Job ID = 4303041 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,695,316 reads read : 15,695,316 reads written : 15,695,316 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1198438.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: 00:04:18 15695316 reads; of these: 15695316 (100.00%) were unpaired; of these: 1827105 (11.64%) aligned 0 times 11334815 (72.22%) aligned exactly 1 time 2533396 (16.14%) aligned >1 times 88.36% overall alignment rate Time searching: 00:04:18 Overall time: 00:04:18 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1282211 / 13868211 = 0.0925 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:44:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.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 @ Thu, 12 Dec 2019 00:44:01: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:44:01: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:44:09: 1000000 INFO @ Thu, 12 Dec 2019 00:44:18: 2000000 INFO @ Thu, 12 Dec 2019 00:44:27: 3000000 INFO @ Thu, 12 Dec 2019 00:44:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.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 @ Thu, 12 Dec 2019 00:44:31: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:44:31: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:44:35: 4000000 INFO @ Thu, 12 Dec 2019 00:44:39: 1000000 INFO @ Thu, 12 Dec 2019 00:44:43: 5000000 INFO @ Thu, 12 Dec 2019 00:44:48: 2000000 INFO @ Thu, 12 Dec 2019 00:44:52: 6000000 INFO @ Thu, 12 Dec 2019 00:44:56: 3000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:45:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.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 @ Thu, 12 Dec 2019 00:45:00: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:45:00: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:45:01: 7000000 INFO @ Thu, 12 Dec 2019 00:45:06: 4000000 INFO @ Thu, 12 Dec 2019 00:45:10: 1000000 INFO @ Thu, 12 Dec 2019 00:45:11: 8000000 INFO @ Thu, 12 Dec 2019 00:45:16: 5000000 INFO @ Thu, 12 Dec 2019 00:45:20: 2000000 INFO @ Thu, 12 Dec 2019 00:45:21: 9000000 INFO @ Thu, 12 Dec 2019 00:45:26: 6000000 INFO @ Thu, 12 Dec 2019 00:45:30: 3000000 INFO @ Thu, 12 Dec 2019 00:45:31: 10000000 INFO @ Thu, 12 Dec 2019 00:45:35: 7000000 INFO @ Thu, 12 Dec 2019 00:45:39: 4000000 INFO @ Thu, 12 Dec 2019 00:45:40: 11000000 INFO @ Thu, 12 Dec 2019 00:45:44: 8000000 INFO @ Thu, 12 Dec 2019 00:45:49: 5000000 INFO @ Thu, 12 Dec 2019 00:45:50: 12000000 INFO @ Thu, 12 Dec 2019 00:45:54: 9000000 INFO @ Thu, 12 Dec 2019 00:45:56: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:45:56: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:45:56: #1 total tags in treatment: 12586000 INFO @ Thu, 12 Dec 2019 00:45:56: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:45:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:45:56: #1 tags after filtering in treatment: 12586000 INFO @ Thu, 12 Dec 2019 00:45:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:45:56: #1 finished! INFO @ Thu, 12 Dec 2019 00:45:56: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:45:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:45:57: #2 number of paired peaks: 356 WARNING @ Thu, 12 Dec 2019 00:45:57: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Thu, 12 Dec 2019 00:45:57: start model_add_line... INFO @ Thu, 12 Dec 2019 00:45:57: start X-correlation... INFO @ Thu, 12 Dec 2019 00:45:58: end of X-cor INFO @ Thu, 12 Dec 2019 00:45:58: #2 finished! INFO @ Thu, 12 Dec 2019 00:45:58: #2 predicted fragment length is 46 bps INFO @ Thu, 12 Dec 2019 00:45:58: #2 alternative fragment length(s) may be 2,46 bps INFO @ Thu, 12 Dec 2019 00:45:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.05_model.r WARNING @ Thu, 12 Dec 2019 00:45:58: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:45:58: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Thu, 12 Dec 2019 00:45:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:45:58: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:45:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:45:58: 6000000 INFO @ Thu, 12 Dec 2019 00:46:03: 10000000 INFO @ Thu, 12 Dec 2019 00:46:07: 7000000 INFO @ Thu, 12 Dec 2019 00:46:13: 11000000 INFO @ Thu, 12 Dec 2019 00:46:16: 8000000 INFO @ Thu, 12 Dec 2019 00:46:23: 12000000 INFO @ Thu, 12 Dec 2019 00:46:26: 9000000 INFO @ Thu, 12 Dec 2019 00:46:28: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:46:28: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:46:28: #1 total tags in treatment: 12586000 INFO @ Thu, 12 Dec 2019 00:46:28: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:46:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:46:28: #1 tags after filtering in treatment: 12586000 INFO @ Thu, 12 Dec 2019 00:46:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:46:28: #1 finished! INFO @ Thu, 12 Dec 2019 00:46:28: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:46:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:46:29: #2 number of paired peaks: 356 WARNING @ Thu, 12 Dec 2019 00:46:29: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Thu, 12 Dec 2019 00:46:29: start model_add_line... INFO @ Thu, 12 Dec 2019 00:46:30: start X-correlation... INFO @ Thu, 12 Dec 2019 00:46:30: end of X-cor INFO @ Thu, 12 Dec 2019 00:46:30: #2 finished! INFO @ Thu, 12 Dec 2019 00:46:30: #2 predicted fragment length is 46 bps INFO @ Thu, 12 Dec 2019 00:46:30: #2 alternative fragment length(s) may be 2,46 bps INFO @ Thu, 12 Dec 2019 00:46:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.10_model.r WARNING @ Thu, 12 Dec 2019 00:46:30: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:46:30: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Thu, 12 Dec 2019 00:46:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:46:30: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:46:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:46:33: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:46:34: 10000000 INFO @ Thu, 12 Dec 2019 00:46:42: 11000000 INFO @ Thu, 12 Dec 2019 00:46:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:46:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:46:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.05_summits.bed INFO @ Thu, 12 Dec 2019 00:46:50: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (661 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:46:51: 12000000 INFO @ Thu, 12 Dec 2019 00:46:56: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:46:56: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:46:56: #1 total tags in treatment: 12586000 INFO @ Thu, 12 Dec 2019 00:46:56: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:46:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:46:56: #1 tags after filtering in treatment: 12586000 INFO @ Thu, 12 Dec 2019 00:46:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:46:56: #1 finished! INFO @ Thu, 12 Dec 2019 00:46:56: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:46:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:46:57: #2 number of paired peaks: 356 WARNING @ Thu, 12 Dec 2019 00:46:57: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Thu, 12 Dec 2019 00:46:57: start model_add_line... INFO @ Thu, 12 Dec 2019 00:46:57: start X-correlation... INFO @ Thu, 12 Dec 2019 00:46:57: end of X-cor INFO @ Thu, 12 Dec 2019 00:46:57: #2 finished! INFO @ Thu, 12 Dec 2019 00:46:57: #2 predicted fragment length is 46 bps INFO @ Thu, 12 Dec 2019 00:46:57: #2 alternative fragment length(s) may be 2,46 bps INFO @ Thu, 12 Dec 2019 00:46:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.20_model.r WARNING @ Thu, 12 Dec 2019 00:46:57: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:46:57: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Thu, 12 Dec 2019 00:46:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:46:57: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:46:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:47:04: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:47:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:47:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:47:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.10_summits.bed INFO @ Thu, 12 Dec 2019 00:47:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (485 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:47:31: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:47:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:47:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:47:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494906/SRX494906.20_summits.bed INFO @ Thu, 12 Dec 2019 00:47:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (198 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。