Job ID = 2007859 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 175,829 reads read : 351,658 reads written : 351,658 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:00:06 175829 reads; of these: 175829 (100.00%) were paired; of these: 18129 (10.31%) aligned concordantly 0 times 141451 (80.45%) aligned concordantly exactly 1 time 16249 (9.24%) aligned concordantly >1 times ---- 18129 pairs aligned concordantly 0 times; of these: 3942 (21.74%) aligned discordantly 1 time ---- 14187 pairs aligned 0 times concordantly or discordantly; of these: 28374 mates make up the pairs; of these: 25862 (91.15%) aligned 0 times 1342 (4.73%) aligned exactly 1 time 1170 (4.12%) aligned >1 times 92.65% overall alignment rate Time searching: 00:00:06 Overall time: 00:00:06 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] 549 / 161240 = 0.0034 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, 05 Jul 2019 16:35:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.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, 05 Jul 2019 16:35:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:35:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:35:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.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, 05 Jul 2019 16:35:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:35:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:35:25: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:35:25: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:35:25: #1 total tags in treatment: 157160 INFO @ Fri, 05 Jul 2019 16:35:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:35:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:35:25: #1 tags after filtering in treatment: 155857 INFO @ Fri, 05 Jul 2019 16:35:25: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:35:25: #1 finished! INFO @ Fri, 05 Jul 2019 16:35:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:35:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:35:26: #2 number of paired peaks: 169 WARNING @ Fri, 05 Jul 2019 16:35:26: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Fri, 05 Jul 2019 16:35:26: start model_add_line... INFO @ Fri, 05 Jul 2019 16:35:26: start X-correlation... INFO @ Fri, 05 Jul 2019 16:35:26: end of X-cor INFO @ Fri, 05 Jul 2019 16:35:26: #2 finished! INFO @ Fri, 05 Jul 2019 16:35:26: #2 predicted fragment length is 154 bps INFO @ Fri, 05 Jul 2019 16:35:26: #2 alternative fragment length(s) may be 4,32,59,74,95,103,154,176,197,221,246,261,284,302,337,363,383,409,422,443,492,528,566 bps INFO @ Fri, 05 Jul 2019 16:35:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.05_model.r INFO @ Fri, 05 Jul 2019 16:35:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:35:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:35:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.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, 05 Jul 2019 16:35:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:35:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:35:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:35:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:35:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:35:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.05_summits.bed INFO @ Fri, 05 Jul 2019 16:35:26: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 6 millis INFO @ Fri, 05 Jul 2019 16:35:26: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:35:26: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:35:26: #1 total tags in treatment: 157160 INFO @ Fri, 05 Jul 2019 16:35:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:35:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:35:26: #1 tags after filtering in treatment: 155857 INFO @ Fri, 05 Jul 2019 16:35:26: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:35:26: #1 finished! INFO @ Fri, 05 Jul 2019 16:35:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:35:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:35:26: #2 number of paired peaks: 169 WARNING @ Fri, 05 Jul 2019 16:35:26: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Fri, 05 Jul 2019 16:35:26: start model_add_line... INFO @ Fri, 05 Jul 2019 16:35:26: start X-correlation... INFO @ Fri, 05 Jul 2019 16:35:27: end of X-cor INFO @ Fri, 05 Jul 2019 16:35:27: #2 finished! INFO @ Fri, 05 Jul 2019 16:35:27: #2 predicted fragment length is 154 bps INFO @ Fri, 05 Jul 2019 16:35:27: #2 alternative fragment length(s) may be 4,32,59,74,95,103,154,176,197,221,246,261,284,302,337,363,383,409,422,443,492,528,566 bps INFO @ Fri, 05 Jul 2019 16:35:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.10_model.r INFO @ Fri, 05 Jul 2019 16:35:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:35:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:35:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:35:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:35:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:35:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.10_summits.bed INFO @ Fri, 05 Jul 2019 16:35:27: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:35:28: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:35:28: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:35:28: #1 total tags in treatment: 157160 INFO @ Fri, 05 Jul 2019 16:35:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:35:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:35:28: #1 tags after filtering in treatment: 155857 INFO @ Fri, 05 Jul 2019 16:35:28: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:35:28: #1 finished! INFO @ Fri, 05 Jul 2019 16:35:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:35:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:35:28: #2 number of paired peaks: 169 WARNING @ Fri, 05 Jul 2019 16:35:28: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Fri, 05 Jul 2019 16:35:28: start model_add_line... INFO @ Fri, 05 Jul 2019 16:35:28: start X-correlation... INFO @ Fri, 05 Jul 2019 16:35:28: end of X-cor INFO @ Fri, 05 Jul 2019 16:35:28: #2 finished! INFO @ Fri, 05 Jul 2019 16:35:28: #2 predicted fragment length is 154 bps INFO @ Fri, 05 Jul 2019 16:35:28: #2 alternative fragment length(s) may be 4,32,59,74,95,103,154,176,197,221,246,261,284,302,337,363,383,409,422,443,492,528,566 bps INFO @ Fri, 05 Jul 2019 16:35:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.20_model.r INFO @ Fri, 05 Jul 2019 16:35:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:35:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:35:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:35:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:35:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:35:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462400/ERX462400.20_summits.bed INFO @ Fri, 05 Jul 2019 16:35:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling