Job ID = 2008321 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,320,009 reads read : 4,640,018 reads written : 4,640,018 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR629032.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: 00:02:26 2320009 reads; of these: 2320009 (100.00%) were paired; of these: 181502 (7.82%) aligned concordantly 0 times 1999408 (86.18%) aligned concordantly exactly 1 time 139099 (6.00%) aligned concordantly >1 times ---- 181502 pairs aligned concordantly 0 times; of these: 8488 (4.68%) aligned discordantly 1 time ---- 173014 pairs aligned 0 times concordantly or discordantly; of these: 346028 mates make up the pairs; of these: 337081 (97.41%) aligned 0 times 6487 (1.87%) aligned exactly 1 time 2460 (0.71%) aligned >1 times 92.74% overall alignment rate Time searching: 00:02:26 Overall time: 00:02:26 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] 1988900 / 2145312 = 0.9271 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 18:35:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.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 18:35:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:35:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:35:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.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 18:35:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:35:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:35:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.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 18:35:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:35:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:35:59: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:35:59: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:35:59: #1 total tags in treatment: 152549 INFO @ Fri, 05 Jul 2019 18:35:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:35:59: #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 18:35:59: #1 tags after filtering in treatment: 140512 INFO @ Fri, 05 Jul 2019 18:35:59: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 05 Jul 2019 18:35:59: #1 finished! INFO @ Fri, 05 Jul 2019 18:35:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:35:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:35:59: #2 number of paired peaks: 175 WARNING @ Fri, 05 Jul 2019 18:35:59: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Fri, 05 Jul 2019 18:35:59: start model_add_line... INFO @ Fri, 05 Jul 2019 18:35:59: start X-correlation... INFO @ Fri, 05 Jul 2019 18:35:59: end of X-cor INFO @ Fri, 05 Jul 2019 18:35:59: #2 finished! INFO @ Fri, 05 Jul 2019 18:35:59: #2 predicted fragment length is 186 bps INFO @ Fri, 05 Jul 2019 18:35:59: #2 alternative fragment length(s) may be 0,17,52,161,186,220,248,281,308,333,352,374,472,514,534,561,574 bps INFO @ Fri, 05 Jul 2019 18:35:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.05_model.r INFO @ Fri, 05 Jul 2019 18:36:00: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:36:00: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:36:00: #1 total tags in treatment: 152549 INFO @ Fri, 05 Jul 2019 18:36:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:36:00: #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 18:36:00: #1 tags after filtering in treatment: 140512 INFO @ Fri, 05 Jul 2019 18:36:00: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 05 Jul 2019 18:36:00: #1 finished! INFO @ Fri, 05 Jul 2019 18:36:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:36:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:36:00: #2 number of paired peaks: 175 WARNING @ Fri, 05 Jul 2019 18:36:00: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Fri, 05 Jul 2019 18:36:00: start model_add_line... INFO @ Fri, 05 Jul 2019 18:36:00: start X-correlation... INFO @ Fri, 05 Jul 2019 18:36:00: end of X-cor INFO @ Fri, 05 Jul 2019 18:36:00: #2 finished! INFO @ Fri, 05 Jul 2019 18:36:00: #2 predicted fragment length is 186 bps INFO @ Fri, 05 Jul 2019 18:36:00: #2 alternative fragment length(s) may be 0,17,52,161,186,220,248,281,308,333,352,374,472,514,534,561,574 bps INFO @ Fri, 05 Jul 2019 18:36:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.10_model.r INFO @ Fri, 05 Jul 2019 18:36:00: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:36:00: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:36:00: #1 total tags in treatment: 152549 INFO @ Fri, 05 Jul 2019 18:36:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:36:00: #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 18:36:00: #1 tags after filtering in treatment: 140512 INFO @ Fri, 05 Jul 2019 18:36:00: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 05 Jul 2019 18:36:00: #1 finished! INFO @ Fri, 05 Jul 2019 18:36:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:36:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:36:00: #2 number of paired peaks: 175 WARNING @ Fri, 05 Jul 2019 18:36:00: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Fri, 05 Jul 2019 18:36:00: start model_add_line... INFO @ Fri, 05 Jul 2019 18:36:00: start X-correlation... INFO @ Fri, 05 Jul 2019 18:36:00: end of X-cor INFO @ Fri, 05 Jul 2019 18:36:00: #2 finished! INFO @ Fri, 05 Jul 2019 18:36:00: #2 predicted fragment length is 186 bps INFO @ Fri, 05 Jul 2019 18:36:00: #2 alternative fragment length(s) may be 0,17,52,161,186,220,248,281,308,333,352,374,472,514,534,561,574 bps INFO @ Fri, 05 Jul 2019 18:36:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.20_model.r BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 18:36:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:36:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:36:09: #3 Call peaks... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 18:36:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:36:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:36:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:36:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:36:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:36:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:36:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:36:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:36:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:36:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:36:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.20_summits.bed INFO @ Fri, 05 Jul 2019 18:36:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:36:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:36:23: Done! INFO @ Fri, 05 Jul 2019 18:36:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.10_summits.bed INFO @ Fri, 05 Jul 2019 18:36:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585830/ERX585830.05_summits.bed INFO @ Fri, 05 Jul 2019 18:36:23: Done! INFO @ Fri, 05 Jul 2019 18:36:23: Done! pass1 - making usageList (11 chroms): 2 millis pass1 - making usageList (0 chroms): 3 millis pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass2 - checking and writing primary data (22 records, 4 fields): 8 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling