Job ID = 2008290 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,658,249 reads read : 23,316,498 reads written : 23,316,498 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR628934.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: 00:07:39 11658249 reads; of these: 11658249 (100.00%) were paired; of these: 1316480 (11.29%) aligned concordantly 0 times 9708393 (83.27%) aligned concordantly exactly 1 time 633376 (5.43%) aligned concordantly >1 times ---- 1316480 pairs aligned concordantly 0 times; of these: 42634 (3.24%) aligned discordantly 1 time ---- 1273846 pairs aligned 0 times concordantly or discordantly; of these: 2547692 mates make up the pairs; of these: 2510206 (98.53%) aligned 0 times 26233 (1.03%) aligned exactly 1 time 11253 (0.44%) aligned >1 times 89.23% overall alignment rate Time searching: 00:07:39 Overall time: 00:07:39 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_sort_core] merging from 8 files... [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] 9599154 / 10377955 = 0.9250 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 18:43:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.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 18:43:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:43:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:43:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.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 18:43:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:43:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:44:00: 1000000 INFO @ Fri, 05 Jul 2019 18:44:01: 1000000 INFO @ Fri, 05 Jul 2019 18:44:04: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:44:04: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:44:04: #1 total tags in treatment: 756019 INFO @ Fri, 05 Jul 2019 18:44:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:44:04: #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 18:44:04: #1 tags after filtering in treatment: 621979 INFO @ Fri, 05 Jul 2019 18:44:04: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 05 Jul 2019 18:44:04: #1 finished! INFO @ Fri, 05 Jul 2019 18:44:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:44:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:44:04: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:44:04: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:44:04: #1 total tags in treatment: 756019 INFO @ Fri, 05 Jul 2019 18:44:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:44:04: #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 18:44:04: #1 tags after filtering in treatment: 621979 INFO @ Fri, 05 Jul 2019 18:44:04: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 05 Jul 2019 18:44:04: #1 finished! INFO @ Fri, 05 Jul 2019 18:44:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:44:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:44:04: #2 number of paired peaks: 109 WARNING @ Fri, 05 Jul 2019 18:44:04: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Fri, 05 Jul 2019 18:44:04: start model_add_line... INFO @ Fri, 05 Jul 2019 18:44:04: start X-correlation... INFO @ Fri, 05 Jul 2019 18:44:04: end of X-cor INFO @ Fri, 05 Jul 2019 18:44:04: #2 finished! INFO @ Fri, 05 Jul 2019 18:44:04: #2 predicted fragment length is 177 bps INFO @ Fri, 05 Jul 2019 18:44:04: #2 alternative fragment length(s) may be 94,177,275,359,376,437,460,542,560,576 bps INFO @ Fri, 05 Jul 2019 18:44:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.05_model.r INFO @ Fri, 05 Jul 2019 18:44:04: #2 number of paired peaks: 109 WARNING @ Fri, 05 Jul 2019 18:44:04: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Fri, 05 Jul 2019 18:44:04: start model_add_line... INFO @ Fri, 05 Jul 2019 18:44:04: start X-correlation... INFO @ Fri, 05 Jul 2019 18:44:04: end of X-cor INFO @ Fri, 05 Jul 2019 18:44:04: #2 finished! INFO @ Fri, 05 Jul 2019 18:44:04: #2 predicted fragment length is 177 bps INFO @ Fri, 05 Jul 2019 18:44:04: #2 alternative fragment length(s) may be 94,177,275,359,376,437,460,542,560,576 bps INFO @ Fri, 05 Jul 2019 18:44:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.10_model.r INFO @ Fri, 05 Jul 2019 18:44:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:44:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:44:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:44:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:44:30: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:44:30: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:44:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.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 18:44:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:44:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:44:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:44:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:44:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.10_summits.bed INFO @ Fri, 05 Jul 2019 18:44:32: Done! INFO @ Fri, 05 Jul 2019 18:44:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:44:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:44:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.05_summits.bed INFO @ Fri, 05 Jul 2019 18:44:33: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (13 records, 4 fields): 3 millis pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (85 records, 4 fields): 4 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:44:38: 1000000 INFO @ Fri, 05 Jul 2019 18:44:42: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:44:42: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:44:42: #1 total tags in treatment: 756019 INFO @ Fri, 05 Jul 2019 18:44:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:44:42: #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 18:44:42: #1 tags after filtering in treatment: 621979 INFO @ Fri, 05 Jul 2019 18:44:42: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 05 Jul 2019 18:44:42: #1 finished! INFO @ Fri, 05 Jul 2019 18:44:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:44:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:44:42: #2 number of paired peaks: 109 WARNING @ Fri, 05 Jul 2019 18:44:42: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Fri, 05 Jul 2019 18:44:42: start model_add_line... INFO @ Fri, 05 Jul 2019 18:44:42: start X-correlation... INFO @ Fri, 05 Jul 2019 18:44:42: end of X-cor INFO @ Fri, 05 Jul 2019 18:44:42: #2 finished! INFO @ Fri, 05 Jul 2019 18:44:42: #2 predicted fragment length is 177 bps INFO @ Fri, 05 Jul 2019 18:44:42: #2 alternative fragment length(s) may be 94,177,275,359,376,437,460,542,560,576 bps INFO @ Fri, 05 Jul 2019 18:44:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.20_model.r INFO @ Fri, 05 Jul 2019 18:44:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:44:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:44:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:44:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:44:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:44:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585802/ERX585802.20_summits.bed INFO @ Fri, 05 Jul 2019 18:44:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。