Job ID = 2006302 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,602,522 reads read : 1,602,522 reads written : 1,602,522 spots read : 1,525,220 reads read : 1,525,220 reads written : 1,525,220 spots read : 1,503,655 reads read : 1,503,655 reads written : 1,503,655 spots read : 1,594,756 reads read : 1,594,756 reads written : 1,594,756 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529466.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529467.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529468.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529469.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: 00:05:34 6226153 reads; of these: 6226153 (100.00%) were unpaired; of these: 282874 (4.54%) aligned 0 times 4870706 (78.23%) aligned exactly 1 time 1072573 (17.23%) aligned >1 times 95.46% overall alignment rate Time searching: 00:05:34 Overall time: 00:05:34 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_rmdupse_core] 5877449 / 5943279 = 0.9889 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 15:37:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.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 15:37:07: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:37:07: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:37:08: #1 tag size is determined as 128 bps INFO @ Fri, 05 Jul 2019 15:37:08: #1 tag size = 128 INFO @ Fri, 05 Jul 2019 15:37:08: #1 total tags in treatment: 65830 INFO @ Fri, 05 Jul 2019 15:37:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:37:08: #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 15:37:08: #1 tags after filtering in treatment: 65830 INFO @ Fri, 05 Jul 2019 15:37:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:37:08: #1 finished! INFO @ Fri, 05 Jul 2019 15:37:08: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:37:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:37:08: #2 number of paired peaks: 324 WARNING @ Fri, 05 Jul 2019 15:37:08: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Fri, 05 Jul 2019 15:37:08: start model_add_line... INFO @ Fri, 05 Jul 2019 15:37:08: start X-correlation... INFO @ Fri, 05 Jul 2019 15:37:08: end of X-cor INFO @ Fri, 05 Jul 2019 15:37:08: #2 finished! INFO @ Fri, 05 Jul 2019 15:37:08: #2 predicted fragment length is 122 bps INFO @ Fri, 05 Jul 2019 15:37:08: #2 alternative fragment length(s) may be 40,90,122,148,185,226,253,402,437,463,489,516,554 bps INFO @ Fri, 05 Jul 2019 15:37:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.05_model.r WARNING @ Fri, 05 Jul 2019 15:37:08: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:37:08: #2 You may need to consider one of the other alternative d(s): 40,90,122,148,185,226,253,402,437,463,489,516,554 WARNING @ Fri, 05 Jul 2019 15:37:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 15:37:08: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:37:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:37:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:37:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.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 15:37:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:37:08: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:37:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:37:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:37:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.05_summits.bed INFO @ Fri, 05 Jul 2019 15:37:08: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:37:09: #1 tag size is determined as 128 bps INFO @ Fri, 05 Jul 2019 15:37:09: #1 tag size = 128 INFO @ Fri, 05 Jul 2019 15:37:09: #1 total tags in treatment: 65830 INFO @ Fri, 05 Jul 2019 15:37:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:37:09: #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 15:37:09: #1 tags after filtering in treatment: 65830 INFO @ Fri, 05 Jul 2019 15:37:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:37:09: #1 finished! INFO @ Fri, 05 Jul 2019 15:37:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:37:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:37:09: #2 number of paired peaks: 324 WARNING @ Fri, 05 Jul 2019 15:37:09: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Fri, 05 Jul 2019 15:37:09: start model_add_line... INFO @ Fri, 05 Jul 2019 15:37:09: start X-correlation... INFO @ Fri, 05 Jul 2019 15:37:09: end of X-cor INFO @ Fri, 05 Jul 2019 15:37:09: #2 finished! INFO @ Fri, 05 Jul 2019 15:37:09: #2 predicted fragment length is 122 bps INFO @ Fri, 05 Jul 2019 15:37:09: #2 alternative fragment length(s) may be 40,90,122,148,185,226,253,402,437,463,489,516,554 bps INFO @ Fri, 05 Jul 2019 15:37:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.10_model.r WARNING @ Fri, 05 Jul 2019 15:37:09: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:37:09: #2 You may need to consider one of the other alternative d(s): 40,90,122,148,185,226,253,402,437,463,489,516,554 WARNING @ Fri, 05 Jul 2019 15:37:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 15:37:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:37:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:37:09: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 15:37:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:37:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:37:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.10_summits.bed INFO @ Fri, 05 Jul 2019 15:37:09: Done! INFO @ Fri, 05 Jul 2019 15:37:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.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 15:37:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:37:09: #1 read treatment tags... pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 15:37:10: #1 tag size is determined as 128 bps INFO @ Fri, 05 Jul 2019 15:37:10: #1 tag size = 128 INFO @ Fri, 05 Jul 2019 15:37:10: #1 total tags in treatment: 65830 INFO @ Fri, 05 Jul 2019 15:37:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:37:10: #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 15:37:10: #1 tags after filtering in treatment: 65830 INFO @ Fri, 05 Jul 2019 15:37:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:37:10: #1 finished! INFO @ Fri, 05 Jul 2019 15:37:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:37:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:37:10: #2 number of paired peaks: 324 WARNING @ Fri, 05 Jul 2019 15:37:10: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Fri, 05 Jul 2019 15:37:10: start model_add_line... INFO @ Fri, 05 Jul 2019 15:37:10: start X-correlation... INFO @ Fri, 05 Jul 2019 15:37:10: end of X-cor INFO @ Fri, 05 Jul 2019 15:37:10: #2 finished! INFO @ Fri, 05 Jul 2019 15:37:10: #2 predicted fragment length is 122 bps INFO @ Fri, 05 Jul 2019 15:37:10: #2 alternative fragment length(s) may be 40,90,122,148,185,226,253,402,437,463,489,516,554 bps INFO @ Fri, 05 Jul 2019 15:37:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.20_model.r WARNING @ Fri, 05 Jul 2019 15:37:10: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:37:10: #2 You may need to consider one of the other alternative d(s): 40,90,122,148,185,226,253,402,437,463,489,516,554 WARNING @ Fri, 05 Jul 2019 15:37:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 15:37:10: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:37:10: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 15:37:10: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:37:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:37:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:37:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548150/ERX2548150.20_summits.bed INFO @ Fri, 05 Jul 2019 15:37:11: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling