Job ID = 2640491 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,855,369 reads read : 63,710,738 reads written : 31,855,369 reads 0-length : 31,855,369 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: 00:00:01 Time loading forward index: 00:00:04 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:30:27 31855369 reads; of these: 31855369 (100.00%) were unpaired; of these: 790709 (2.48%) aligned 0 times 22642276 (71.08%) aligned exactly 1 time 8422384 (26.44%) aligned >1 times 97.52% overall alignment rate Time searching: 00:30:34 Overall time: 00:30:34 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 3213368 / 31064660 = 0.1034 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:07:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:07:33: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:07:33: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:07:40: 1000000 INFO @ Sat, 24 Aug 2019 18:07:48: 2000000 INFO @ Sat, 24 Aug 2019 18:07:55: 3000000 INFO @ Sat, 24 Aug 2019 18:08:02: 4000000 INFO @ Sat, 24 Aug 2019 18:08:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:08:02: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:08:02: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:08:09: 5000000 INFO @ Sat, 24 Aug 2019 18:08:10: 1000000 INFO @ Sat, 24 Aug 2019 18:08:16: 6000000 INFO @ Sat, 24 Aug 2019 18:08:18: 2000000 INFO @ Sat, 24 Aug 2019 18:08:24: 7000000 INFO @ Sat, 24 Aug 2019 18:08:26: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:08:31: 8000000 INFO @ Sat, 24 Aug 2019 18:08:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:08:32: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:08:32: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:08:34: 4000000 INFO @ Sat, 24 Aug 2019 18:08:38: 9000000 INFO @ Sat, 24 Aug 2019 18:08:39: 1000000 INFO @ Sat, 24 Aug 2019 18:08:43: 5000000 INFO @ Sat, 24 Aug 2019 18:08:46: 10000000 INFO @ Sat, 24 Aug 2019 18:08:46: 2000000 INFO @ Sat, 24 Aug 2019 18:08:51: 6000000 INFO @ Sat, 24 Aug 2019 18:08:53: 3000000 INFO @ Sat, 24 Aug 2019 18:08:53: 11000000 INFO @ Sat, 24 Aug 2019 18:08:59: 7000000 INFO @ Sat, 24 Aug 2019 18:08:59: 4000000 INFO @ Sat, 24 Aug 2019 18:09:00: 12000000 INFO @ Sat, 24 Aug 2019 18:09:06: 5000000 INFO @ Sat, 24 Aug 2019 18:09:07: 8000000 INFO @ Sat, 24 Aug 2019 18:09:07: 13000000 INFO @ Sat, 24 Aug 2019 18:09:13: 6000000 INFO @ Sat, 24 Aug 2019 18:09:15: 14000000 INFO @ Sat, 24 Aug 2019 18:09:16: 9000000 INFO @ Sat, 24 Aug 2019 18:09:19: 7000000 INFO @ Sat, 24 Aug 2019 18:09:22: 15000000 INFO @ Sat, 24 Aug 2019 18:09:24: 10000000 INFO @ Sat, 24 Aug 2019 18:09:26: 8000000 INFO @ Sat, 24 Aug 2019 18:09:29: 16000000 INFO @ Sat, 24 Aug 2019 18:09:32: 11000000 INFO @ Sat, 24 Aug 2019 18:09:33: 9000000 INFO @ Sat, 24 Aug 2019 18:09:36: 17000000 INFO @ Sat, 24 Aug 2019 18:09:39: 10000000 INFO @ Sat, 24 Aug 2019 18:09:40: 12000000 INFO @ Sat, 24 Aug 2019 18:09:44: 18000000 INFO @ Sat, 24 Aug 2019 18:09:46: 11000000 INFO @ Sat, 24 Aug 2019 18:09:49: 13000000 INFO @ Sat, 24 Aug 2019 18:09:51: 19000000 INFO @ Sat, 24 Aug 2019 18:09:53: 12000000 INFO @ Sat, 24 Aug 2019 18:09:57: 14000000 INFO @ Sat, 24 Aug 2019 18:09:58: 20000000 INFO @ Sat, 24 Aug 2019 18:10:00: 13000000 INFO @ Sat, 24 Aug 2019 18:10:05: 15000000 INFO @ Sat, 24 Aug 2019 18:10:06: 21000000 INFO @ Sat, 24 Aug 2019 18:10:06: 14000000 INFO @ Sat, 24 Aug 2019 18:10:13: 22000000 INFO @ Sat, 24 Aug 2019 18:10:13: 15000000 INFO @ Sat, 24 Aug 2019 18:10:13: 16000000 INFO @ Sat, 24 Aug 2019 18:10:22: 16000000 INFO @ Sat, 24 Aug 2019 18:10:25: 23000000 INFO @ Sat, 24 Aug 2019 18:10:27: 17000000 INFO @ Sat, 