Job ID = 1292971 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,621,262 reads read : 8,621,262 reads written : 8,621,262 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: 00:02:05 8621262 reads; of these: 8621262 (100.00%) were unpaired; of these: 467140 (5.42%) aligned 0 times 6868394 (79.67%) aligned exactly 1 time 1285728 (14.91%) aligned >1 times 94.58% overall alignment rate Time searching: 00:02:05 Overall time: 00:02:05 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] 443415 / 8154122 = 0.0544 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 21:18:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.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 21:18:33: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:18:33: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:18:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.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 21:18:33: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:18:33: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:18:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.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 21:18:33: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:18:33: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:18:40: 1000000 INFO @ Sun, 02 Jun 2019 21:18:41: 1000000 INFO @ Sun, 02 Jun 2019 21:18:42: 1000000 INFO @ Sun, 02 Jun 2019 21:18:47: 2000000 INFO @ Sun, 02 Jun 2019 21:18:49: 2000000 INFO @ Sun, 02 Jun 2019 21:18:50: 2000000 INFO @ Sun, 02 Jun 2019 21:18:53: 3000000 INFO @ Sun, 02 Jun 2019 21:18:56: 3000000 INFO @ Sun, 02 Jun 2019 21:18:58: 3000000 INFO @ Sun, 02 Jun 2019 21:19:00: 4000000 INFO @ Sun, 02 Jun 2019 21:19:04: 4000000 INFO @ Sun, 02 Jun 2019 21:19:06: 4000000 INFO @ Sun, 02 Jun 2019 21:19:07: 5000000 INFO @ Sun, 02 Jun 2019 21:19:12: 5000000 INFO @ Sun, 02 Jun 2019 21:19:14: 6000000 INFO @ Sun, 02 Jun 2019 21:19:15: 5000000 INFO @ Sun, 02 Jun 2019 21:19:19: 6000000 INFO @ Sun, 02 Jun 2019 21:19:21: 7000000 INFO @ Sun, 02 Jun 2019 21:19:23: 6000000 INFO @ Sun, 02 Jun 2019 21:19:25: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:19:25: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:19:25: #1 total tags in treatment: 7710707 INFO @ Sun, 02 Jun 2019 21:19:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:19:25: #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 21:19:26: #1 tags after filtering in treatment: 7710707 INFO @ Sun, 02 Jun 2019 21:19:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:19:26: #1 finished! INFO @ Sun, 02 Jun 2019 21:19:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:19:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:19:26: #2 number of paired peaks: 305 WARNING @ Sun, 02 Jun 2019 21:19:26: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Sun, 02 Jun 2019 21:19:26: start model_add_line... INFO @ Sun, 02 Jun 2019 21:19:26: start X-correlation... INFO @ Sun, 02 Jun 2019 21:19:26: end of X-cor INFO @ Sun, 02 Jun 2019 21:19:26: #2 finished! INFO @ Sun, 02 Jun 2019 21:19:26: #2 predicted fragment length is 52 bps INFO @ Sun, 02 Jun 2019 21:19:26: #2 alternative fragment length(s) may be 4,52,565 bps INFO @ Sun, 02 Jun 2019 21:19:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.20_model.r WARNING @ Sun, 02 Jun 2019 21:19:26: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:19:26: #2 You may need to consider one of the other alternative d(s): 4,52,565 WARNING @ Sun, 02 Jun 2019 21:19:26: #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 21:19:26: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:19:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:19:27: 7000000 INFO @ Sun, 02 Jun 2019 21:19:31: 7000000 INFO @ Sun, 02 Jun 2019 21:19:32: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:19:32: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:19:32: #1 total tags in treatment: 7710707 INFO @ Sun, 02 Jun 2019 21:19:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:19:32: #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 21:19:32: #1 tags after filtering in treatment: 7710707 INFO @ Sun, 02 Jun 2019 21:19:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:19:32: #1 finished! INFO @ Sun, 02 Jun 2019 21:19:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:19:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:19:33: #2 number of paired peaks: 305 WARNING @ Sun, 02 Jun 2019 21:19:33: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Sun, 02 Jun 2019 21:19:33: start model_add_line... INFO @ Sun, 02 Jun 2019 21:19:33: start X-correlation... INFO @ Sun, 02 Jun 2019 21:19:33: end of X-cor INFO @ Sun, 02 Jun 2019 21:19:33: #2 finished! INFO @ Sun, 02 Jun 2019 21:19:33: #2 predicted fragment length is 52 bps INFO @ Sun, 02 Jun 2019 21:19:33: #2 alternative fragment length(s) may be 4,52,565 bps INFO @ Sun, 02 Jun 2019 21:19:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.10_model.r WARNING @ Sun, 02 Jun 2019 21:19:33: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:19:33: #2 You may need to consider one of the other alternative d(s): 4,52,565 WARNING @ Sun, 02 Jun 2019 21:19:33: #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 21:19:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:19:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:19:37: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:19:37: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:19:37: #1 total tags in treatment: 7710707 INFO @ Sun, 02 Jun 2019 21:19:37: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:19:37: #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 21:19:37: #1 tags after filtering in treatment: 7710707 INFO @ Sun, 02 Jun 2019 21:19:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:19:37: #1 finished! INFO @ Sun, 02 Jun 2019 21:19:37: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:19:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:19:38: #2 number of paired peaks: 305 WARNING @ Sun, 02 Jun 2019 21:19:38: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Sun, 02 Jun 2019 21:19:38: start model_add_line... INFO @ Sun, 02 Jun 2019 21:19:38: start X-correlation... INFO @ Sun, 02 Jun 2019 21:19:38: end of X-cor INFO @ Sun, 02 Jun 2019 21:19:38: #2 finished! INFO @ Sun, 02 Jun 2019 21:19:38: #2 predicted fragment length is 52 bps INFO @ Sun, 02 Jun 2019 21:19:38: #2 alternative fragment length(s) may be 4,52,565 bps INFO @ Sun, 02 Jun 2019 21:19:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.05_model.r WARNING @ Sun, 02 Jun 2019 21:19:38: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:19:38: #2 You may need to consider one of the other alternative d(s): 4,52,565 WARNING @ Sun, 02 Jun 2019 21:19:38: #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 21:19:38: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:19:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:19:48: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:19:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:19:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:19:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:19:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.20_summits.bed INFO @ Sun, 02 Jun 2019 21:19:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (123 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:19:59: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:20:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:20:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:20:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.10_summits.bed INFO @ Sun, 02 Jun 2019 21:20:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (300 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:20:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:20:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:20:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020751/SRX5020751.05_summits.bed INFO @ Sun, 02 Jun 2019 21:20:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (618 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。