Job ID = 2007995 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,725,767 reads read : 3,451,534 reads written : 3,451,534 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: 00:04:32 1725767 reads; of these: 1725767 (100.00%) were paired; of these: 139628 (8.09%) aligned concordantly 0 times 1449521 (83.99%) aligned concordantly exactly 1 time 136618 (7.92%) aligned concordantly >1 times ---- 139628 pairs aligned concordantly 0 times; of these: 36928 (26.45%) aligned discordantly 1 time ---- 102700 pairs aligned 0 times concordantly or discordantly; of these: 205400 mates make up the pairs; of these: 176444 (85.90%) aligned 0 times 18872 (9.19%) aligned exactly 1 time 10084 (4.91%) aligned >1 times 94.89% overall alignment rate Time searching: 00:04:32 Overall time: 00:04:32 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] 90731 / 1612861 = 0.0563 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 17:09:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.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 17:09:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:09:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:09:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.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 17:09:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:09:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:09:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.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 17:09:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:09:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:09:25: 1000000 INFO @ Fri, 05 Jul 2019 17:09:26: 1000000 INFO @ Fri, 05 Jul 2019 17:09:27: 1000000 INFO @ Fri, 05 Jul 2019 17:09:37: 2000000 INFO @ Fri, 05 Jul 2019 17:09:38: 2000000 INFO @ Fri, 05 Jul 2019 17:09:41: 2000000 INFO @ Fri, 05 Jul 2019 17:09:48: 3000000 INFO @ Fri, 05 Jul 2019 17:09:49: 3000000 INFO @ Fri, 05 Jul 2019 17:09:49: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:09:49: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:09:49: #1 total tags in treatment: 1496168 INFO @ Fri, 05 Jul 2019 17:09:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:09:49: #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 17:09:49: #1 tags after filtering in treatment: 1423426 INFO @ Fri, 05 Jul 2019 17:09:49: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:09:49: #1 finished! INFO @ Fri, 05 Jul 2019 17:09:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:09:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:09:49: #2 number of paired peaks: 153 WARNING @ Fri, 05 Jul 2019 17:09:49: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Fri, 05 Jul 2019 17:09:49: start model_add_line... INFO @ Fri, 05 Jul 2019 17:09:49: start X-correlation... INFO @ Fri, 05 Jul 2019 17:09:49: end of X-cor INFO @ Fri, 05 Jul 2019 17:09:49: #2 finished! INFO @ Fri, 05 Jul 2019 17:09:49: #2 predicted fragment length is 218 bps INFO @ Fri, 05 Jul 2019 17:09:49: #2 alternative fragment length(s) may be 1,28,69,91,117,137,152,187,218,262,291,296,327,354,371,389,405,411,446,475,490,519,571,594 bps INFO @ Fri, 05 Jul 2019 17:09:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.10_model.r INFO @ Fri, 05 Jul 2019 17:09:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:09:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:09:50: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:09:50: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:09:50: #1 total tags in treatment: 1496168 INFO @ Fri, 05 Jul 2019 17:09:50: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:09:50: #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 17:09:50: #1 tags after filtering in treatment: 1423426 INFO @ Fri, 05 Jul 2019 17:09:50: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:09:50: #1 finished! INFO @ Fri, 05 Jul 2019 17:09:50: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:09:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:09:50: #2 number of paired peaks: 153 WARNING @ Fri, 05 Jul 2019 17:09:50: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Fri, 05 Jul 2019 17:09:50: start model_add_line... INFO @ Fri, 05 Jul 2019 17:09:50: start X-correlation... INFO @ Fri, 05 Jul 2019 17:09:50: end of X-cor INFO @ Fri, 05 Jul 2019 17:09:50: #2 finished! INFO @ Fri, 05 Jul 2019 17:09:50: #2 predicted fragment length is 218 bps INFO @ Fri, 05 Jul 2019 17:09:50: #2 alternative fragment length(s) may be 1,28,69,91,117,137,152,187,218,262,291,296,327,354,371,389,405,411,446,475,490,519,571,594 bps INFO @ Fri, 05 Jul 2019 17:09:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.20_model.r INFO @ Fri, 05 Jul 2019 17:09:50: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:09:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:09:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:09:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:09:54: 3000000 INFO @ Fri, 05 Jul 2019 17:09:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:09:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:09:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.10_summits.bed INFO @ Fri, 05 Jul 2019 17:09:55: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (22 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 17:09:56: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:09:56: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:09:56: #1 total tags in treatment: 1496168 INFO @ Fri, 05 Jul 2019 17:09:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:09:56: #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 17:09:56: #1 tags after filtering in treatment: 1423426 INFO @ Fri, 05 Jul 2019 17:09:56: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:09:56: #1 finished! INFO @ Fri, 05 Jul 2019 17:09:56: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:09:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:09:56: #2 number of paired peaks: 153 WARNING @ Fri, 05 Jul 2019 17:09:56: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Fri, 05 Jul 2019 17:09:56: start model_add_line... INFO @ Fri, 05 Jul 2019 17:09:56: start X-correlation... INFO @ Fri, 05 Jul 2019 17:09:56: end of X-cor INFO @ Fri, 05 Jul 2019 17:09:56: #2 finished! INFO @ Fri, 05 Jul 2019 17:09:56: #2 predicted fragment length is 218 bps INFO @ Fri, 05 Jul 2019 17:09:56: #2 alternative fragment length(s) may be 1,28,69,91,117,137,152,187,218,262,291,296,327,354,371,389,405,411,446,475,490,519,571,594 bps INFO @ Fri, 05 Jul 2019 17:09:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.05_model.r INFO @ Fri, 05 Jul 2019 17:09:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:09:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:09:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:09:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:09:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.20_summits.bed INFO @ Fri, 05 Jul 2019 17:09:56: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:10:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:10:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:10:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:10:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471785/ERX471785.05_summits.bed INFO @ Fri, 05 Jul 2019 17:10:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (63 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。