Job ID = 10937338 sra ファイルのダウンロード中... Completed: 244690K bytes transferred in 6 seconds (320906K 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 3422303 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198707/SRR4304437.sra Written 3422303 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198707/SRR4304437.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: 00:02:48 3422303 reads; of these: 3422303 (100.00%) were paired; of these: 615079 (17.97%) aligned concordantly 0 times 2070742 (60.51%) aligned concordantly exactly 1 time 736482 (21.52%) aligned concordantly >1 times ---- 615079 pairs aligned concordantly 0 times; of these: 24108 (3.92%) aligned discordantly 1 time ---- 590971 pairs aligned 0 times concordantly or discordantly; of these: 1181942 mates make up the pairs; of these: 1067300 (90.30%) aligned 0 times 63714 (5.39%) aligned exactly 1 time 50928 (4.31%) aligned >1 times 84.41% overall alignment rate Time searching: 00:02:48 Overall time: 00:02:48 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] 321325 / 2825735 = 0.1137 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 01:50:09: # Command line: callpeak -t SRX2198707.bam -f BAM -g 12100000 -n SRX2198707.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2198707.20 # format = BAM # ChIP-seq file = ['SRX2198707.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 01:50:09: #1 read tag files... INFO @ Fri, 10 Aug 2018 01:50:09: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 01:50:09: # Command line: callpeak -t SRX2198707.bam -f BAM -g 12100000 -n SRX2198707.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2198707.10 # format = BAM # ChIP-seq file = ['SRX2198707.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 01:50:09: #1 read tag files... INFO @ Fri, 10 Aug 2018 01:50:09: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 01:50:09: # Command line: callpeak -t SRX2198707.bam -f BAM -g 12100000 -n SRX2198707.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2198707.05 # format = BAM # ChIP-seq file = ['SRX2198707.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 01:50:09: #1 read tag files... INFO @ Fri, 10 Aug 2018 01:50:09: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 01:50:17: 1000000 INFO @ Fri, 10 Aug 2018 01:50:17: 1000000 INFO @ Fri, 10 Aug 2018 01:50:17: 1000000 INFO @ Fri, 10 Aug 2018 01:50:24: 2000000 INFO @ Fri, 10 Aug 2018 01:50:24: 2000000 INFO @ Fri, 10 Aug 2018 01:50:26: 2000000 INFO @ Fri, 10 Aug 2018 01:50:31: 3000000 INFO @ Fri, 10 Aug 2018 01:50:31: 3000000 INFO @ Fri, 10 Aug 2018 01:50:34: 3000000 INFO @ Fri, 10 Aug 2018 01:50:39: 4000000 INFO @ Fri, 10 Aug 2018 01:50:39: 4000000 INFO @ Fri, 10 Aug 2018 01:50:42: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Aug 2018 01:50:46: 5000000 INFO @ Fri, 10 Aug 2018 01:50:46: 5000000 BigWig に変換しました。 INFO @ Fri, 10 Aug 2018 01:50:47: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 01:50:47: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 01:50:47: #1 total tags in treatment: 2486516 INFO @ Fri, 10 Aug 2018 01:50:47: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 01:50:47: #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 01:50:47: #1 tags after filtering in treatment: 977823 INFO @ Fri, 10 Aug 2018 01:50:47: #1 Redundant rate of treatment: 0.61 INFO @ Fri, 10 Aug 2018 01:50:47: #1 finished! INFO @ Fri, 10 Aug 2018 01:50:47: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 01:50:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 01:50:47: #2 number of paired peaks: 1087 INFO @ Fri, 10 Aug 2018 01:50:47: start model_add_line... INFO @ Fri, 10 Aug 2018 01:50:47: start X-correlation... INFO @ Fri, 10 Aug 2018 01:50:47: end of X-cor INFO @ Fri, 10 Aug 2018 01:50:47: #2 finished! INFO @ Fri, 10 Aug 2018 01:50:47: #2 predicted fragment length is 1 bps INFO @ Fri, 10 Aug 2018 01:50:47: #2 alternative fragment length(s) may be 1,82,103,125 bps INFO @ Fri, 10 Aug 2018 01:50:47: #2.2 Generate R script for model : SRX2198707.10_model.r INFO @ Fri, 10 Aug 2018 01:50:47: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 01:50:47: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 01:50:47: #1 total tags in treatment: 2486516 INFO @ Fri, 10 Aug 2018 01:50:47: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 01:50:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) WARNING @ Fri, 10 Aug 