Job ID = 11632739 sra ファイルのダウンロード中... Completed: 245859K bytes transferred in 6 seconds (314304K 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 2336817 spots for /home/okishinya/chipatlas/results/sacCer3/DRX123809/DRR131071.sra Written 2336817 spots for /home/okishinya/chipatlas/results/sacCer3/DRX123809/DRR131071.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: 00:02:27 2336817 reads; of these: 2336817 (100.00%) were paired; of these: 225394 (9.65%) aligned concordantly 0 times 1947467 (83.34%) aligned concordantly exactly 1 time 163956 (7.02%) aligned concordantly >1 times ---- 225394 pairs aligned concordantly 0 times; of these: 90193 (40.02%) aligned discordantly 1 time ---- 135201 pairs aligned 0 times concordantly or discordantly; of these: 270402 mates make up the pairs; of these: 217741 (80.52%) aligned 0 times 33093 (12.24%) aligned exactly 1 time 19568 (7.24%) aligned >1 times 95.34% overall alignment rate Time searching: 00:02:28 Overall time: 00:02:28 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] 3276 / 2195700 = 0.0015 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 @ Fri, 15 Feb 2019 06:59:04: # Command line: callpeak -t DRX123809.bam -f BAM -g 12100000 -n DRX123809.05 -q 1e-05 # ARGUMENTS LIST: # name = DRX123809.05 # format = BAM # ChIP-seq file = ['DRX123809.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 @ Fri, 15 Feb 2019 06:59:04: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:59:04: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:59:04: # Command line: callpeak -t DRX123809.bam -f BAM -g 12100000 -n DRX123809.20 -q 1e-20 # ARGUMENTS LIST: # name = DRX123809.20 # format = BAM # ChIP-seq file = ['DRX123809.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 @ Fri, 15 Feb 2019 06:59:04: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:59:04: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:59:04: # Command line: callpeak -t DRX123809.bam -f BAM -g 12100000 -n DRX123809.10 -q 1e-10 # ARGUMENTS LIST: # name = DRX123809.10 # format = BAM # ChIP-seq file = ['DRX123809.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 @ Fri, 15 Feb 2019 06:59:04: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:59:04: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:59:11: 1000000 INFO @ Fri, 15 Feb 2019 06:59:12: 1000000 INFO @ Fri, 15 Feb 2019 06:59:12: 1000000 INFO @ Fri, 15 Feb 2019 06:59:18: 2000000 INFO @ Fri, 15 Feb 2019 06:59:18: 2000000 INFO @ Fri, 15 Feb 2019 06:59:19: 2000000 INFO @ Fri, 15 Feb 2019 06:59:25: 3000000 INFO @ Fri, 15 Feb 2019 06:59:26: 3000000 INFO @ Fri, 15 Feb 2019 06:59:26: 3000000 INFO @ Fri, 15 Feb 2019 06:59:32: 4000000 INFO @ Fri, 15 Feb 2019 06:59:33: 4000000 INFO @ Fri, 15 Feb 2019 06:59:33: 4000000 INFO @ Fri, 15 Feb 2019 06:59:35: #1 tag size is determined as 75 bps INFO @ Fri, 15 Feb 2019 06:59:35: #1 tag size = 75 INFO @ Fri, 15 Feb 2019 06:59:35: #1 total tags in treatment: 2108190 INFO @ Fri, 15 Feb 2019 06:59:35: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:59:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:59:35: #1 tags after filtering in treatment: 1920201 INFO @ Fri, 15 Feb 2019 06:59:35: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 15 Feb 2019 06:59:35: #1 finished! INFO @ Fri, 15 Feb 2019 06:59:35: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:59:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:59:35: #2 number of paired peaks: 188 WARNING @ Fri, 15 Feb 2019 06:59:35: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Fri, 15 Feb 2019 06:59:35: start model_add_line... INFO @ Fri, 15 Feb 2019 06:59:35: start X-correlation... INFO @ Fri, 15 Feb 2019 06:59:35: end of X-cor INFO @ Fri, 15 Feb 2019 06:59:35: #2 finished! INFO @ Fri, 15 Feb 2019 06:59:35: #2 predicted fragment length is 171 bps INFO @ Fri, 15 Feb 2019 06:59:35: #2 alternative fragment length(s) may be 0,54,87,108,134,171,198,226,248,273,311,318,344,412,462,513,519,542,573,585,598 bps INFO @ Fri, 15 Feb 2019 06:59:35: #2.2 Generate R script for model : DRX123809.20_model.r INFO @ Fri, 15 Feb 2019 06:59:35: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:59:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:59:36: #1 tag size is determined as 75 bps