Job ID = 10937320 sra ファイルのダウンロード中... Completed: 207487K bytes transferred in 4 seconds (342003K 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 2911585 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198703/SRR4304433.sra Written 2911585 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198703/SRR4304433.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: 00:02:14 2911585 reads; of these: 2911585 (100.00%) were paired; of these: 348938 (11.98%) aligned concordantly 0 times 2116747 (72.70%) aligned concordantly exactly 1 time 445900 (15.31%) aligned concordantly >1 times ---- 348938 pairs aligned concordantly 0 times; of these: 39520 (11.33%) aligned discordantly 1 time ---- 309418 pairs aligned 0 times concordantly or discordantly; of these: 618836 mates make up the pairs; of these: 441077 (71.28%) aligned 0 times 131044 (21.18%) aligned exactly 1 time 46715 (7.55%) aligned >1 times 92.43% overall alignment rate Time searching: 00:02:15 Overall time: 00:02:15 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] 399599 / 2572965 = 0.1553 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 01:44:21: # Command line: callpeak -t SRX2198703.bam -f BAM -g 12100000 -n SRX2198703.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2198703.10 # format = BAM # ChIP-seq file = ['SRX2198703.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 01:44:21: #1 read tag files... INFO @ Fri, 10 Aug 2018 01:44:21: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 01:44:21: # Command line: callpeak -t SRX2198703.bam -f BAM -g 12100000 -n SRX2198703.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2198703.05 # format = BAM # ChIP-seq file = ['SRX2198703.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 01:44:21: #1 read tag files... INFO @ Fri, 10 Aug 2018 01:44:21: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 01:44:21: # Command line: callpeak -t SRX2198703.bam -f BAM -g 12100000 -n SRX2198703.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2198703.20 # format = BAM # ChIP-seq file = ['SRX2198703.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 01:44:21: #1 read tag files... INFO @ Fri, 10 Aug 2018 01:44:21: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 01:44:28: 1000000 INFO @ Fri, 10 Aug 2018 01:44:28: 1000000 INFO @ Fri, 10 Aug 2018 01:44:28: 1000000 INFO @ Fri, 10 Aug 2018 01:44:35: 2000000 INFO @ Fri, 10 Aug 2018 01:44:35: 2000000 INFO @ Fri, 10 Aug 2018 01:44:35: 2000000 INFO @ Fri, 10 Aug 2018 01:44:42: 3000000 INFO @ Fri, 10 Aug 2018 01:44:42: 3000000 INFO @ Fri, 10 Aug 2018 01:44:42: 3000000 INFO @ Fri, 10 Aug 2018 01:44:49: 4000000 INFO @ Fri, 10 Aug 2018 01:44:49: 4000000 INFO @ Fri, 10 Aug 2018 01:44:50: 4000000 INFO @ Fri, 10 Aug 2018 01:44:53: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 01:44:53: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 01:44:53: #1 total tags in treatment: 2163974 INFO @ Fri, 10 Aug 2018 01:44:53: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 01:44:53: #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 01:44:53: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 01:44:53: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 01:44:53: #1 total tags in treatment: 2163974 INFO @ Fri, 10 Aug 2018 01:44:53: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 01:44:53: #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 01:44:53: #1 tags after filtering in treatment: 1720187 INFO @ Fri, 10 Aug 2018 01:44:53: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 10 Aug 2018 01:44:53: #1 finished! INFO @ Fri, 10 Aug 2018 01:44:53: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 01:44:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 01:44:53: #1 tags after filtering in treatment: 1720187 INFO @ Fri, 10 Aug 2018 01:44:53: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 10 Aug 2018 01:44:53: #1 finished! INFO @ Fri, 10 Aug 2018 01:44:53: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 01:44:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 01:44:53: #2 number of paired peaks: 193 WARNING @ Fri, 10 Aug 2018 01:44:53: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Fri, 10 Aug 2018 01:44:53: start model_add_line... INFO @ Fri, 10 Aug 2018 01:44:53: start X-correlation... INFO @ Fri, 10 Aug 2018 01:44:53: end of X-cor INFO @ Fri, 10 Aug 2018 01:44:53: #2 finished! INFO @ Fri, 10 Aug 2018 01:44:53: #2 predicted fragment length is 136 bps INFO @ Fri, 10 Aug 2018 01:44:53: #2 alternative fragment length(s) may be 0,12,43,92,136,151,176,195,231,449,484,506,570,590 bps INFO @ Fri, 10 Aug 2018 01:44:53: #2.2 Generate R script for model : SRX2198703.10_model.r INFO @ Fri, 10 Aug 2018 01:44:53: #3 Call peaks... INFO @ Fri, 10 Aug 2018 01:44:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 01:44:53: #2 number of paired peaks: 193 WARNING @ Fri, 10 Aug 2018 01:44:53: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Fri, 10 Aug 2018 01:44:53: start model_add_line... INFO @ Fri, 10 Aug 2018 01:44:53: start X-correlation... INFO @ Fri, 10 Aug 2018 01:44:53: end of X-cor INFO @ Fri, 10 Aug 2018 01:44:53: #2 finished! INFO @ Fri, 10 Aug 2018 01:44:53: #2 predicted fragment length is 136 bps INFO @ Fri, 10 Aug 2018 01:44:53: #2 alternative fragment length(s) may be 0,12,43,92,136,151,176,195,231,449,484,506,570,590 bps INFO @ Fri, 10 Aug 2018 01:44:53: #2.2 Generate R script for model : SRX2198703.05_model.r INFO @ Fri, 10 Aug 2018 01:44:53: #3 Call peaks... INFO @ Fri, 10 Aug 2018 01:44:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 01:44:54: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 01:44:54: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 01:44:54: #1 total tags in treatment: 2163974 INFO @ Fri, 10 Aug 2018 01:44:54: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 01:44:54: #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 01:44:54: #1 tags after filtering in treatment: 1720187 INFO @ Fri, 10 Aug 2018 01:44:54: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 10 Aug 2018 01:44:54: #1 finished! INFO @ Fri, 10 Aug 2018 01:44:54: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 01:44:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 01:44:54: #2 number of paired peaks: 193 WARNING @ Fri, 10 Aug 2018 01:44:54: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Fri, 10 Aug 2018 01:44:54: start model_add_line... INFO @ Fri, 10 Aug 2018 01:44:54: start X-correlation... INFO @ Fri, 10 Aug 2018 01:44:54: end of X-cor INFO @ Fri, 10 Aug 2018 01:44:54: #2 finished! INFO @ Fri, 10 Aug 2018 01:44:54: #2 predicted fragment length is 136 bps INFO @ Fri, 10 Aug 2018 01:44:54: #2 alternative fragment length(s) may be 0,12,43,92,136,151,176,195,231,449,484,506,570,590 bps INFO @ Fri, 10 Aug 2018 01:44:54: #2.2 Generate R script for model : SRX2198703.20_model.r INFO @ Fri, 10 Aug 2018 01:44:54: #3 Call peaks... INFO @ Fri, 10 Aug 2018 01:44:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 01:44:57: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 01:44:57: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 01:44:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 01:44:59: #4 Write output xls file... SRX2198703.05_peaks.xls INFO @ Fri, 10 Aug 2018 01:44:59: #4 Write peak in narrowPeak format file... SRX2198703.05_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 01:44:59: #4 Write summits bed file... SRX2198703.05_summits.bed INFO @ Fri, 10 Aug 2018 01:44:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (16 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 01:44:59: #4 Write output xls file... SRX2198703.10_peaks.xls INFO @ Fri, 10 Aug 2018 01:44:59: #4 Write peak in narrowPeak format file... SRX2198703.10_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 01:44:59: #4 Write summits bed file... SRX2198703.10_summits.bed INFO @ Fri, 10 Aug 2018 01:44:59: Done! pass1 - making usageList (4 chroms): 2 millis pass2 - checking and writing primary data (12 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 01:45:00: #4 Write output xls file... SRX2198703.20_peaks.xls INFO @ Fri, 10 Aug 2018 01:45:00: #4 Write peak in narrowPeak format file... SRX2198703.20_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 01:45:00: #4 Write summits bed file... SRX2198703.20_summits.bed INFO @ Fri, 10 Aug 2018 01:45:00: Done! pass1 - making usageList (1 chroms): 1 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。