Job ID = 2007905 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 181,775 reads read : 363,550 reads written : 363,550 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: 00:00:07 181775 reads; of these: 181775 (100.00%) were paired; of these: 24137 (13.28%) aligned concordantly 0 times 144236 (79.35%) aligned concordantly exactly 1 time 13402 (7.37%) aligned concordantly >1 times ---- 24137 pairs aligned concordantly 0 times; of these: 15437 (63.96%) aligned discordantly 1 time ---- 8700 pairs aligned 0 times concordantly or discordantly; of these: 17400 mates make up the pairs; of these: 10743 (61.74%) aligned 0 times 3211 (18.45%) aligned exactly 1 time 3446 (19.80%) aligned >1 times 97.04% overall alignment rate Time searching: 00:00:07 Overall time: 00:00:07 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] 646 / 170298 = 0.0038 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 16:39:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.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 16:39:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:39:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:39:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.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 16:39:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:39:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:39:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.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 16:39:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:39:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:39:58: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:39:58: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:39:58: #1 total tags in treatment: 157034 INFO @ Fri, 05 Jul 2019 16:39:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:39:58: #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 16:39:58: #1 tags after filtering in treatment: 155716 INFO @ Fri, 05 Jul 2019 16:39:58: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:39:58: #1 finished! INFO @ Fri, 05 Jul 2019 16:39:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:39:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:39:58: #2 number of paired peaks: 216 WARNING @ Fri, 05 Jul 2019 16:39:58: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Fri, 05 Jul 2019 16:39:58: start model_add_line... INFO @ Fri, 05 Jul 2019 16:39:58: start X-correlation... INFO @ Fri, 05 Jul 2019 16:39:58: end of X-cor INFO @ Fri, 05 Jul 2019 16:39:58: #2 finished! INFO @ Fri, 05 Jul 2019 16:39:58: #2 predicted fragment length is 257 bps INFO @ Fri, 05 Jul 2019 16:39:58: #2 alternative fragment length(s) may be 162,190,206,227,257 bps INFO @ Fri, 05 Jul 2019 16:39:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.05_model.r INFO @ Fri, 05 Jul 2019 16:39:58: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:39:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:39:59: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:39:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:39:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:39:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.05_summits.bed INFO @ Fri, 05 Jul 2019 16:39:59: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (129 records, 4 fields): 25 millis INFO @ Fri, 05 Jul 2019 16:39:59: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:39:59: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:39:59: #1 total tags in treatment: 157034 INFO @ Fri, 05 Jul 2019 16:39:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:39:59: #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 16:39:59: #1 tags after filtering in treatment: 155716 INFO @ Fri, 05 Jul 2019 16:39:59: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:39:59: #1 finished! INFO @ Fri, 05 Jul 2019 16:39:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:39:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:39:59: #2 number of paired peaks: 216 WARNING @ Fri, 05 Jul 2019 16:39:59: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Fri, 05 Jul 2019 16:39:59: start model_add_line... INFO @ Fri, 05 Jul 2019 16:39:59: start X-correlation... INFO @ Fri, 05 Jul 2019 16:40:00: end of X-cor INFO @ Fri, 05 Jul 2019 16:40:00: #2 finished! INFO @ Fri, 05 Jul 2019 16:40:00: #2 predicted fragment length is 257 bps INFO @ Fri, 05 Jul 2019 16:40:00: #2 alternative fragment length(s) may be 162,190,206,227,257 bps INFO @ Fri, 05 Jul 2019 16:40:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.10_model.r INFO @ Fri, 05 Jul 2019 16:40:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:40:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:40:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:40:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:40:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:40:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.10_summits.bed INFO @ Fri, 05 Jul 2019 16:40:00: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (43 records, 4 fields): 20 millis INFO @ Fri, 05 Jul 2019 16:40:00: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:40:00: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:40:00: #1 total tags in treatment: 157034 INFO @ Fri, 05 Jul 2019 16:40:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:40:00: #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 16:40:00: #1 tags after filtering in treatment: 155716 INFO @ Fri, 05 Jul 2019 16:40:00: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:40:00: #1 finished! INFO @ Fri, 05 Jul 2019 16:40:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:40:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:40:00: #2 number of paired peaks: 216 WARNING @ Fri, 05 Jul 2019 16:40:00: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Fri, 05 Jul 2019 16:40:00: start model_add_line... INFO @ Fri, 05 Jul 2019 16:40:00: start X-correlation... INFO @ Fri, 05 Jul 2019 16:40:00: end of X-cor INFO @ Fri, 05 Jul 2019 16:40:00: #2 finished! INFO @ Fri, 05 Jul 2019 16:40:00: #2 predicted fragment length is 257 bps INFO @ Fri, 05 Jul 2019 16:40:00: #2 alternative fragment length(s) may be 162,190,206,227,257 bps INFO @ Fri, 05 Jul 2019 16:40:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.20_model.r INFO @ Fri, 05 Jul 2019 16:40:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:40:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:40:01: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:40:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:40:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:40:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462436/ERX462436.20_summits.bed INFO @ Fri, 05 Jul 2019 16:40:01: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (11 records, 4 fields): 33 millis BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling CompletedMACS2peakCalling