Job ID = 10536493 sra ファイルのダウンロード中... Completed: 1326935K bytes transferred in 47 seconds (226840K 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 28136311 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3671189/SRR6696941.sra Written 28136311 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: 00:14:03 28136311 reads; of these: 28136311 (100.00%) were paired; of these: 13086730 (46.51%) aligned concordantly 0 times 13052206 (46.39%) aligned concordantly exactly 1 time 1997375 (7.10%) aligned concordantly >1 times ---- 13086730 pairs aligned concordantly 0 times; of these: 17826 (0.14%) aligned discordantly 1 time ---- 13068904 pairs aligned 0 times concordantly or discordantly; of these: 26137808 mates make up the pairs; of these: 25851445 (98.90%) aligned 0 times 230869 (0.88%) aligned exactly 1 time 55494 (0.21%) aligned >1 times 54.06% overall alignment rate Time searching: 00:14:03 Overall time: 00:14:03 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] 12712258 / 15058200 = 0.8442 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 10:08:38: # Command line: callpeak -t SRX3671189.bam -f BAM -g 12100000 -n SRX3671189.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3671189.20 # format = BAM # ChIP-seq file = ['SRX3671189.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 10:08:38: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:08:38: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:08:38: # Command line: callpeak -t SRX3671189.bam -f BAM -g 12100000 -n SRX3671189.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3671189.10 # format = BAM # ChIP-seq file = ['SRX3671189.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 10:08:38: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:08:38: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:08:38: # Command line: callpeak -t SRX3671189.bam -f BAM -g 12100000 -n SRX3671189.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3671189.05 # format = BAM # ChIP-seq file = ['SRX3671189.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 10:08:38: #1 read tag files... INFO @ Thu, 05 Apr 2018 10:08:38: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 10:08:44: 1000000 INFO @ Thu, 05 Apr 2018 10:08:44: 1000000 INFO @ Thu, 05 Apr 2018 10:08:44: 1000000 INFO @ Thu, 05 Apr 2018 10:08:49: 2000000 INFO @ Thu, 05 Apr 2018 10:08:49: 2000000 INFO @ Thu, 05 Apr 2018 10:08:50: 2000000 INFO @ Thu, 05 Apr 2018 10:08:55: 3000000 INFO @ Thu, 05 Apr 2018 10:08:55: 3000000 INFO @ Thu, 05 Apr 2018 10:08:56: 3000000 INFO @ Thu, 05 Apr 2018 10:09:00: 4000000 INFO @ Thu, 05 Apr 2018 10:09:01: 4000000 INFO @ Thu, 05 Apr 2018 10:09:02: 4000000 INFO @ Thu, 05 Apr 2018 10:09:06: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:09:06: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:09:06: #1 total tags in treatment: 2347886 INFO @ Thu, 05 Apr 2018 10:09:06: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:09:06: #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 10:09:06: #1 tags after filtering in treatment: 1948918 INFO @ Thu, 05 Apr 2018 10:09:06: #1 Redundant rate of treatment: 0.17 INFO @ Thu, 05 Apr 2018 10:09:06: #1 finished! INFO @ Thu, 05 Apr 2018 10:09:06: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:09:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:09:06: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:09:06: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:09:06: #1 total tags in treatment: 2347886 INFO @ Thu, 05 Apr 2018 10:09:06: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:09:06: #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 10:09:06: #1 tags after filtering in treatment: 1948918 INFO @ Thu, 05 Apr 2018 10:09:06: #1 Redundant rate of treatment: 0.17 INFO @ Thu, 05 Apr 2018 10:09:06: #1 finished! INFO @ Thu, 05 Apr 2018 10:09:06: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:09:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:09:06: #2 number of paired peaks: 298 WARNING @ Thu, 05 Apr 2018 10:09:06: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Thu, 05 Apr 2018 10:09:06: start model_add_line... INFO @ Thu, 05 Apr 2018 10:09:06: start X-correlation... INFO @ Thu, 05 Apr 2018 10:09:06: end of X-cor INFO @ Thu, 05 Apr 2018 10:09:06: #2 finished! INFO @ Thu, 05 Apr 2018 10:09:06: #2 predicted fragment length is 132 bps INFO @ Thu, 05 Apr 2018 10:09:06: #2 alternative fragment length(s) may be 2,66,90,119,123,132,156 bps INFO @ Thu, 05 Apr 2018 10:09:06: #2.2 Generate R script for model : SRX3671189.20_model.r INFO @ Thu, 05 Apr 2018 10:09:06: #3 Call peaks... INFO @ Thu, 05 Apr 2018 10:09:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 10:09:07: #2 number of paired peaks: 298 WARNING @ Thu, 05 Apr 2018 10:09:07: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Thu, 05 Apr 2018 10:09:07: start model_add_line... INFO @ Thu, 05 Apr 2018 10:09:07: start X-correlation... INFO @ Thu, 05 Apr 2018 10:09:07: end of X-cor INFO @ Thu, 05 Apr 2018 10:09:07: #2 finished! INFO @ Thu, 05 Apr 2018 10:09:07: #2 predicted fragment length is 132 bps INFO @ Thu, 05 Apr 2018 10:09:07: #2 alternative fragment length(s) may be 2,66,90,119,123,132,156 bps INFO @ Thu, 05 Apr 2018 10:09:07: #2.2 Generate R script for model : SRX3671189.10_model.r INFO @ Thu, 05 Apr 2018 10:09:07: #3 Call peaks... INFO @ Thu, 05 Apr 2018 10:09:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 10:09:09: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 10:09:09: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 10:09:09: #1 total tags in treatment: 2347886 INFO @ Thu, 05 Apr 2018 10:09:09: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 10:09:09: #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 10:09:09: #1 tags after filtering in treatment: 1948918 INFO @ Thu, 05 Apr 2018 10:09:09: #1 Redundant rate of treatment: 0.17 INFO @ Thu, 05 Apr 2018 10:09:09: #1 finished! INFO @ Thu, 05 Apr 2018 10:09:09: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 10:09:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 10:09:09: #2 number of paired peaks: 298 WARNING @ Thu, 05 Apr 2018 10:09:09: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Thu, 05 Apr 2018 10:09:09: start model_add_line... INFO @ Thu, 05 Apr 2018 10:09:09: start X-correlation... INFO @ Thu, 05 Apr 2018 10:09:09: end of X-cor INFO @ Thu, 05 Apr 2018 10:09:09: #2 finished! INFO @ Thu, 05 Apr 2018 10:09:09: #2 predicted fragment length is 132 bps INFO @ Thu, 05 Apr 2018 10:09:09: #2 alternative fragment length(s) may be 2,66,90,119,123,132,156 bps INFO @ Thu, 05 Apr 2018 10:09:09: #2.2 Generate R script for model : SRX3671189.05_model.r INFO @ Thu, 05 Apr 2018 10:09:09: #3 Call peaks... INFO @ Thu, 05 Apr 2018 10:09:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 10:09:13: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 10:09:13: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 10:09:15: #4 Write output xls file... SRX3671189.20_peaks.xls INFO @ Thu, 05 Apr 2018 10:09:15: #4 Write peak in narrowPeak format file... SRX3671189.20_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 10:09:15: #4 Write summits bed file... SRX3671189.20_summits.bed INFO @ Thu, 05 Apr 2018 10:09:15: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (178 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Apr 2018 10:09:15: #4 Write output xls file... SRX3671189.10_peaks.xls INFO @ Thu, 05 Apr 2018 10:09:15: #4 Write peak in narrowPeak format file... SRX3671189.10_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 10:09:15: #4 Write summits bed file... SRX3671189.10_summits.bed INFO @ Thu, 05 Apr 2018 10:09:15: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (542 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Apr 2018 10:09:15: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 10:09:18: #4 Write output xls file... SRX3671189.05_peaks.xls INFO @ Thu, 05 Apr 2018 10:09:18: #4 Write peak in narrowPeak format file... SRX3671189.05_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 10:09:18: #4 Write summits bed file... SRX3671189.05_summits.bed INFO @ Thu, 05 Apr 2018 10:09:18: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (832 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。