Job ID = 2009998 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,435,511 reads read : 6,871,022 reads written : 6,871,022 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: 00:02:44 3435511 reads; of these: 3435511 (100.00%) were paired; of these: 462709 (13.47%) aligned concordantly 0 times 2511381 (73.10%) aligned concordantly exactly 1 time 461421 (13.43%) aligned concordantly >1 times ---- 462709 pairs aligned concordantly 0 times; of these: 34072 (7.36%) aligned discordantly 1 time ---- 428637 pairs aligned 0 times concordantly or discordantly; of these: 857274 mates make up the pairs; of these: 763065 (89.01%) aligned 0 times 58738 (6.85%) aligned exactly 1 time 35471 (4.14%) aligned >1 times 88.89% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:44 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] 197181 / 3000143 = 0.0657 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 20:52:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.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 20:52:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:52:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:52:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.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 20:52:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:52:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:52:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.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 20:52:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:52:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:52:21: 1000000 INFO @ Fri, 05 Jul 2019 20:52:23: 1000000 INFO @ Fri, 05 Jul 2019 20:52:24: 1000000 INFO @ Fri, 05 Jul 2019 20:52:28: 2000000 INFO @ Fri, 05 Jul 2019 20:52:31: 2000000 INFO @ Fri, 05 Jul 2019 20:52:32: 2000000 INFO @ Fri, 05 Jul 2019 20:52:35: 3000000 INFO @ Fri, 05 Jul 2019 20:52:39: 3000000 INFO @ Fri, 05 Jul 2019 20:52:40: 3000000 INFO @ Fri, 05 Jul 2019 20:52:43: 4000000 INFO @ Fri, 05 Jul 2019 20:52:47: 4000000 INFO @ Fri, 05 Jul 2019 20:52:49: 4000000 INFO @ Fri, 05 Jul 2019 20:52:50: 5000000 INFO @ Fri, 05 Jul 2019 20:52:55: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:52:55: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:52:55: #1 total tags in treatment: 2776441 INFO @ Fri, 05 Jul 2019 20:52:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:52:55: #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 20:52:55: #1 tags after filtering in treatment: 1331207 INFO @ Fri, 05 Jul 2019 20:52:55: #1 Redundant rate of treatment: 0.52 INFO @ Fri, 05 Jul 2019 20:52:55: #1 finished! INFO @ Fri, 05 Jul 2019 20:52:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:52:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:52:55: #2 number of paired peaks: 916 WARNING @ Fri, 05 Jul 2019 20:52:55: Fewer paired peaks (916) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 916 pairs to build model! INFO @ Fri, 05 Jul 2019 20:52:55: start model_add_line... INFO @ Fri, 05 Jul 2019 20:52:55: start X-correlation... INFO @ Fri, 05 Jul 2019 20:52:55: end of X-cor INFO @ Fri, 05 Jul 2019 20:52:55: #2 finished! INFO @ Fri, 05 Jul 2019 20:52:55: #2 predicted fragment length is 212 bps INFO @ Fri, 05 Jul 2019 20:52:55: #2 alternative fragment length(s) may be 0,145,148,180,212,241,259 bps INFO @ Fri, 05 Jul 2019 20:52:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.05_model.r INFO @ Fri, 05 Jul 2019 20:52:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:52:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:52:55: 5000000 INFO @ Fri, 05 Jul 2019 20:52:57: 5000000 INFO @ Fri, 05 Jul 2019 20:53:01: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:53:01: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:53:01: #1 total tags in treatment: 2776441 INFO @ Fri, 05 Jul 2019 20:53:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:53:01: #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 20:53:01: #1 tags after filtering in treatment: 1331207 INFO @ Fri, 05 Jul 2019 20:53:01: #1 Redundant rate of treatment: 0.52 INFO @ Fri, 05 Jul 2019 20:53:01: #1 finished! INFO @ Fri, 05 Jul 2019 20:53:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:53:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:53:01: #2 number of paired peaks: 916 WARNING @ Fri, 05 Jul 2019 20:53:01: Fewer paired peaks (916) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 916 pairs to build model! INFO @ Fri, 05 Jul 2019 20:53:01: start model_add_line... INFO @ Fri, 05 Jul 2019 20:53:01: start X-correlation... INFO @ Fri, 05 Jul 2019 20:53:01: end of X-cor INFO @ Fri, 05 Jul 2019 20:53:01: #2 finished! INFO @ Fri, 05 Jul 2019 20:53:01: #2 predicted fragment length is 212 bps INFO @ Fri, 05 Jul 2019 20:53:01: #2 alternative fragment length(s) may be 0,145,148,180,212,241,259 bps INFO @ Fri, 05 Jul 2019 20:53:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.10_model.r INFO @ Fri, 05 Jul 2019 20:53:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:53:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:53:02: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:53:02: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:53:02: #1 total tags in treatment: 2776441 INFO @ Fri, 05 Jul 2019 20:53:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:53:02: #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 20:53:02: #1 tags after filtering in treatment: 1331207 INFO @ Fri, 05 Jul 2019 20:53:02: #1 Redundant rate of treatment: 0.52 INFO @ Fri, 05 Jul 2019 20:53:02: #1 finished! INFO @ Fri, 05 Jul 2019 20:53:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:53:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:53:03: #2 number of paired peaks: 916 WARNING @ Fri, 05 Jul 2019 20:53:03: Fewer paired peaks (916) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 916 pairs to build model! INFO @ Fri, 05 Jul 2019 20:53:03: start model_add_line... INFO @ Fri, 05 Jul 2019 20:53:03: start X-correlation... INFO @ Fri, 05 Jul 2019 20:53:03: end of X-cor INFO @ Fri, 05 Jul 2019 20:53:03: #2 finished! INFO @ Fri, 05 Jul 2019 20:53:03: #2 predicted fragment length is 212 bps INFO @ Fri, 05 Jul 2019 20:53:03: #2 alternative fragment length(s) may be 0,145,148,180,212,241,259 bps INFO @ Fri, 05 Jul 2019 20:53:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.20_model.r INFO @ Fri, 05 Jul 2019 20:53:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:53:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:53:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:53:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.05_peaks.xls INFO @ Fri, 05 Jul 2019 20:53:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:53:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.05_summits.bed INFO @ Fri, 05 Jul 2019 20:53:05: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (571 records, 4 fields): 5 millis BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:53:09: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:53:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:53:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.10_peaks.xls INFO @ Fri, 05 Jul 2019 20:53:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:53:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.10_summits.bed INFO @ Fri, 05 Jul 2019 20:53:11: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (384 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:53:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.20_peaks.xls INFO @ Fri, 05 Jul 2019 20:53:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:53:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339861/SRX2339861.20_summits.bed INFO @ Fri, 05 Jul 2019 20:53:12: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (206 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。