INFO @ Fri, 15 Feb 2019 06:59:36: #1 tag size = 75 INFO @ Fri, 15 Feb 2019 06:59:36: #1 total tags in treatment: 2108190 INFO @ Fri, 15 Feb 2019 06:59:36: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:59:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:59:36: #1 tags after filtering in treatment: 1920201 INFO @ Fri, 15 Feb 2019 06:59:36: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 15 Feb 2019 06:59:36: #1 finished! INFO @ Fri, 15 Feb 2019 06:59:36: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:59:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:59:37: #2 number of paired peaks: 188 WARNING @ Fri, 15 Feb 2019 06:59:37: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Fri, 15 Feb 2019 06:59:37: start model_add_line... INFO @ Fri, 15 Feb 2019 06:59:37: start X-correlation... INFO @ Fri, 15 Feb 2019 06:59:37: end of X-cor INFO @ Fri, 15 Feb 2019 06:59:37: #2 finished! INFO @ Fri, 15 Feb 2019 06:59:37: #2 predicted fragment length is 171 bps INFO @ Fri, 15 Feb 2019 06:59:37: #2 alternative fragment length(s) may be 0,54,87,108,134,171,198,226,248,273,311,318,344,412,462,513,519,542,573,585,598 bps INFO @ Fri, 15 Feb 2019 06:59:37: #2.2 Generate R script for model : DRX123809.05_model.r INFO @ Fri, 15 Feb 2019 06:59:37: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:59:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:59:37: #1 tag size is determined as 75 bps INFO @ Fri, 15 Feb 2019 06:59:37: #1 tag size = 75 INFO @ Fri, 15 Feb 2019 06:59:37: #1 total tags in treatment: 2108190 INFO @ Fri, 15 Feb 2019 06:59:37: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:59:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:59:37: #1 tags after filtering in treatment: 1920201 INFO @ Fri, 15 Feb 2019 06:59:37: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 15 Feb 2019 06:59:37: #1 finished! INFO @ Fri, 15 Feb 2019 06:59:37: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:59:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:59:37: #2 number of paired peaks: 188 WARNING @ Fri, 15 Feb 2019 06:59:37: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Fri, 15 Feb 2019 06:59:37: start model_add_line... INFO @ Fri, 15 Feb 2019 06:59:37: start X-correlation... INFO @ Fri, 15 Feb 2019 06:59:37: end of X-cor INFO @ Fri, 15 Feb 2019 06:59:37: #2 finished! INFO @ Fri, 15 Feb 2019 06:59:37: #2 predicted fragment length is 171 bps INFO @ Fri, 15 Feb 2019 06:59:37: #2 alternative fragment length(s) may be 0,54,87,108,134,171,198,226,248,273,311,318,344,412,462,513,519,542,573,585,598 bps INFO @ Fri, 15 Feb 2019 06:59:37: #2.2 Generate R script for model : DRX123809.10_model.r INFO @ Fri, 15 Feb 2019 06:59:37: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:59:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:59:40: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:59:41: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:59:41: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:59:42: #4 Write output xls file... DRX123809.20_peaks.xls INFO @ Fri, 15 Feb 2019 06:59:42: #4 Write peak in narrowPeak format file... DRX123809.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:59:42: #4 Write summits bed file... DRX123809.20_summits.bed INFO @ Fri, 15 Feb 2019 06:59:42: Done! pass1 - making usageList (1 chroms): 2 millis pass2 - checking and writing primary data (1 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 06:59:43: #4 Write output xls file... DRX123809.05_peaks.xls INFO @ Fri, 15 Feb 2019 06:59:43: #4 Write peak in narrowPeak format file... DRX123809.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:59:43: #4 Write summits bed file... DRX123809.05_summits.bed INFO @ Fri, 15 Feb 2019 06:59:43: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (18 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 06:59:43: #4 Write output xls file... DRX123809.10_peaks.xls INFO @ Fri, 15 Feb 2019 06:59:43: #4 Write peak in narrowPeak format file... DRX123809.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:59:43: #4 Write summits bed file... DRX123809.10_summits.bed INFO @ Fri, 15 Feb 2019 06:59:43: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (11 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。