Job ID = 2589159 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,650,007 reads read : 3,650,007 reads written : 3,650,007 spots read : 3,167,329 reads read : 3,167,329 reads written : 3,167,329 spots read : 5,439,564 reads read : 5,439,564 reads written : 5,439,564 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107540.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107541.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107542.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: 00:01:06 12256900 reads; of these: 12256900 (100.00%) were unpaired; of these: 11583321 (94.50%) aligned 0 times 595291 (4.86%) aligned exactly 1 time 78288 (0.64%) aligned >1 times 5.50% overall alignment rate Time searching: 00:01:06 Overall time: 00:01:06 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 22076 / 673579 = 0.0328 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 @ Mon, 12 Aug 2019 17:05:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 17:05:04: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:05:04: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:05:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 17:05:05: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:05:05: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:05:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 17:05:06: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:05:06: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:05:09: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:05:09: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:05:09: #1 total tags in treatment: 651503 INFO @ Mon, 12 Aug 2019 17:05:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:05:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:05:09: #1 tags after filtering in treatment: 651503 INFO @ Mon, 12 Aug 2019 17:05:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:05:09: #1 finished! INFO @ Mon, 12 Aug 2019 17:05:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:05:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:05:09: #2 number of paired peaks: 206 WARNING @ Mon, 12 Aug 2019 17:05:09: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Mon, 12 Aug 2019 17:05:09: start model_add_line... INFO @ Mon, 12 Aug 2019 17:05:09: start X-correlation... INFO @ Mon, 12 Aug 2019 17:05:09: end of X-cor INFO @ Mon, 12 Aug 2019 17:05:09: #2 finished! INFO @ Mon, 12 Aug 2019 17:05:09: #2 predicted fragment length is 41 bps INFO @ Mon, 12 Aug 2019 17:05:09: #2 alternative fragment length(s) may be 41,90,124,169,203,289,292,336,389,422,468,573 bps INFO @ Mon, 12 Aug 2019 17:05:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.05_model.r WARNING @ Mon, 12 Aug 2019 17:05:09: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:05:09: #2 You may need to consider one of the other alternative d(s): 41,90,124,169,203,289,292,336,389,422,468,573 WARNING @ Mon, 12 Aug 2019 17:05:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:05:09: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:05:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:05:10: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:05:10: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:05:10: #1 total tags in treatment: 651503 INFO @ Mon, 12 Aug 2019 17:05:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:05:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:05:10: #1 tags after filtering in treatment: 651503 INFO @ Mon, 12 Aug 2019 17:05:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:05:10: #1 finished! INFO @ Mon, 12 Aug 2019 17:05:10: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:05:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:05:10: #2 number of paired peaks: 206 WARNING @ Mon, 12 Aug 2019 17:05:10: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Mon, 12 Aug 2019 17:05:10: start model_add_line... INFO @ Mon, 12 Aug 2019 17:05:10: start X-correlation... INFO @ Mon, 12 Aug 2019 17:05:10: end of X-cor INFO @ Mon, 12 Aug 2019 17:05:10: #2 finished! INFO @ Mon, 12 Aug 2019 17:05:10: #2 predicted fragment length is 41 bps INFO @ Mon, 12 Aug 2019 17:05:10: #2 alternative fragment length(s) may be 41,90,124,169,203,289,292,336,389,422,468,573 bps INFO @ Mon, 12 Aug 2019 17:05:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.10_model.r WARNING @ Mon, 12 Aug 2019 17:05:10: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:05:10: #2 You may need to consider one of the other alternative d(s): 41,90,124,169,203,289,292,336,389,422,468,573 WARNING @ Mon, 12 Aug 2019 17:05:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:05:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:05:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:05:11: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:05:11: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:05:11: #1 total tags in treatment: 651503 INFO @ Mon, 12 Aug 2019 17:05:11: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:05:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:05:11: #1 tags after filtering in treatment: 651503 INFO @ Mon, 12 Aug 2019 17:05:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:05:11: #1 finished! INFO @ Mon, 12 Aug 2019 17:05:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:05:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:05:11: #2 number of paired peaks: 206 WARNING @ Mon, 12 Aug 2019 17:05:11: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Mon, 12 Aug 2019 17:05:11: start model_add_line... INFO @ Mon, 12 Aug 2019 17:05:11: start X-correlation... INFO @ Mon, 12 Aug 2019 17:05:11: end of X-cor INFO @ Mon, 12 Aug 2019 17:05:11: #2 finished! INFO @ Mon, 12 Aug 2019 17:05:11: #2 predicted fragment length is 41 bps INFO @ Mon, 12 Aug 2019 17:05:11: #2 alternative fragment length(s) may be 41,90,124,169,203,289,292,336,389,422,468,573 bps INFO @ Mon, 12 Aug 2019 17:05:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.20_model.r WARNING @ Mon, 12 Aug 2019 17:05:11: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:05:11: #2 You may need to consider one of the other alternative d(s): 41,90,124,169,203,289,292,336,389,422,468,573 WARNING @ Mon, 12 Aug 2019 17:05:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:05:11: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:05:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:05:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:05:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:05:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:05:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:05:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.05_summits.bed INFO @ Mon, 12 Aug 2019 17:05:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (29 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:05:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:05:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:05:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.10_summits.bed INFO @ Mon, 12 Aug 2019 17:05:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:05:13: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 12 Aug 2019 17:05:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:05:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:05:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043967/SRX043967.20_summits.bed INFO @ Mon, 12 Aug 2019 17:05:14: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。