Job ID = 4178396 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,605,029 reads read : 18,605,029 reads written : 18,605,029 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: 00:00:00 Multiseed full-index search: 00:03:48 18605029 reads; of these: 18605029 (100.00%) were unpaired; of these: 1291538 (6.94%) aligned 0 times 14531103 (78.10%) aligned exactly 1 time 2782388 (14.96%) aligned >1 times 93.06% overall alignment rate Time searching: 00:03:48 Overall time: 00:03:48 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] 2330440 / 17313491 = 0.1346 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:33:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.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 12:33:41: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:33:41: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:33:51: 1000000 INFO @ Thu, 05 Dec 2019 12:33:58: 2000000 INFO @ Thu, 05 Dec 2019 12:34:05: 3000000 INFO @ Thu, 05 Dec 2019 12:34:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.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 12:34:10: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:34:10: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:34:12: 4000000 INFO @ Thu, 05 Dec 2019 12:34:17: 1000000 INFO @ Thu, 05 Dec 2019 12:34:19: 5000000 INFO @ Thu, 05 Dec 2019 12:34:25: 2000000 INFO @ Thu, 05 Dec 2019 12:34:26: 6000000 INFO @ Thu, 05 Dec 2019 12:34:32: 3000000 INFO @ Thu, 05 Dec 2019 12:34:34: 7000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:34:39: 4000000 INFO @ Thu, 05 Dec 2019 12:34:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.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 12:34:41: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:34:41: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:34:41: 8000000 INFO @ Thu, 05 Dec 2019 12:34:46: 5000000 INFO @ Thu, 05 Dec 2019 12:34:48: 9000000 INFO @ Thu, 05 Dec 2019 12:34:50: 1000000 INFO @ Thu, 05 Dec 2019 12:34:54: 6000000 INFO @ Thu, 05 Dec 2019 12:34:55: 10000000 INFO @ Thu, 05 Dec 2019 12:34:59: 2000000 INFO @ Thu, 05 Dec 2019 12:35:01: 7000000 INFO @ Thu, 05 Dec 2019 12:35:02: 11000000 INFO @ Thu, 05 Dec 2019 12:35:06: 3000000 INFO @ Thu, 05 Dec 2019 12:35:08: 8000000 INFO @ Thu, 05 Dec 2019 12:35:10: 12000000 INFO @ Thu, 05 Dec 2019 12:35:14: 4000000 INFO @ Thu, 05 Dec 2019 12:35:15: 9000000 INFO @ Thu, 05 Dec 2019 12:35:17: 13000000 INFO @ Thu, 05 Dec 2019 12:35:21: 5000000 INFO @ Thu, 05 Dec 2019 12:35:23: 10000000 INFO @ Thu, 05 Dec 2019 12:35:24: 14000000 INFO @ Thu, 05 Dec 2019 12:35:28: 6000000 INFO @ Thu, 05 Dec 2019 12:35:30: 11000000 INFO @ Thu, 05 Dec 2019 12:35:31: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:35:31: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:35:31: #1 total tags in treatment: 14983051 INFO @ Thu, 05 Dec 2019 12:35:31: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:35:31: #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 12:35:32: #1 tags after filtering in treatment: 14983051 INFO @ Thu, 05 Dec 2019 12:35:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:35:32: #1 finished! INFO @ Thu, 05 Dec 2019 12:35:32: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:35:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:35:33: #2 number of paired peaks: 283 WARNING @ Thu, 05 Dec 2019 12:35:33: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Thu, 05 Dec 2019 12:35:33: start model_add_line... INFO @ Thu, 05 Dec 2019 12:35:33: start X-correlation... INFO @ Thu, 05 Dec 2019 12:35:33: end of X-cor INFO @ Thu, 05 Dec 2019 12:35:33: #2 finished! INFO @ Thu, 05 Dec 2019 12:35:33: #2 predicted fragment length is 65 bps INFO @ Thu, 05 Dec 2019 12:35:33: #2 alternative fragment length(s) may be 4,65 bps INFO @ Thu, 05 Dec 2019 12:35:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.05_model.r WARNING @ Thu, 05 Dec 2019 12:35:33: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:35:33: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Thu, 05 Dec 2019 12:35:33: #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 12:35:33: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:35:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:35:35: 7000000 INFO @ Thu, 05 Dec 2019 12:35:37: 12000000 INFO @ Thu, 05 Dec 2019 12:35:43: 8000000 INFO @ Thu, 05 Dec 2019 12:35:45: 13000000 INFO @ Thu, 05 Dec 2019 12:35:50: 9000000 INFO @ Thu, 05 Dec 2019 12:35:52: 14000000 INFO @ Thu, 05 Dec 2019 12:35:57: 10000000 INFO @ Thu, 05 Dec 2019 12:35:59: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:35:59: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:35:59: #1 total tags in treatment: 14983051 INFO @ Thu, 05 Dec 2019 12:35:59: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:35:59: #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 12:35:59: #1 tags after filtering in treatment: 14983051 INFO @ Thu, 05 Dec 2019 12:35:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:35:59: #1 finished! INFO @ Thu, 05 Dec 2019 12:35:59: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:35:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:36:01: #2 number of paired peaks: 283 WARNING @ Thu, 05 Dec 2019 12:36:01: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Thu, 05 Dec 2019 12:36:01: start model_add_line... INFO @ Thu, 05 Dec 2019 12:36:01: start X-correlation... INFO @ Thu, 05 Dec 2019 12:36:01: end of X-cor INFO @ Thu, 05 Dec 2019 12:36:01: #2 finished! INFO @ Thu, 05 Dec 2019 12:36:01: #2 predicted fragment length is 65 bps INFO @ Thu, 05 Dec 2019 12:36:01: #2 alternative fragment length(s) may be 4,65 bps INFO @ Thu, 05 Dec 2019 12:36:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.10_model.r WARNING @ Thu, 05 Dec 2019 12:36:01: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:36:01: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Thu, 05 Dec 2019 12:36:01: #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 12:36:01: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:36:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:36:04: 11000000 INFO @ Thu, 05 Dec 2019 12:36:11: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:36:11: 12000000 INFO @ Thu, 05 Dec 2019 12:36:19: 13000000 INFO @ Thu, 05 Dec 2019 12:36:26: 14000000 INFO @ Thu, 05 Dec 2019 12:36:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:36:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:36:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.05_summits.bed INFO @ Thu, 05 Dec 2019 12:36:30: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (4963 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:36:33: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:36:33: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:36:33: #1 total tags in treatment: 14983051 INFO @ Thu, 05 Dec 2019 12:36:33: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:36:33: #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 12:36:33: #1 tags after filtering in treatment: 14983051 INFO @ Thu, 05 Dec 2019 12:36:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:36:33: #1 finished! INFO @ Thu, 05 Dec 2019 12:36:33: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:36:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:36:35: #2 number of paired peaks: 283 WARNING @ Thu, 05 Dec 2019 12:36:35: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Thu, 05 Dec 2019 12:36:35: start model_add_line... INFO @ Thu, 05 Dec 2019 12:36:35: start X-correlation... INFO @ Thu, 05 Dec 2019 12:36:35: end of X-cor INFO @ Thu, 05 Dec 2019 12:36:35: #2 finished! INFO @ Thu, 05 Dec 2019 12:36:35: #2 predicted fragment length is 65 bps INFO @ Thu, 05 Dec 2019 12:36:35: #2 alternative fragment length(s) may be 4,65 bps INFO @ Thu, 05 Dec 2019 12:36:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.20_model.r WARNING @ Thu, 05 Dec 2019 12:36:35: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:36:35: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Thu, 05 Dec 2019 12:36:35: #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 12:36:35: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:36:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:36:39: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:36:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:36:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:36:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.10_summits.bed INFO @ Thu, 05 Dec 2019 12:36:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2284 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:37:13: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:37:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:37:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:37:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107874/SRX4107874.20_summits.bed INFO @ Thu, 05 Dec 2019 12:37:34: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (675 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。