Job ID = 1293189 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,212,115 reads read : 32,212,115 reads written : 32,212,115 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:50 32212115 reads; of these: 32212115 (100.00%) were unpaired; of these: 7761361 (24.09%) aligned 0 times 12600964 (39.12%) aligned exactly 1 time 11849790 (36.79%) aligned >1 times 75.91% overall alignment rate Time searching: 00:08:51 Overall time: 00:08:51 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 12 files... [bam_rmdupse_core] 9376359 / 24450754 = 0.3835 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 22:38:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.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 22:38:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:38:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:38:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.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 22:38:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:38:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:38:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.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 22:38:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:38:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:38:15: 1000000 INFO @ Sun, 02 Jun 2019 22:38:16: 1000000 INFO @ Sun, 02 Jun 2019 22:38:17: 1000000 INFO @ Sun, 02 Jun 2019 22:38:23: 2000000 INFO @ Sun, 02 Jun 2019 22:38:26: 2000000 INFO @ Sun, 02 Jun 2019 22:38:27: 2000000 INFO @ Sun, 02 Jun 2019 22:38:31: 3000000 INFO @ Sun, 02 Jun 2019 22:38:35: 3000000 INFO @ Sun, 02 Jun 2019 22:38:36: 3000000 INFO @ Sun, 02 Jun 2019 22:38:40: 4000000 INFO @ Sun, 02 Jun 2019 22:38:45: 4000000 INFO @ Sun, 02 Jun 2019 22:38:46: 4000000 INFO @ Sun, 02 Jun 2019 22:38:48: 5000000 INFO @ Sun, 02 Jun 2019 22:38:54: 5000000 INFO @ Sun, 02 Jun 2019 22:38:56: 5000000 INFO @ Sun, 02 Jun 2019 22:38:56: 6000000 INFO @ Sun, 02 Jun 2019 22:39:03: 6000000 INFO @ Sun, 02 Jun 2019 22:39:05: 7000000 INFO @ Sun, 02 Jun 2019 22:39:06: 6000000 INFO @ Sun, 02 Jun 2019 22:39:13: 7000000 INFO @ Sun, 02 Jun 2019 22:39:13: 8000000 INFO @ Sun, 02 Jun 2019 22:39:16: 7000000 INFO @ Sun, 02 Jun 2019 22:39:21: 9000000 INFO @ Sun, 02 Jun 2019 22:39:22: 8000000 INFO @ Sun, 02 Jun 2019 22:39:26: 8000000 INFO @ Sun, 02 Jun 2019 22:39:30: 10000000 INFO @ Sun, 02 Jun 2019 22:39:32: 9000000 INFO @ Sun, 02 Jun 2019 22:39:36: 9000000 INFO @ Sun, 02 Jun 2019 22:39:38: 11000000 INFO @ Sun, 02 Jun 2019 22:39:41: 10000000 INFO @ Sun, 02 Jun 2019 22:39:46: 10000000 INFO @ Sun, 02 Jun 2019 22:39:46: 12000000 INFO @ Sun, 02 Jun 2019 22:39:51: 11000000 INFO @ Sun, 02 Jun 2019 22:39:55: 13000000 INFO @ Sun, 02 Jun 2019 22:39:56: 11000000 INFO @ Sun, 02 Jun 2019 22:40:00: 12000000 INFO @ Sun, 02 Jun 2019 22:40:04: 14000000 INFO @ Sun, 02 Jun 2019 22:40:06: 12000000 INFO @ Sun, 02 Jun 2019 22:40:10: 13000000 INFO @ Sun, 02 Jun 2019 22:40:12: 15000000 INFO @ Sun, 02 Jun 2019 22:40:13: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:40:13: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:40:13: #1 total tags in treatment: 15074395 INFO @ Sun, 02 Jun 2019 22:40:13: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:40:13: #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 22:40:13: #1 tags after filtering in treatment: 15074395 INFO @ Sun, 02 Jun 2019 22:40:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:40:13: #1 finished! INFO @ Sun, 02 Jun 2019 22:40:13: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:40:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:40:15: #2 number of paired peaks: 3115 INFO @ Sun, 02 Jun 2019 22:40:15: start model_add_line... INFO @ Sun, 02 Jun 2019 22:40:15: start X-correlation... INFO @ Sun, 02 Jun 2019 22:40:15: end of X-cor INFO @ Sun, 02 Jun 2019 22:40:15: #2 finished! INFO @ Sun, 02 Jun 2019 22:40:15: #2 predicted fragment length is 67 bps INFO @ Sun, 02 Jun 2019 22:40:15: #2 alternative fragment length(s) may be 4,67 bps INFO @ Sun, 02 Jun 2019 22:40:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.20_model.r WARNING @ Sun, 02 Jun 2019 22:40:15: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:40:15: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Sun, 02 Jun 2019 22:40:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:40:15: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:40:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:40:16: 