Job ID = 2008347 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,455,031 reads read : 12,910,062 reads written : 12,910,062 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR628982.sra.cache’: 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: 00:05:13 6455031 reads; of these: 6455031 (100.00%) were paired; of these: 378816 (5.87%) aligned concordantly 0 times 5626740 (87.17%) aligned concordantly exactly 1 time 449475 (6.96%) aligned concordantly >1 times ---- 378816 pairs aligned concordantly 0 times; of these: 52326 (13.81%) aligned discordantly 1 time ---- 326490 pairs aligned 0 times concordantly or discordantly; of these: 652980 mates make up the pairs; of these: 617100 (94.51%) aligned 0 times 22780 (3.49%) aligned exactly 1 time 13100 (2.01%) aligned >1 times 95.22% overall alignment rate Time searching: 00:05:13 Overall time: 00:05:13 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] 5438710 / 6125575 = 0.8879 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 18:50:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.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 18:50:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:50:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:50:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.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 18:50:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:50:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:50:32: 1000000 INFO @ Fri, 05 Jul 2019 18:50:32: 1000000 INFO @ Fri, 05 Jul 2019 18:50:35: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:50:35: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:50:35: #1 total tags in treatment: 648613 INFO @ Fri, 05 Jul 2019 18:50:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:50:35: #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 18:50:35: #1 tags after filtering in treatment: 527602 INFO @ Fri, 05 Jul 2019 18:50:35: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 05 Jul 2019 18:50:35: #1 finished! INFO @ Fri, 05 Jul 2019 18:50:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:50:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:50:35: #2 number of paired peaks: 192 WARNING @ Fri, 05 Jul 2019 18:50:35: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Fri, 05 Jul 2019 18:50:35: start model_add_line... INFO @ Fri, 05 Jul 2019 18:50:35: start X-correlation... INFO @ Fri, 05 Jul 2019 18:50:35: end of X-cor INFO @ Fri, 05 Jul 2019 18:50:35: #2 finished! INFO @ Fri, 05 Jul 2019 18:50:35: #2 predicted fragment length is 180 bps INFO @ Fri, 05 Jul 2019 18:50:35: #2 alternative fragment length(s) may be 0,101,180,260,347,438,554 bps INFO @ Fri, 05 Jul 2019 18:50:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.05_model.r INFO @ Fri, 05 Jul 2019 18:50:35: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:50:35: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:50:35: #1 total tags in treatment: 648613 INFO @ Fri, 05 Jul 2019 18:50:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:50:35: #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 18:50:35: #1 tags after filtering in treatment: 527602 INFO @ Fri, 05 Jul 2019 18:50:35: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 05 Jul 2019 18:50:35: #1 finished! INFO @ Fri, 05 Jul 2019 18:50:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:50:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:50:36: #2 number of paired peaks: 192 WARNING @ Fri, 05 Jul 2019 18:50:36: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Fri, 05 Jul 2019 18:50:36: start model_add_line... INFO @ Fri, 05 Jul 2019 18:50:36: start X-correlation... INFO @ Fri, 05 Jul 2019 18:50:36: end of X-cor INFO @ Fri, 05 Jul 2019 18:50:36: #2 finished! INFO @ Fri, 05 Jul 2019 18:50:36: #2 predicted fragment length is 180 bps INFO @ Fri, 05 Jul 2019 18:50:36: #2 alternative fragment length(s) may be 0,101,180,260,347,438,554 bps INFO @ Fri, 05 Jul 2019 18:50:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.10_model.r INFO @ Fri, 05 Jul 2019 18:50:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:50:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:50:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:50:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:50:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:50:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:50:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:50:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:50:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.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 18:50:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:50:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:50:53: 1000000 INFO @ Fri, 05 Jul 2019 18:50:56: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:50:56: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:50:56: #1 total tags in treatment: 648613 INFO @ Fri, 05 Jul 2019 18:50:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:50:56: #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 18:50:56: #1 tags after filtering in treatment: 527602 INFO @ Fri, 05 Jul 2019 18:50:56: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 05 Jul 2019 18:50:56: #1 finished! INFO @ Fri, 05 Jul 2019 18:50:56: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:50:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:50:56: #2 number of paired peaks: 192 WARNING @ Fri, 05 Jul 2019 18:50:56: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Fri, 05 Jul 2019 18:50:56: start model_add_line... INFO @ Fri, 05 Jul 2019 18:50:56: start X-correlation... INFO @ Fri, 05 Jul 2019 18:50:56: end of X-cor INFO @ Fri, 05 Jul 2019 18:50:56: #2 finished! INFO @ Fri, 05 Jul 2019 18:50:56: #2 predicted fragment length is 180 bps INFO @ Fri, 05 Jul 2019 18:50:56: #2 alternative fragment length(s) may be 0,101,180,260,347,438,554 bps INFO @ Fri, 05 Jul 2019 18:50:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.20_model.r INFO @ Fri, 05 Jul 2019 18:51:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:51:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:51:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.10_summits.bed INFO @ Fri, 05 Jul 2019 18:51:01: Done! INFO @ Fri, 05 Jul 2019 18:51:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.05_summits.bed INFO @ Fri, 05 Jul 2019 18:51:01: Done! INFO @ Fri, 05 Jul 2019 18:51:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:51:01: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (28 records, 4 fields): 1 millis pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (109 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 18:51:02: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:51:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:51:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:51:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585851/ERX585851.20_summits.bed INFO @ Fri, 05 Jul 2019 18:51:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。