2018 01:50:47: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 01:50:47: #2 You may need to consider one of the other alternative d(s): 1,82,103,125 WARNING @ Fri, 10 Aug 2018 01:50:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 01:50:47: #3 Call peaks... INFO @ Fri, 10 Aug 2018 01:50:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 01:50:47: #1 tags after filtering in treatment: 977823 INFO @ Fri, 10 Aug 2018 01:50:47: #1 Redundant rate of treatment: 0.61 INFO @ Fri, 10 Aug 2018 01:50:47: #1 finished! INFO @ Fri, 10 Aug 2018 01:50:47: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 01:50:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 01:50:47: #2 number of paired peaks: 1087 INFO @ Fri, 10 Aug 2018 01:50:47: start model_add_line... INFO @ Fri, 10 Aug 2018 01:50:47: start X-correlation... INFO @ Fri, 10 Aug 2018 01:50:47: end of X-cor INFO @ Fri, 10 Aug 2018 01:50:47: #2 finished! INFO @ Fri, 10 Aug 2018 01:50:47: #2 predicted fragment length is 1 bps INFO @ Fri, 10 Aug 2018 01:50:47: #2 alternative fragment length(s) may be 1,82,103,125 bps INFO @ Fri, 10 Aug 2018 01:50:47: #2.2 Generate R script for model : SRX2198707.20_model.r WARNING @ Fri, 10 Aug 2018 01:50:47: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 01:50:47: #2 You may need to consider one of the other alternative d(s): 1,82,103,125 WARNING @ Fri, 10 Aug 2018 01:50:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 01:50:47: #3 Call peaks... INFO @ Fri, 10 Aug 2018 01:50:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 01:50:49: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 01:50:49: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 01:50:49: #4 Write output xls file... SRX2198707.10_peaks.xls INFO @ Fri, 10 Aug 2018 01:50:49: #4 Write peak in narrowPeak format file... SRX2198707.10_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 01:50:49: #4 Write summits bed file... SRX2198707.10_summits.bed INFO @ Fri, 10 Aug 2018 01:50:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 01:50:50: #4 Write output xls file... SRX2198707.20_peaks.xls INFO @ Fri, 10 Aug 2018 01:50:50: #4 Write peak in narrowPeak format file... SRX2198707.20_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 01:50:50: #4 Write summits bed file... SRX2198707.20_summits.bed INFO @ Fri, 10 Aug 2018 01:50:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 01:50:50: 5000000 INFO @ Fri, 10 Aug 2018 01:50:51: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 01:50:51: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 01:50:51: #1 total tags in treatment: 2486516 INFO @ Fri, 10 Aug 2018 01:50:51: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 01:50:51: #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 01:50:51: #1 tags after filtering in treatment: 977823 INFO @ Fri, 10 Aug 2018 01:50:51: #1 Redundant rate of treatment: 0.61 INFO @ Fri, 10 Aug 2018 01:50:51: #1 finished! INFO @ Fri, 10 Aug 2018 01:50:51: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 01:50:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 01:50:51: #2 number of paired peaks: 1087 INFO @ Fri, 10 Aug 2018 01:50:51: start model_add_line... INFO @ Fri, 10 Aug 2018 01:50:51: start X-correlation... INFO @ Fri, 10 Aug 2018 01:50:51: end of X-cor INFO @ Fri, 10 Aug 2018 01:50:51: #2 finished! INFO @ Fri, 10 Aug 2018 01:50:51: #2 predicted fragment length is 1 bps INFO @ Fri, 10 Aug 2018 01:50:51: #2 alternative fragment length(s) may be 1,82,103,125 bps INFO @ Fri, 10 Aug 2018 01:50:51: #2.2 Generate R script for model : SRX2198707.05_model.r WARNING @ Fri, 10 Aug 2018 01:50:51: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 01:50:51: #2 You may need to consider one of the other alternative d(s): 1,82,103,125 WARNING @ Fri, 10 Aug 2018 01:50:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 01:50:51: #3 Call peaks... INFO @ Fri, 10 Aug 2018 01:50:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 01:50:53: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 01:50:54: #4 Write output xls file... SRX2198707.05_peaks.xls INFO @ Fri, 10 Aug 2018 01:50:54: #4 Write peak in narrowPeak format file... SRX2198707.05_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 01:50:54: #4 Write summits bed file... SRX2198707.05_summits.bed INFO @ Fri, 10 Aug 2018 01:50:54: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling