 INFO @ Wed, 06 Dec 2017 18:14:39: 5000000 INFO @ Wed, 06 Dec 2017 18:14:45: 6000000 INFO @ Wed, 06 Dec 2017 18:14:45: 6000000 INFO @ Wed, 06 Dec 2017 18:14:45: 6000000 INFO @ Wed, 06 Dec 2017 18:14:50: 7000000 INFO @ Wed, 06 Dec 2017 18:14:50: 7000000 INFO @ Wed, 06 Dec 2017 18:14:50: 7000000 INFO @ Wed, 06 Dec 2017 18:14:56: 8000000 INFO @ Wed, 06 Dec 2017 18:14:56: 8000000 INFO @ Wed, 06 Dec 2017 18:14:56: 8000000 INFO @ Wed, 06 Dec 2017 18:15:01: 9000000 INFO @ Wed, 06 Dec 2017 18:15:01: 9000000 INFO @ Wed, 06 Dec 2017 18:15:01: 9000000 INFO @ Wed, 06 Dec 2017 18:15:06: 10000000 INFO @ Wed, 06 Dec 2017 18:15:07: 10000000 INFO @ Wed, 06 Dec 2017 18:15:07: 10000000 INFO @ Wed, 06 Dec 2017 18:15:12: 11000000 INFO @ Wed, 06 Dec 2017 18:15:12: 11000000 INFO @ Wed, 06 Dec 2017 18:15:12: 11000000 INFO @ Wed, 06 Dec 2017 18:15:17: 12000000 INFO @ Wed, 06 Dec 2017 18:15:18: 12000000 INFO @ Wed, 06 Dec 2017 18:15:18: 12000000 INFO @ Wed, 06 Dec 2017 18:15:19: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 18:15:19: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 18:15:19: #1 total tags in treatment: 5836857 INFO @ Wed, 06 Dec 2017 18:15:19: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:15:19: #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 18:15:19: #1 tags after filtering in treatment: 3650553 INFO @ Wed, 06 Dec 2017 18:15:19: #1 Redundant rate of treatment: 0.37 INFO @ Wed, 06 Dec 2017 18:15:19: #1 finished! INFO @ Wed, 06 Dec 2017 18:15:19: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:15:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:15:19: #2 number of paired peaks: 110 WARNING @ Wed, 06 Dec 2017 18:15:19: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Wed, 06 Dec 2017 18:15:19: start model_add_line... INFO @ Wed, 06 Dec 2017 18:15:19: start X-correlation... INFO @ Wed, 06 Dec 2017 18:15:19: end of X-cor INFO @ Wed, 06 Dec 2017 18:15:19: #2 finished! INFO @ Wed, 06 Dec 2017 18:15:19: #2 predicted fragment length is 1 bps INFO @ Wed, 06 Dec 2017 18:15:19: #2 alternative fragment length(s) may be 1,101,118,150,158,188,207,348,539 bps INFO @ Wed, 06 Dec 2017 18:15:19: #2.2 Generate R script for model : SRX2658708.20_model.r WARNING @ Wed, 06 Dec 2017 18:15:19: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 06 Dec 2017 18:15:19: #2 You may need to consider one of the other alternative d(s): 1,101,118,150,158,188,207,348,539 WARNING @ Wed, 06 Dec 2017 18:15:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 06 Dec 2017 18:15:19: #3 Call peaks... INFO @ Wed, 06 Dec 2017 18:15:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 06 Dec 2017 18:15:20: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 18:15:20: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 18:15:20: #1 total tags in treatment: 5836857 INFO @ Wed, 06 Dec 2017 18:15:20: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:15:20: #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 18:15:20: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 18:15:20: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 18:15:20: #1 total tags in treatment: 5836857 INFO @ Wed, 06 Dec 2017 18:15:20: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:15:20: #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 18:15:20: #1 tags after filtering in treatment: 3650553 INFO @ Wed, 06 Dec 2017 18:15:20: #1 Redundant rate of treatment: 0.37 INFO @ Wed, 06 Dec 2017 18:15:20: #1 finished! INFO @ Wed, 06 Dec 2017 18:15:20: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:15:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:15:20: #1 tags after filtering in treatment: 3650553 