Job ID = 9162519 sra ファイルのダウンロード中... Completed: 336249K bytes transferred in 5 seconds (462630K bits/sec), in 1 file, 2 directories. 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 4856087 spots for /home/okishinya/chipatlas/results/sacCer3/SRX360916/SRR1003638.sra Written 4856087 spots total 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: 00:03:18 4856087 reads; of these: 4856087 (100.00%) were paired; of these: 3175419 (65.39%) aligned concordantly 0 times 1552688 (31.97%) aligned concordantly exactly 1 time 127980 (2.64%) aligned concordantly >1 times ---- 3175419 pairs aligned concordantly 0 times; of these: 17265 (0.54%) aligned discordantly 1 time ---- 3158154 pairs aligned 0 times concordantly or discordantly; of these: 6316308 mates make up the pairs; of these: 3724684 (58.97%) aligned 0 times 2374365 (37.59%) aligned exactly 1 time 217259 (3.44%) aligned >1 times 61.65% overall alignment rate Time searching: 00:03:18 Overall time: 00:03:18 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] 1651234 / 1692818 = 0.9754 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 @ Wed, 28 Jun 2017 08:06:03: # Command line: callpeak -t SRX360916.bam -f BAM -g 12100000 -n SRX360916.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX360916.10 # format = BAM # ChIP-seq file = ['SRX360916.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 @ Wed, 28 Jun 2017 08:06:03: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:06:03: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:06:03: # Command line: callpeak -t SRX360916.bam -f BAM -g 12100000 -n SRX360916.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX360916.20 # format = BAM # ChIP-seq file = ['SRX360916.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 @ Wed, 28 Jun 2017 08:06:03: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:06:03: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:06:03: # Command line: callpeak -t SRX360916.bam -f BAM -g 12100000 -n SRX360916.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX360916.05 # format = BAM # ChIP-seq file = ['SRX360916.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 @ Wed, 28 Jun 2017 08:06:03: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:06:03: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:06:08: 1000000 INFO @ Wed, 28 Jun 2017 08:06:08: 1000000 INFO @ Wed, 28 Jun 2017 08:06:08: 1000000 INFO @ Wed, 28 Jun 2017 08:06:13: 2000000 INFO @ Wed, 28 Jun 2017 08:06:13: 2000000 INFO @ Wed, 28 Jun 2017 08:06:14: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 28 Jun 2017 08:06:16: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 08:06:16: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 08:06:16: #1 total tags in treatment: 35442 INFO @ Wed, 28 Jun 2017 08:06:16: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:06:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 08:06:16: #1 tags after filtering in treatment: 32290 INFO @ Wed, 28 Jun 2017 08:06:16: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 28 Jun 2017 08:06:16: #1 finished! INFO @ Wed, 28 Jun 2017 08:06:16: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:06:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:06:16: #2 number of paired peaks: 258 WARNING @ Wed, 28 Jun 2017 08:06:16: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Wed, 28 Jun 2017 08:06:16: start model_add_line... INFO @ Wed, 28 Jun 2017 08:06:16: start X-correlation... INFO @ Wed, 28 Jun 2017 08:06:16: end of X-cor INFO @ Wed, 28 Jun 2017 08:06:16: #2 finished! INFO @ Wed, 28 Jun 2017 08:06:16: #2 predicted fragment length is 216 bps INFO @ Wed, 28 Jun 2017 08:06:16: #2 alternative fragment length(s) may be 37,216,233,270,293,312,368,554 bps INFO @ Wed, 28 Jun 2017 08:06:16: #2.2 Generate R script for model : SRX360916.05_model.r INFO @ Wed, 28 Jun 2017 08:06:16: #3 Call peaks... INFO @ Wed, 28 Jun 2017 08:06:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 08:06:16: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 08:06:16: #4 Write output xls file... SRX360916.05_peaks.xls INFO @ Wed, 28 Jun 2017 08:06:16: #4 Write peak in narrowPeak format file... SRX360916.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 08:06:16: #4 Write summits bed file... SRX360916.05_summits.bed INFO @ Wed, 28 Jun 2017 08:06:16: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (16 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 08:06:17: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 08:06:17: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 08:06:17: #1 total tags in treatment: 35442 INFO @ Wed, 28 Jun 2017 08:06:17: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:06:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 08:06:17: #1 tags after filtering in treatment: 32290 INFO @ Wed, 28 Jun 2017 08:06:17: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 28 Jun 2017 08:06:17: #1 finished! INFO @ Wed, 28 Jun 2017 08:06:17: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:06:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:06:17: #2 number of paired peaks: 258 WARNING @ Wed, 28 Jun 2017 08:06:17: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Wed, 28 Jun 2017 08:06:17: start model_add_line... INFO @ Wed, 28 Jun 2017 08:06:17: start X-correlation... INFO @ Wed, 28 Jun 2017 08:06:17: end of X-cor INFO @ Wed, 28 Jun 2017 08:06:17: #2 finished! INFO @ Wed, 28 Jun 2017 08:06:17: #2 predicted fragment length is 216 bps INFO @ Wed, 28 Jun 2017 08:06:17: #2 alternative fragment length(s) may be 37,216,233,270,293,312,368,554 bps INFO @ Wed, 28 Jun 2017 08:06:17: #2.2 Generate R script for model : SRX360916.20_model.r INFO @ Wed, 28 Jun 2017 08:06:17: #3 Call peaks... INFO @ Wed, 28 Jun 2017 08:06:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 08:06:17: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 08:06:17: #4 Write output xls file... SRX360916.20_peaks.xls BigWig に変換しました。 INFO @ Wed, 28 Jun 2017 08:06:17: #4 Write peak in narrowPeak format file... SRX360916.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 08:06:17: #4 Write summits bed file... SRX360916.20_summits.bed INFO @ Wed, 28 Jun 2017 08:06:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 08:06:17: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 08:06:17: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 08:06:17: #1 total tags in treatment: 35442 INFO @ Wed, 28 Jun 2017 08:06:17: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:06:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 08:06:17: #1 tags after filtering in treatment: 32290 INFO @ Wed, 28 Jun 2017 08:06:17: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 28 Jun 2017 08:06:17: #1 finished! INFO @ Wed, 28 Jun 2017 08:06:17: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:06:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:06:17: #2 number of paired peaks: 258 WARNING @ Wed, 28 Jun 2017 08:06:17: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Wed, 28 Jun 2017 08:06:17: start model_add_line... INFO @ Wed, 28 Jun 2017 08:06:17: start X-correlation... INFO @ Wed, 28 Jun 2017 08:06:17: end of X-cor INFO @ Wed, 28 Jun 2017 08:06:17: #2 finished! INFO @ Wed, 28 Jun 2017 08:06:17: #2 predicted fragment length is 216 bps INFO @ Wed, 28 Jun 2017 08:06:17: #2 alternative fragment length(s) may be 37,216,233,270,293,312,368,554 bps INFO @ Wed, 28 Jun 2017 08:06:17: #2.2 Generate R script for model : SRX360916.10_model.r INFO @ Wed, 28 Jun 2017 08:06:17: #3 Call peaks... INFO @ Wed, 28 Jun 2017 08:06:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 08:06:18: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 08:06:18: #4 Write output xls file... SRX360916.10_peaks.xls INFO @ Wed, 28 Jun 2017 08:06:18: #4 Write peak in narrowPeak format file... SRX360916.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 08:06:18: #4 Write summits bed file... SRX360916.10_summits.bed INFO @ Wed, 28 Jun 2017 08:06:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling