Job ID = 10937326 sra ファイルのダウンロード中... Completed: 219967K bytes transferred in 5 seconds (354485K 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 3077556 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198705/SRR4304435.sra Written 3077556 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198705/SRR4304435.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: 00:02:32 3077556 reads; of these: 3077556 (100.00%) were paired; of these: 317860 (10.33%) aligned concordantly 0 times 2285683 (74.27%) aligned concordantly exactly 1 time 474013 (15.40%) aligned concordantly >1 times ---- 317860 pairs aligned concordantly 0 times; of these: 42076 (13.24%) aligned discordantly 1 time ---- 275784 pairs aligned 0 times concordantly or discordantly; of these: 551568 mates make up the pairs; of these: 358116 (64.93%) aligned 0 times 140027 (25.39%) aligned exactly 1 time 53425 (9.69%) aligned >1 times 94.18% overall alignment rate Time searching: 00:02:32 Overall time: 00:02:32 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] 741723 / 2771458 = 0.2676 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, 10 Aug 2018 01:45:41: # Command line: callpeak -t SRX2198705.bam -f BAM -g 12100000 -n SRX2198705.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2198705.10 # format = BAM # ChIP-seq file = ['SRX2198705.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, 10 Aug 2018 01:45:41: #1 read tag files... INFO @ Fri, 10 Aug 2018 01:45:41: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 01:45:41: # Command line: callpeak -t SRX2198705.bam -f BAM -g 12100000 -n SRX2198705.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2198705.20 # format = BAM # ChIP-seq file = ['SRX2198705.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, 10 Aug 2018 01:45:41: #1 read tag files... INFO @ Fri, 10 Aug 2018 01:45:41: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 01:45:41: # Command line: callpeak -t SRX2198705.bam -f BAM -g 12100000 -n SRX2198705.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2198705.05 # format = BAM # ChIP-seq file = ['SRX2198705.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, 10 Aug 2018 01:45:41: #1 read tag files... INFO @ Fri, 10 Aug 2018 01:45:41: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 01:45:47: 1000000 INFO @ Fri, 10 Aug 2018 01:45:47: 1000000 INFO @ Fri, 10 Aug 2018 01:45:48: 1000000 INFO @ Fri, 10 Aug 2018 01:45:53: 2000000 INFO @ Fri, 10 Aug 2018 01:45:53: 2000000 INFO @ Fri, 10 Aug 2018 01:45:54: 2000000 INFO @ Fri, 10 Aug 2018 01:45:59: 3000000 INFO @ Fri, 10 Aug 2018 01:46:00: 3000000 INFO @ Fri, 10 Aug 2018 01:46:00: 3000000 INFO @ Fri, 10 Aug 2018 01:46:06: 4000000 INFO @ Fri, 10 Aug 2018 01:46:07: 4000000 INFO @ Fri, 10 Aug 2018 01:46:07: 4000000 INFO @ Fri, 10 Aug 2018 01:46:08: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 01:46:08: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 01:46:08: #1 total tags in treatment: 2019840 INFO @ Fri, 10 Aug 2018 01:46:08: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 01:46:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 01:46:08: #1 tags after filtering in treatment: 1597856 INFO @ Fri, 10 Aug 2018 01:46:08: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 10 Aug 2018 01:46:08: #1 finished! INFO @ Fri, 10 Aug 2018 01:46:08: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 01:46:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 01:46:08: #2 number of paired peaks: 189 WARNING @ Fri, 10 Aug 2018 01:46:08: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Fri, 10 Aug 2018 01:46:08: start model_add_line... INFO @ Fri, 10 Aug 2018 01:46:08: start X-correlation... INFO @ Fri, 10 Aug 2018 01:46:08: end of X-cor INFO @ Fri, 10 Aug 2018 01:46:08: #2 finished! INFO @ Fri, 10 Aug 2018 01:46:08: #2 predicted fragment length is 117 bps INFO @ Fri, 10 Aug 2018 01:46:08: #2 alternative fragment length(s) may be 93,117,139,156,203,223,489,521,569,591 bps INFO @ Fri, 10 Aug 2018 01:46:08: #2.2 Generate R script for model : SRX2198705.05_model.r INFO @ Fri, 10 Aug 2018 01:46:08: #3 Call peaks... INFO @ Fri, 10 Aug 2018 01:46:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 01:46:09: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 01:46:09: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 01:46:09: #1 total tags in treatment: 2019840 INFO @ Fri, 10 Aug 2018 01:46:09: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 01:46:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 01:46:09: #1 tags after filtering in treatment: 1597856 INFO @ Fri, 10 Aug 2018 01:46:09: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 10 Aug 2018 01:46:09: #1 finished! INFO @ Fri, 10 Aug 2018 01:46:09: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 01:46:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 01:46:09: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 01:46:09: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 01:46:09: #1 total tags in treatment: 2019840 INFO @ Fri, 10 Aug 2018 01:46:09: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 01:46:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 01:46:09: #2 number of paired peaks: 189 WARNING @ Fri, 10 Aug 2018 01:46:09: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Fri, 10 Aug 2018 01:46:09: start model_add_line... INFO @ Fri, 10 Aug 2018 01:46:09: start X-correlation... INFO @ Fri, 10 Aug 2018 01:46:09: end of X-cor INFO @ Fri, 10 Aug 2018 01:46:09: #2 finished! INFO @ Fri, 10 Aug 2018 01:46:09: #2 predicted fragment length is 117 bps INFO @ Fri, 10 Aug 2018 01:46:09: #2 alternative fragment length(s) may be 93,117,139,156,203,223,489,521,569,591 bps INFO @ Fri, 10 Aug 2018 01:46:09: #2.2 Generate R script for model : SRX2198705.10_model.r INFO @ Fri, 10 Aug 2018 01:46:09: #1 tags after filtering in treatment: 1597856 INFO @ Fri, 10 Aug 2018 01:46:09: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 10 Aug 2018 01:46:09: #1 finished! INFO @ Fri, 10 Aug 2018 01:46:09: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 01:46:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 01:46:09: #3 Call peaks... INFO @ Fri, 10 Aug 2018 01:46:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 01:46:09: #2 number of paired peaks: 189 WARNING @ Fri, 10 Aug 2018 01:46:09: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Fri, 10 Aug 2018 01:46:09: start model_add_line... INFO @ Fri, 10 Aug 2018 01:46:09: start X-correlation... INFO @ Fri, 10 Aug 2018 01:46:09: end of X-cor INFO @ Fri, 10 Aug 2018 01:46:09: #2 finished! INFO @ Fri, 10 Aug 2018 01:46:09: #2 predicted fragment length is 117 bps INFO @ Fri, 10 Aug 2018 01:46:09: #2 alternative fragment length(s) may be 93,117,139,156,203,223,489,521,569,591 bps INFO @ Fri, 10 Aug 2018 01:46:09: #2.2 Generate R script for model : SRX2198705.20_model.r INFO @ Fri, 10 Aug 2018 01:46:09: #3 Call peaks... INFO @ Fri, 10 Aug 2018 01:46:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 01:46:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 01:46:13: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 01:46:13: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 01:46:14: #4 Write output xls file... SRX2198705.05_peaks.xls INFO @ Fri, 10 Aug 2018 01:46:14: #4 Write peak in narrowPeak format file... SRX2198705.05_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 01:46:14: #4 Write summits bed file... SRX2198705.05_summits.bed INFO @ Fri, 10 Aug 2018 01:46:14: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (25 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 01:46:14: #4 Write output xls file... SRX2198705.10_peaks.xls INFO @ Fri, 10 Aug 2018 01:46:14: #4 Write peak in narrowPeak format file... SRX2198705.10_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 01:46:14: #4 Write summits bed file... SRX2198705.10_summits.bed INFO @ Fri, 10 Aug 2018 01:46:14: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (13 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 01:46:15: #4 Write output xls file... SRX2198705.20_peaks.xls INFO @ Fri, 10 Aug 2018 01:46:15: #4 Write peak in narrowPeak format file... SRX2198705.20_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 01:46:15: #4 Write summits bed file... SRX2198705.20_summits.bed INFO @ Fri, 10 Aug 2018 01:46:15: Done! pass1 - making usageList (1 chroms): 2 millis pass2 - checking and writing primary data (1 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。