Job ID = 1292333 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,812,743 reads read : 18,812,743 reads written : 18,812,743 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:04:46 18812743 reads; of these: 18812743 (100.00%) were unpaired; of these: 150233 (0.80%) aligned 0 times 15590725 (82.87%) aligned exactly 1 time 3071785 (16.33%) aligned >1 times 99.20% overall alignment rate Time searching: 00:04:46 Overall time: 00:04:46 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] 8433062 / 18662510 = 0.4519 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 @ Sun, 02 Jun 2019 18:10:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.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 @ Sun, 02 Jun 2019 18:10:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:10:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:10:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.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 @ Sun, 02 Jun 2019 18:10:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:10:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:10:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.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 @ Sun, 02 Jun 2019 18:10:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:10:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:10:20: 1000000 INFO @ Sun, 02 Jun 2019 18:10:20: 1000000 INFO @ Sun, 02 Jun 2019 18:10:22: 1000000 INFO @ Sun, 02 Jun 2019 18:10:28: 2000000 INFO @ Sun, 02 Jun 2019 18:10:28: 2000000 INFO @ Sun, 02 Jun 2019 18:10:33: 2000000 INFO @ Sun, 02 Jun 2019 18:10:35: 3000000 INFO @ Sun, 02 Jun 2019 18:10:36: 3000000 INFO @ Sun, 02 Jun 2019 18:10:42: 4000000 INFO @ Sun, 02 Jun 2019 18:10:43: 3000000 INFO @ Sun, 02 Jun 2019 18:10:44: 4000000 INFO @ Sun, 02 Jun 2019 18:10:50: 5000000 INFO @ Sun, 02 Jun 2019 18:10:51: 5000000 INFO @ Sun, 02 Jun 2019 18:10:53: 4000000 INFO @ Sun, 02 Jun 2019 18:10:57: 6000000 INFO @ Sun, 02 Jun 2019 18:10:59: 6000000 INFO @ Sun, 02 Jun 2019 18:11:03: 5000000 INFO @ Sun, 02 Jun 2019 18:11:05: 7000000 INFO @ Sun, 02 Jun 2019 18:11:08: 7000000 INFO @ Sun, 02 Jun 2019 18:11:12: 8000000 INFO @ Sun, 02 Jun 2019 18:11:13: 6000000 INFO @ Sun, 02 Jun 2019 18:11:16: 8000000 INFO @ Sun, 02 Jun 2019 18:11:19: 9000000 INFO @ Sun, 02 Jun 2019 18:11:22: 7000000 INFO @ Sun, 02 Jun 2019 18:11:23: 9000000 INFO @ Sun, 02 Jun 2019 18:11:26: 10000000 INFO @ Sun, 02 Jun 2019 18:11:28: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:11:28: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:11:28: #1 total tags in treatment: 10229448 INFO @ Sun, 02 Jun 2019 18:11:28: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:11:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:11:28: #1 tags after filtering in treatment: 10229448 INFO @ Sun, 02 Jun 2019 18:11:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:11:28: #1 finished! INFO @ Sun, 02 Jun 2019 18:11:28: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:11:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:11:29: #2 number of paired peaks: 422 WARNING @ Sun, 02 Jun 2019 18:11:29: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Sun, 02 Jun 2019 18:11:29: start model_add_line... INFO @ Sun, 02 Jun 2019 18:11:29: start X-correlation... INFO @ Sun, 02 Jun 2019 18:11:29: end of X-cor INFO @ Sun, 02 Jun 2019 18:11:29: #2 finished! INFO @ Sun, 02 Jun 2019 18:11:29: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 18:11:29: #2 alternative fragment length(s) may be 1,48,518,560 bps INFO @ Sun, 02 Jun 2019 18:11:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.20_model.r WARNING @ Sun, 02 Jun 2019 18:11:29: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:11:29: #2 You may need to consider one of the other alternative d(s): 1,48,518,560 WARNING @ Sun, 02 Jun 2019 18:11:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:11:29: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:11:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:11:31: 10000000 INFO @ Sun, 02 Jun 2019 18:11:32: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:11:32: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:11:32: #1 total tags in treatment: 10229448 INFO @ Sun, 02 Jun 2019 18:11:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:11:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:11:32: #1 tags after filtering in treatment: 10229448 INFO @ Sun, 02 Jun 2019 18:11:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:11:32: #1 finished! INFO @ Sun, 02 Jun 2019 18:11:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:11:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:11:33: 8000000 INFO @ Sun, 02 Jun 2019 18:11:33: #2 number of paired peaks: 422 WARNING @ Sun, 02 Jun 2019 18:11:33: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Sun, 02 Jun 2019 18:11:33: start model_add_line... INFO @ Sun, 02 Jun 2019 18:11:33: start X-correlation... INFO @ Sun, 02 Jun 2019 18:11:33: end of X-cor INFO @ Sun, 02 Jun 2019 18:11:33: #2 finished! INFO @ Sun, 02 Jun 2019 18:11:33: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 18:11:33: #2 alternative fragment length(s) may be 1,48,518,560 bps INFO @ Sun, 02 Jun 2019 18:11:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.05_model.r WARNING @ Sun, 02 Jun 2019 18:11:33: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:11:33: #2 You may need to consider one of the other alternative d(s): 1,48,518,560 WARNING @ Sun, 02 Jun 2019 18:11:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:11:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:11:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:11:43: 9000000 INFO @ Sun, 02 Jun 2019 18:11:52: 10000000 INFO @ Sun, 02 Jun 2019 18:11:54: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:11:54: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:11:54: #1 total tags in treatment: 10229448 INFO @ Sun, 02 Jun 2019 18:11:54: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:11:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:11:54: #1 tags after filtering in treatment: 10229448 INFO @ Sun, 02 Jun 2019 18:11:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:11:54: #1 finished! INFO @ Sun, 02 Jun 2019 18:11:54: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:11:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:11:55: #2 number of paired peaks: 422 WARNING @ Sun, 02 Jun 2019 18:11:55: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Sun, 02 Jun 2019 18:11:55: start model_add_line... INFO @ Sun, 02 Jun 2019 18:11:55: start X-correlation... INFO @ Sun, 02 Jun 2019 18:11:55: end of X-cor INFO @ Sun, 02 Jun 2019 18:11:55: #2 finished! INFO @ Sun, 02 Jun 2019 18:11:55: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 18:11:55: #2 alternative fragment length(s) may be 1,48,518,560 bps INFO @ Sun, 02 Jun 2019 18:11:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.10_model.r WARNING @ Sun, 02 Jun 2019 18:11:55: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:11:55: #2 You may need to consider one of the other alternative d(s): 1,48,518,560 WARNING @ Sun, 02 Jun 2019 18:11:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:11:55: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:11:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:11:57: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:12:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:12:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:12:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:12:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.20_summits.bed INFO @ Sun, 02 Jun 2019 18:12:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (217 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:12:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:12:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:12:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.05_summits.bed INFO @ Sun, 02 Jun 2019 18:12:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (753 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:12:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:12:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:12:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:12:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331357/SRX331357.10_summits.bed INFO @ Sun, 02 Jun 2019 18:12:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (560 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。