Job ID = 4178400 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,313,276 reads read : 22,626,552 reads written : 11,313,276 reads 0-length : 11,313,276 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:01 Multiseed full-index search: 00:04:48 11313276 reads; of these: 11313276 (100.00%) were unpaired; of these: 1217069 (10.76%) aligned 0 times 8238162 (72.82%) aligned exactly 1 time 1858045 (16.42%) aligned >1 times 89.24% overall alignment rate Time searching: 00:04:49 Overall time: 00:04:49 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] 867507 / 10096207 = 0.0859 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:29:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.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, 05 Dec 2019 12:29:29: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:29:29: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:29:40: 1000000 INFO @ Thu, 05 Dec 2019 12:29:49: 2000000 INFO @ Thu, 05 Dec 2019 12:29:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.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, 05 Dec 2019 12:29:58: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:29:58: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:29:58: 3000000 INFO @ Thu, 05 Dec 2019 12:30:08: 4000000 INFO @ Thu, 05 Dec 2019 12:30:10: 1000000 INFO @ Thu, 05 Dec 2019 12:30:18: 5000000 INFO @ Thu, 05 Dec 2019 12:30:23: 2000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:30:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.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, 05 Dec 2019 12:30:28: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:30:28: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:30:28: 6000000 INFO @ Thu, 05 Dec 2019 12:30:37: 3000000 INFO @ Thu, 05 Dec 2019 12:30:38: 7000000 INFO @ Thu, 05 Dec 2019 12:30:38: 1000000 INFO @ Thu, 05 Dec 2019 12:30:47: 8000000 INFO @ Thu, 05 Dec 2019 12:30:48: 4000000 INFO @ Thu, 05 Dec 2019 12:30:51: 2000000 INFO @ Thu, 05 Dec 2019 12:30:58: 9000000 INFO @ Thu, 05 Dec 2019 12:31:00: #1 tag size is determined as 75 bps INFO @ Thu, 05 Dec 2019 12:31:00: #1 tag size = 75 INFO @ Thu, 05 Dec 2019 12:31:00: #1 total tags in treatment: 9228700 INFO @ Thu, 05 Dec 2019 12:31:00: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:31:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:31:00: #1 tags after filtering in treatment: 9228700 INFO @ Thu, 05 Dec 2019 12:31:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:31:00: #1 finished! INFO @ Thu, 05 Dec 2019 12:31:00: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:31:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:31:01: 5000000 INFO @ Thu, 05 Dec 2019 12:31:01: #2 number of paired peaks: 336 WARNING @ Thu, 05 Dec 2019 12:31:01: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Thu, 05 Dec 2019 12:31:01: start model_add_line... INFO @ Thu, 05 Dec 2019 12:31:01: start X-correlation... INFO @ Thu, 05 Dec 2019 12:31:01: end of X-cor INFO @ Thu, 05 Dec 2019 12:31:01: #2 finished! INFO @ Thu, 05 Dec 2019 12:31:01: #2 predicted fragment length is 70 bps INFO @ Thu, 05 Dec 2019 12:31:01: #2 alternative fragment length(s) may be 4,70,526 bps INFO @ Thu, 05 Dec 2019 12:31:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.05_model.r WARNING @ Thu, 05 Dec 2019 12:31:01: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:31:01: #2 You may need to consider one of the other alternative d(s): 4,70,526 WARNING @ Thu, 05 Dec 2019 12:31:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:31:01: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:31:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:31:04: 3000000 INFO @ Thu, 05 Dec 2019 12:31:14: 6000000 INFO @ Thu, 05 Dec 2019 12:31:16: 4000000 INFO @ Thu, 05 Dec 2019 12:31:27: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:31:28: 7000000 INFO @ Thu, 05 Dec 2019 12:31:29: 5000000 INFO @ Thu, 05 Dec 2019 12:31:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:31:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:31:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.05_summits.bed INFO @ Thu, 05 Dec 2019 12:31:41: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (923 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:31:41: 6000000 INFO @ Thu, 05 Dec 2019 12:31:43: 8000000 INFO @ Thu, 05 Dec 2019 12:31:53: 7000000 INFO @ Thu, 05 Dec 2019 12:31:55: 9000000 INFO @ Thu, 05 Dec 2019 12:31:58: #1 tag size is determined as 75 bps INFO @ Thu, 05 Dec 2019 12:31:58: #1 tag size = 75 INFO @ Thu, 05 Dec 2019 12:31:58: #1 total tags in treatment: 9228700 INFO @ Thu, 05 Dec 2019 12:31:58: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:31:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:31:58: #1 tags after filtering in treatment: 9228700 INFO @ Thu, 05 Dec 2019 12:31:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:31:58: #1 finished! INFO @ Thu, 05 Dec 2019 12:31:58: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:31:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:31:59: #2 number of paired peaks: 336 WARNING @ Thu, 05 Dec 2019 12:31:59: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Thu, 05 Dec 2019 12:31:59: start model_add_line... INFO @ Thu, 05 Dec 2019 12:31:59: start X-correlation... INFO @ Thu, 05 Dec 2019 12:31:59: end of X-cor INFO @ Thu, 05 Dec 2019 12:31:59: #2 finished! INFO @ Thu, 05 Dec 2019 12:31:59: #2 predicted fragment length is 70 bps INFO @ Thu, 05 Dec 2019 12:31:59: #2 alternative fragment length(s) may be 4,70,526 bps INFO @ Thu, 05 Dec 2019 12:31:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.10_model.r WARNING @ Thu, 05 Dec 2019 12:31:59: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:31:59: #2 You may need to consider one of the other alternative d(s): 4,70,526 WARNING @ Thu, 05 Dec 2019 12:31:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:31:59: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:31:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:32:05: 8000000 INFO @ Thu, 05 Dec 2019 12:32:17: 9000000 INFO @ Thu, 05 Dec 2019 12:32:20: #1 tag size is determined as 75 bps INFO @ Thu, 05 Dec 2019 12:32:20: #1 tag size = 75 INFO @ Thu, 05 Dec 2019 12:32:20: #1 total tags in treatment: 9228700 INFO @ Thu, 05 Dec 2019 12:32:20: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:32:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:32:20: #1 tags after filtering in treatment: 9228700 INFO @ Thu, 05 Dec 2019 12:32:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:32:20: #1 finished! INFO @ Thu, 05 Dec 2019 12:32:20: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:32:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:32:21: #2 number of paired peaks: 336 WARNING @ Thu, 05 Dec 2019 12:32:21: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Thu, 05 Dec 2019 12:32:21: start model_add_line... INFO @ Thu, 05 Dec 2019 12:32:21: start X-correlation... INFO @ Thu, 05 Dec 2019 12:32:21: end of X-cor INFO @ Thu, 05 Dec 2019 12:32:21: #2 finished! INFO @ Thu, 05 Dec 2019 12:32:21: #2 predicted fragment length is 70 bps INFO @ Thu, 05 Dec 2019 12:32:21: #2 alternative fragment length(s) may be 4,70,526 bps INFO @ Thu, 05 Dec 2019 12:32:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.20_model.r WARNING @ Thu, 05 Dec 2019 12:32:21: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:32:21: #2 You may need to consider one of the other alternative d(s): 4,70,526 WARNING @ Thu, 05 Dec 2019 12:32:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:32:21: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:32:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:32:25: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:32:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:32:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:32:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.10_summits.bed INFO @ Thu, 05 Dec 2019 12:32:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (467 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:32:47: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:32:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:32:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:32:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5729148/SRX5729148.20_summits.bed INFO @ Thu, 05 Dec 2019 12:32:59: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (214 records, 4 fields): 44 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。