Job ID = 2589856 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,201,747 reads read : 7,201,747 reads written : 7,201,747 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947489.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: 00:01:11 7201747 reads; of these: 7201747 (100.00%) were unpaired; of these: 183083 (2.54%) aligned 0 times 5947801 (82.59%) aligned exactly 1 time 1070863 (14.87%) aligned >1 times 97.46% overall alignment rate Time searching: 00:01:11 Overall time: 00:01:11 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] 819844 / 7018664 = 0.1168 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 18:39:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.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 18:39:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:39:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:39:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.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 18:39:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:39:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:39:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.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 18:39:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:39:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:39:40: 1000000 INFO @ Mon, 12 Aug 2019 18:39:40: 1000000 INFO @ Mon, 12 Aug 2019 18:39:41: 1000000 INFO @ Mon, 12 Aug 2019 18:39:45: 2000000 INFO @ Mon, 12 Aug 2019 18:39:47: 2000000 INFO @ Mon, 12 Aug 2019 18:39:48: 2000000 INFO @ Mon, 12 Aug 2019 18:39:51: 3000000 INFO @ Mon, 12 Aug 2019 18:39:53: 3000000 INFO @ Mon, 12 Aug 2019 18:39:54: 3000000 INFO @ Mon, 12 Aug 2019 18:39:57: 4000000 INFO @ Mon, 12 Aug 2019 18:39:59: 4000000 INFO @ Mon, 12 Aug 2019 18:40:00: 4000000 INFO @ Mon, 12 Aug 2019 18:40:03: 5000000 INFO @ Mon, 12 Aug 2019 18:40:06: 5000000 INFO @ Mon, 12 Aug 2019 18:40:06: 5000000 INFO @ Mon, 12 Aug 2019 18:40:09: 6000000 INFO @ Mon, 12 Aug 2019 18:40:10: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:40:10: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:40:10: #1 total tags in treatment: 6198820 INFO @ Mon, 12 Aug 2019 18:40:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:40:10: #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 18:40:10: #1 tags after filtering in treatment: 6198820 INFO @ Mon, 12 Aug 2019 18:40:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:40:10: #1 finished! INFO @ Mon, 12 Aug 2019 18:40:10: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:40:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:40:11: #2 number of paired peaks: 403 WARNING @ Mon, 12 Aug 2019 18:40:11: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Mon, 12 Aug 2019 18:40:11: start model_add_line... INFO @ Mon, 12 Aug 2019 18:40:11: start X-correlation... INFO @ Mon, 12 Aug 2019 18:40:11: end of X-cor INFO @ Mon, 12 Aug 2019 18:40:11: #2 finished! INFO @ Mon, 12 Aug 2019 18:40:11: #2 predicted fragment length is 30 bps INFO @ Mon, 12 Aug 2019 18:40:11: #2 alternative fragment length(s) may be 2,30 bps INFO @ Mon, 12 Aug 2019 18:40:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.05_model.r WARNING @ Mon, 12 Aug 2019 18:40:11: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:40:11: #2 You may need to consider one of the other alternative d(s): 2,30 WARNING @ Mon, 12 Aug 2019 18:40:11: #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 18:40:11: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:40:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:40:12: 6000000 INFO @ Mon, 12 Aug 2019 18:40:13: 6000000 INFO @ Mon, 12 Aug 2019 18:40:13: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:40:13: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:40:13: #1 total tags in treatment: 6198820 INFO @ Mon, 12 Aug 2019 18:40:13: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:40:13: #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 18:40:13: #1 tags after filtering in treatment: 6198820 INFO @ Mon, 12 Aug 2019 18:40:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:40:13: #1 finished! INFO @ Mon, 12 Aug 2019 18:40:13: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:40:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:40:14: #2 number of paired peaks: 403 WARNING @ Mon, 12 Aug 2019 18:40:14: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Mon, 12 Aug 2019 18:40:14: start model_add_line... INFO @ Mon, 12 Aug 2019 18:40:14: start X-correlation... INFO @ Mon, 12 Aug 2019 18:40:14: end of X-cor INFO @ Mon, 12 Aug 2019 18:40:14: #2 finished! INFO @ Mon, 12 Aug 2019 18:40:14: #2 predicted fragment length is 30 bps INFO @ Mon, 12 Aug 2019 18:40:14: #2 alternative fragment length(s) may be 2,30 bps INFO @ Mon, 12 Aug 2019 18:40:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.10_model.r WARNING @ Mon, 12 Aug 2019 18:40:14: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:40:14: #2 You may need to consider one of the other alternative d(s): 2,30 WARNING @ Mon, 12 Aug 2019 18:40:14: #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 18:40:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:40:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:40:14: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:40:14: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:40:14: #1 total tags in treatment: 6198820 INFO @ Mon, 12 Aug 2019 18:40:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:40:14: #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 18:40:14: #1 tags after filtering in treatment: 6198820 INFO @ Mon, 12 Aug 2019 18:40:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:40:14: #1 finished! INFO @ Mon, 12 Aug 2019 18:40:14: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:40:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:40:15: #2 number of paired peaks: 403 WARNING @ Mon, 12 Aug 2019 18:40:15: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Mon, 12 Aug 2019 18:40:15: start model_add_line... INFO @ Mon, 12 Aug 2019 18:40:15: start X-correlation... INFO @ Mon, 12 Aug 2019 18:40:15: end of X-cor INFO @ Mon, 12 Aug 2019 18:40:15: #2 finished! INFO @ Mon, 12 Aug 2019 18:40:15: #2 predicted fragment length is 30 bps INFO @ Mon, 12 Aug 2019 18:40:15: #2 alternative fragment length(s) may be 2,30 bps INFO @ Mon, 12 Aug 2019 18:40:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.20_model.r WARNING @ Mon, 12 Aug 2019 18:40:15: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:40:15: #2 You may need to consider one of the other alternative d(s): 2,30 WARNING @ Mon, 12 Aug 2019 18:40:15: #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 18:40:15: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:40:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:40:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:40:31: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:40:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:40:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:40:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:40:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.05_summits.bed INFO @ Mon, 12 Aug 2019 18:40:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (492 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:40:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:40:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:40:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.10_summits.bed INFO @ Mon, 12 Aug 2019 18:40:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (227 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:40:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:40:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:40:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331257/SRX331257.20_summits.bed INFO @ Mon, 12 Aug 2019 18:40:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (56 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。