INFO @ Wed, 06 Dec 2017 18:15:20: #1 Redundant rate of treatment: 0.37 INFO @ Wed, 06 Dec 2017 18:15:20: #1 finished! INFO @ Wed, 06 Dec 2017 18:15:20: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:15:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:15:20: #2 number of paired peaks: 110 WARNING @ Wed, 06 Dec 2017 18:15:20: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Wed, 06 Dec 2017 18:15:20: start model_add_line... INFO @ Wed, 06 Dec 2017 18:15:20: start X-correlation... INFO @ Wed, 06 Dec 2017 18:15:20: end of X-cor INFO @ Wed, 06 Dec 2017 18:15:20: #2 finished! INFO @ Wed, 06 Dec 2017 18:15:20: #2 predicted fragment length is 1 bps INFO @ Wed, 06 Dec 2017 18:15:20: #2 alternative fragment length(s) may be 1,101,118,150,158,188,207,348,539 bps INFO @ Wed, 06 Dec 2017 18:15:20: #2.2 Generate R script for model : SRX2658708.05_model.r WARNING @ Wed, 06 Dec 2017 18:15:20: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 06 Dec 2017 18:15:20: #2 You may need to consider one of the other alternative d(s): 1,101,118,150,158,188,207,348,539 WARNING @ Wed, 06 Dec 2017 18:15:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 06 Dec 2017 18:15:20: #3 Call peaks... INFO @ Wed, 06 Dec 2017 18:15:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 06 Dec 2017 18:15:20: #2 number of paired peaks: 110 WARNING @ Wed, 06 Dec 2017 18:15:20: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Wed, 06 Dec 2017 18:15:20: start model_add_line... INFO @ Wed, 06 Dec 2017 18:15:20: start X-correlation... INFO @ Wed, 06 Dec 2017 18:15:20: end of X-cor INFO @ Wed, 06 Dec 2017 18:15:20: #2 finished! INFO @ Wed, 06 Dec 2017 18:15:20: #2 predicted fragment length is 1 bps INFO @ Wed, 06 Dec 2017 18:15:20: #2 alternative fragment length(s) may be 1,101,118,150,158,188,207,348,539 bps INFO @ Wed, 06 Dec 2017 18:15:20: #2.2 Generate R script for model : SRX2658708.10_model.r WARNING @ Wed, 06 Dec 2017 18:15:20: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 06 Dec 2017 18:15:20: #2 You may need to consider one of the other alternative d(s): 1,101,118,150,158,188,207,348,539 WARNING @ Wed, 06 Dec 2017 18:15:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 06 Dec 2017 18:15:20: #3 Call peaks... INFO @ Wed, 06 Dec 2017 18:15:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 06 Dec 2017 18:15:24: #3 Call peaks for each chromosome... INFO @ Wed, 06 Dec 2017 18:15:25: #3 Call peaks for each chromosome... INFO @ Wed, 06 Dec 2017 18:15:25: #3 Call peaks for each chromosome... INFO @ Wed, 06 Dec 2017 18:15:27: #4 Write output xls file... SRX2658708.20_peaks.xls INFO @ Wed, 06 Dec 2017 18:15:27: #4 Write peak in narrowPeak format file... SRX2658708.20_peaks.narrowPeak INFO @ Wed, 06 Dec 2017 18:15:27: #4 Write summits bed file... SRX2658708.20_summits.bed INFO @ Wed, 06 Dec 2017 18:15:27: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 06 Dec 2017 18:15:27: #4 Write output xls file... SRX2658708.05_peaks.xls INFO @ Wed, 06 Dec 2017 18:15:27: #4 Write peak in narrowPeak format file... SRX2658708.05_peaks.narrowPeak INFO @ Wed, 06 Dec 2017 18:15:27: #4 Write summits bed file... SRX2658708.05_summits.bed INFO @ Wed, 06 Dec 2017 18:15:27: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Wed, 06 Dec 2017 18:15:27: #4 Write output xls file... SRX2658708.10_peaks.xls INFO @ Wed, 06 Dec 2017 18:15:27: #4 Write peak in narrowPeak format file... SRX2658708.10_peaks.narrowPeak INFO @ Wed, 06 Dec 2017 18:15:27: #4 Write summits bed file... SRX2658708.10_summits.bed CompletedMACS2peakCalling INFO @ Wed, 06 Dec 2017 18:15:27: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。