Job ID = 2589420 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,185,898 reads read : 5,185,898 reads written : 5,185,898 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR494630.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: 00:00:43 5185898 reads; of these: 5185898 (100.00%) were unpaired; of these: 2016654 (38.89%) aligned 0 times 2597463 (50.09%) aligned exactly 1 time 571781 (11.03%) aligned >1 times 61.11% overall alignment rate Time searching: 00:00:43 Overall time: 00:00:43 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] 120304 / 3169244 = 0.0380 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 17:38:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.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 17:38:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:38:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:38:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.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 17:38:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:38:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:38:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.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 17:38:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:38:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:38:42: 1000000 INFO @ Mon, 12 Aug 2019 17:38:43: 1000000 INFO @ Mon, 12 Aug 2019 17:38:44: 1000000 INFO @ Mon, 12 Aug 2019 17:38:49: 2000000 INFO @ Mon, 12 Aug 2019 17:38:50: 2000000 INFO @ Mon, 12 Aug 2019 17:38:51: 2000000 INFO @ Mon, 12 Aug 2019 17:38:56: 3000000 INFO @ Mon, 12 Aug 2019 17:38:56: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:38:56: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:38:56: #1 total tags in treatment: 3048940 INFO @ Mon, 12 Aug 2019 17:38:56: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:38:56: #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 17:38:56: #1 tags after filtering in treatment: 3048940 INFO @ Mon, 12 Aug 2019 17:38:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:38:56: #1 finished! INFO @ Mon, 12 Aug 2019 17:38:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:38:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:38:57: #2 number of paired peaks: 427 WARNING @ Mon, 12 Aug 2019 17:38:57: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Mon, 12 Aug 2019 17:38:57: start model_add_line... INFO @ Mon, 12 Aug 2019 17:38:57: start X-correlation... INFO @ Mon, 12 Aug 2019 17:38:57: end of X-cor INFO @ Mon, 12 Aug 2019 17:38:57: #2 finished! INFO @ Mon, 12 Aug 2019 17:38:57: #2 predicted fragment length is 33 bps INFO @ Mon, 12 Aug 2019 17:38:57: #2 alternative fragment length(s) may be 33,446,564,594 bps INFO @ Mon, 12 Aug 2019 17:38:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.10_model.r WARNING @ Mon, 12 Aug 2019 17:38:57: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:38:57: #2 You may need to consider one of the other alternative d(s): 33,446,564,594 WARNING @ Mon, 12 Aug 2019 17:38:57: #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 17:38:57: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:38:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:38:57: 3000000 INFO @ Mon, 12 Aug 2019 17:38:57: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:38:57: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:38:57: #1 total tags in treatment: 3048940 INFO @ Mon, 12 Aug 2019 17:38:57: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:38:57: #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 17:38:57: #1 tags after filtering in treatment: 3048940 INFO @ Mon, 12 Aug 2019 17:38:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:38:57: #1 finished! INFO @ Mon, 12 Aug 2019 17:38:57: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:38:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:38:58: #2 number of paired peaks: 427 WARNING @ Mon, 12 Aug 2019 17:38:58: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Mon, 12 Aug 2019 17:38:58: start model_add_line... INFO @ Mon, 12 Aug 2019 17:38:58: start X-correlation... INFO @ Mon, 12 Aug 2019 17:38:58: end of X-cor INFO @ Mon, 12 Aug 2019 17:38:58: #2 finished! INFO @ Mon, 12 Aug 2019 17:38:58: #2 predicted fragment length is 33 bps INFO @ Mon, 12 Aug 2019 17:38:58: #2 alternative fragment length(s) may be 33,446,564,594 bps INFO @ Mon, 12 Aug 2019 17:38:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.05_model.r WARNING @ Mon, 12 Aug 2019 17:38:58: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:38:58: #2 You may need to consider one of the other alternative d(s): 33,446,564,594 WARNING @ Mon, 12 Aug 2019 17:38:58: #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 17:38:58: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:38:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:38:58: 3000000 INFO @ Mon, 12 Aug 2019 17:38:59: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:38:59: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:38:59: #1 total tags in treatment: 3048940 INFO @ Mon, 12 Aug 2019 17:38:59: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:38:59: #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 17:38:59: #1 tags after filtering in treatment: 3048940 INFO @ Mon, 12 Aug 2019 17:38:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:38:59: #1 finished! INFO @ Mon, 12 Aug 2019 17:38:59: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:38:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:38:59: #2 number of paired peaks: 427 WARNING @ Mon, 12 Aug 2019 17:38:59: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Mon, 12 Aug 2019 17:38:59: start model_add_line... INFO @ Mon, 12 Aug 2019 17:38:59: start X-correlation... INFO @ Mon, 12 Aug 2019 17:38:59: end of X-cor INFO @ Mon, 12 Aug 2019 17:38:59: #2 finished! INFO @ Mon, 12 Aug 2019 17:38:59: #2 predicted fragment length is 33 bps INFO @ Mon, 12 Aug 2019 17:38:59: #2 alternative fragment length(s) may be 33,446,564,594 bps INFO @ Mon, 12 Aug 2019 17:38:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.20_model.r WARNING @ Mon, 12 Aug 2019 17:38:59: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:38:59: #2 You may need to consider one of the other alternative d(s): 33,446,564,594 WARNING @ Mon, 12 Aug 2019 17:38:59: #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 17:38:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:38:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:39:06: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:39:07: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:39:08: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:39:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:39:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:39:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.10_summits.bed INFO @ Mon, 12 Aug 2019 17:39:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (191 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:39:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:39:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:39:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.05_summits.bed INFO @ Mon, 12 Aug 2019 17:39:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (393 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:39:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:39:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:39:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX146469/SRX146469.20_summits.bed INFO @ Mon, 12 Aug 2019 17:39:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (54 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。