13000000 INFO @ Sun, 02 Jun 2019 22:40:20: 14000000 INFO @ Sun, 02 Jun 2019 22:40:26: 14000000 INFO @ Sun, 02 Jun 2019 22:40:29: 15000000 INFO @ Sun, 02 Jun 2019 22:40:30: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:40:30: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:40:30: #1 total tags in treatment: 15074395 INFO @ Sun, 02 Jun 2019 22:40:30: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:40:30: #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 22:40:30: #1 tags after filtering in treatment: 15074395 INFO @ Sun, 02 Jun 2019 22:40:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:40:30: #1 finished! INFO @ Sun, 02 Jun 2019 22:40:30: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:40:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:40:32: #2 number of paired peaks: 3115 INFO @ Sun, 02 Jun 2019 22:40:32: start model_add_line... INFO @ Sun, 02 Jun 2019 22:40:32: start X-correlation... INFO @ Sun, 02 Jun 2019 22:40:32: end of X-cor INFO @ Sun, 02 Jun 2019 22:40:32: #2 finished! INFO @ Sun, 02 Jun 2019 22:40:32: #2 predicted fragment length is 67 bps INFO @ Sun, 02 Jun 2019 22:40:32: #2 alternative fragment length(s) may be 4,67 bps INFO @ Sun, 02 Jun 2019 22:40:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.05_model.r WARNING @ Sun, 02 Jun 2019 22:40:32: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:40:32: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Sun, 02 Jun 2019 22:40:32: #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 22:40:32: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:40:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:40:36: 15000000 INFO @ Sun, 02 Jun 2019 22:40:37: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:40:37: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:40:37: #1 total tags in treatment: 15074395 INFO @ Sun, 02 Jun 2019 22:40:37: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:40:37: #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 22:40:37: #1 tags after filtering in treatment: 15074395 INFO @ Sun, 02 Jun 2019 22:40:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:40:37: #1 finished! INFO @ Sun, 02 Jun 2019 22:40:37: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:40:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:40:39: #2 number of paired peaks: 3115 INFO @ Sun, 02 Jun 2019 22:40:39: start model_add_line... INFO @ Sun, 02 Jun 2019 22:40:39: start X-correlation... INFO @ Sun, 02 Jun 2019 22:40:39: end of X-cor INFO @ Sun, 02 Jun 2019 22:40:39: #2 finished! INFO @ Sun, 02 Jun 2019 22:40:39: #2 predicted fragment length is 67 bps INFO @ Sun, 02 Jun 2019 22:40:39: #2 alternative fragment length(s) may be 4,67 bps INFO @ Sun, 02 Jun 2019 22:40:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.10_model.r WARNING @ Sun, 02 Jun 2019 22:40:39: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:40:39: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Sun, 02 Jun 2019 22:40:39: #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 22:40:39: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:40:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:40:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:41:13: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:41:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:41:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:41:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.20_summits.bed INFO @ Sun, 02 Jun 2019 22:41:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3711 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:41:20: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:41:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:41:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:41:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.05_summits.bed INFO @ Sun, 02 Jun 2019 22:41:32: Done! pass1 - making usageList (7 chroms): 6 millis pass2 - checking and writing primary data (11873 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:41:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:41:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:41:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402747/SRX5402747.10_summits.bed INFO @ Sun, 02 Jun 2019 22:41:40: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (7896 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。