Job ID = 10536334 sra ファイルのダウンロード中... Completed: 1277885K bytes transferred in 86 seconds (120851K 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 20259323 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3433201/SRR6333842.sra Written 20259323 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: 00:11:57 20259323 reads; of these: 20259323 (100.00%) were paired; of these: 6934194 (34.23%) aligned concordantly 0 times 11601831 (57.27%) aligned concordantly exactly 1 time 1723298 (8.51%) aligned concordantly >1 times ---- 6934194 pairs aligned concordantly 0 times; of these: 15226 (0.22%) aligned discordantly 1 time ---- 6918968 pairs aligned 0 times concordantly or discordantly; of these: 13837936 mates make up the pairs; of these: 13229633 (95.60%) aligned 0 times 506425 (3.66%) aligned exactly 1 time 101878 (0.74%) aligned >1 times 67.35% overall alignment rate Time searching: 00:11:57 Overall time: 00:11:57 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 12 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] 12425749 / 13331749 = 0.9320 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, 05 Apr 2018 08:54:15: # Command line: callpeak -t SRX3433201.bam -f BAM -g 12100000 -n SRX3433201.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3433201.20 # format = BAM # ChIP-seq file = ['SRX3433201.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, 05 Apr 2018 08:54:15: #1 read tag files... INFO @ Thu, 05 Apr 2018 08:54:15: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 08:54:15: # Command line: callpeak -t SRX3433201.bam -f BAM -g 12100000 -n SRX3433201.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3433201.05 # format = BAM # ChIP-seq file = ['SRX3433201.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, 05 Apr 2018 08:54:15: #1 read tag files... INFO @ Thu, 05 Apr 2018 08:54:15: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 08:54:15: # Command line: callpeak -t SRX3433201.bam -f BAM -g 12100000 -n SRX3433201.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3433201.10 # format = BAM # ChIP-seq file = ['SRX3433201.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, 05 Apr 2018 08:54:15: #1 read tag files... INFO @ Thu, 05 Apr 2018 08:54:15: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 08:54:21: 1000000 INFO @ Thu, 05 Apr 2018 08:54:22: 1000000 INFO @ Thu, 05 Apr 2018 08:54:22: 1000000 INFO @ Thu, 05 Apr 2018 08:54:27: 2000000 INFO @ Thu, 05 Apr 2018 08:54:29: 2000000 INFO @ Thu, 05 Apr 2018 08:54:29: 2000000 INFO @ Thu, 05 Apr 2018 08:54:30: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 08:54:30: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 08:54:30: #1 total tags in treatment: 902576 INFO @ Thu, 05 Apr 2018 08:54:30: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 08:54:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 08:54:30: #1 tags after filtering in treatment: 813400 INFO @ Thu, 05 Apr 2018 08:54:30: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 05 Apr 2018 08:54:30: #1 finished! INFO @ Thu, 05 Apr 2018 08:54:30: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 08:54:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 08:54:30: #2 number of paired peaks: 136 WARNING @ Thu, 05 Apr 2018 08:54:30: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Thu, 05 Apr 2018 08:54:30: start model_add_line... INFO @ Thu, 05 Apr 2018 08:54:30: start X-correlation... INFO @ Thu, 05 Apr 2018 08:54:30: end of X-cor INFO @ Thu, 05 Apr 2018 08:54:30: #2 finished! INFO @ Thu, 05 Apr 2018 08:54:30: #2 predicted fragment length is 300 bps INFO @ Thu, 05 Apr 2018 08:54:30: #2 alternative fragment length(s) may be 2,10,98,104,111,144,163,225,270,300,343,491,579 bps INFO @ Thu, 05 Apr 2018 08:54:30: #2.2 Generate R script for model : SRX3433201.20_model.r INFO @ Thu, 05 Apr 2018 08:54:30: #3 Call peaks... INFO @ Thu, 05 Apr 2018 08:54:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 08:54:33: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 08:54:33: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 08:54:33: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 08:54:33: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 08:54:33: #1 total tags in treatment: 902576 INFO @ Thu, 05 Apr 2018 08:54:33: #1 total tags in treatment: 902576 INFO @ Thu, 05 Apr 2018 08:54:33: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 08:54:33: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 08:54:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 08:54:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 08:54:33: #1 tags after filtering in treatment: 813400 INFO @ Thu, 05 Apr 2018 08:54:33: #1 tags after filtering in treatment: 813400 INFO @ Thu, 05 Apr 2018 08:54:33: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 05 Apr 2018 08:54:33: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 05 Apr 2018 08:54:33: #1 finished! INFO @ Thu, 05 Apr 2018 08:54:33: #1 finished! INFO @ Thu, 05 Apr 2018 08:54:33: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 08:54:33: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 08:54:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 08:54:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 08:54:33: #2 number of paired peaks: 136 WARNING @ Thu, 05 Apr 2018 08:54:33: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Thu, 05 Apr 2018 08:54:33: start model_add_line... INFO @ Thu, 05 Apr 2018 08:54:33: #2 number of paired peaks: 136 WARNING @ Thu, 05 Apr 2018 08:54:33: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Thu, 05 Apr 2018 08:54:33: start model_add_line... INFO @ Thu, 05 Apr 2018 08:54:33: start X-correlation... INFO @ Thu, 05 Apr 2018 08:54:33: start X-correlation... INFO @ Thu, 05 Apr 2018 08:54:33: end of X-cor INFO @ Thu, 05 Apr 2018 08:54:33: #2 finished! INFO @ Thu, 05 Apr 2018 08:54:33: #2 predicted fragment length is 300 bps INFO @ Thu, 05 Apr 2018 08:54:33: #2 alternative fragment length(s) may be 2,10,98,104,111,144,163,225,270,300,343,491,579 bps INFO @ Thu, 05 Apr 2018 08:54:33: #2.2 Generate R script for model : SRX3433201.10_model.r INFO @ Thu, 05 Apr 2018 08:54:33: end of X-cor INFO @ Thu, 05 Apr 2018 08:54:33: #2 finished! INFO @ Thu, 05 Apr 2018 08:54:33: #2 predicted fragment length is 300 bps INFO @ Thu, 05 Apr 2018 08:54:33: #2 alternative fragment length(s) may be 2,10,98,104,111,144,163,225,270,300,343,491,579 bps INFO @ Thu, 05 Apr 2018 08:54:33: #2.2 Generate R script for model : SRX3433201.05_model.r INFO @ Thu, 05 Apr 2018 08:54:33: #3 Call peaks... INFO @ Thu, 05 Apr 2018 08:54:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 08:54:33: #3 Call peaks... INFO @ Thu, 05 Apr 2018 08:54:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 08:54:33: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 08:54:35: #4 Write output xls file... SRX3433201.20_peaks.xls INFO @ Thu, 05 Apr 2018 08:54:35: #4 Write peak in narrowPeak format file... SRX3433201.20_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 08:54:35: #4 Write summits bed file... SRX3433201.20_summits.bed INFO @ Thu, 05 Apr 2018 08:54:35: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (12 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 05 Apr 2018 08:54:36: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 08:54:36: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 08:54:37: #4 Write output xls file... SRX3433201.05_peaks.xls INFO @ Thu, 05 Apr 2018 08:54:37: #4 Write peak in narrowPeak format file... SRX3433201.05_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 08:54:37: #4 Write summits bed file... SRX3433201.05_summits.bed INFO @ Thu, 05 Apr 2018 08:54:37: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (120 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 05 Apr 2018 08:54:37: #4 Write output xls file... SRX3433201.10_peaks.xls INFO @ Thu, 05 Apr 2018 08:54:37: #4 Write peak in narrowPeak format file... SRX3433201.10_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 08:54:37: #4 Write summits bed file... SRX3433201.10_summits.bed INFO @ Thu, 05 Apr 2018 08:54:37: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (45 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。