24 Aug 2019 18:10:34: 17000000 INFO @ Sat, 24 Aug 2019 18:10:36: 24000000 INFO @ Sat, 24 Aug 2019 18:10:37: 18000000 INFO @ Sat, 24 Aug 2019 18:10:45: 18000000 INFO @ Sat, 24 Aug 2019 18:10:46: 25000000 INFO @ Sat, 24 Aug 2019 18:10:47: 19000000 INFO @ Sat, 24 Aug 2019 18:10:55: 19000000 INFO @ Sat, 24 Aug 2019 18:10:56: 26000000 INFO @ Sat, 24 Aug 2019 18:10:59: 20000000 INFO @ Sat, 24 Aug 2019 18:11:05: 20000000 INFO @ Sat, 24 Aug 2019 18:11:06: 27000000 INFO @ Sat, 24 Aug 2019 18:11:09: 21000000 INFO @ Sat, 24 Aug 2019 18:11:12: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:11:12: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:11:12: #1 total tags in treatment: 27851292 INFO @ Sat, 24 Aug 2019 18:11:12: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:11:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:11:13: #1 tags after filtering in treatment: 27851180 INFO @ Sat, 24 Aug 2019 18:11:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:11:13: #1 finished! INFO @ Sat, 24 Aug 2019 18:11:13: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:11:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:11:13: 21000000 INFO @ Sat, 24 Aug 2019 18:11:16: #2 number of paired peaks: 5814 INFO @ Sat, 24 Aug 2019 18:11:16: start model_add_line... INFO @ Sat, 24 Aug 2019 18:11:17: start X-correlation... INFO @ Sat, 24 Aug 2019 18:11:17: end of X-cor INFO @ Sat, 24 Aug 2019 18:11:17: #2 finished! INFO @ Sat, 24 Aug 2019 18:11:17: #2 predicted fragment length is 52 bps INFO @ Sat, 24 Aug 2019 18:11:17: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 24 Aug 2019 18:11:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.05_model.r WARNING @ Sat, 24 Aug 2019 18:11:17: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:11:17: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 24 Aug 2019 18:11:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 18:11:17: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:11:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:11:17: 22000000 INFO @ Sat, 24 Aug 2019 18:11:22: 22000000 INFO @ Sat, 24 Aug 2019 18:11:25: 23000000 INFO @ Sat, 24 Aug 2019 18:11:30: 23000000 INFO @ Sat, 24 Aug 2019 18:11:37: 24000000 INFO @ Sat, 24 Aug 2019 18:11:43: 24000000 INFO @ Sat, 24 Aug 2019 18:11:48: 25000000 INFO @ Sat, 24 Aug 2019 18:11:51: 25000000 INFO @ Sat, 24 Aug 2019 18:11:57: 26000000 INFO @ Sat, 24 Aug 2019 18:12:00: 26000000 INFO @ Sat, 24 Aug 2019 18:12:05: 27000000 INFO @ Sat, 24 Aug 2019 18:12:09: 27000000 INFO @ Sat, 24 Aug 2019 18:12:12: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:12:12: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:12:12: #1 total tags in treatment: 27851292 INFO @ Sat, 24 Aug 2019 18:12:12: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:12:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:12:12: #1 tags after filtering in treatment: 27851180 INFO @ Sat, 24 Aug 2019 18:12:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:12:12: #1 finished! INFO @ Sat, 24 Aug 2019 18:12:12: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:12:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:12:16: #2 number of paired peaks: 5814 INFO @ Sat, 24 Aug 2019 18:12:16: start model_add_line... INFO @ Sat, 24 Aug 2019 18:12:16: start X-correlation... INFO @ Sat, 24 Aug 2019 18:12:16: end of X-cor INFO @ Sat, 24 Aug 2019 18:12:16: #2 finished! INFO @ Sat, 24 Aug 2019 18:12:16: #2 predicted fragment length is 52 bps INFO @ Sat, 24 Aug 2019 18:12:16: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 24 Aug 2019 18:12:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.10_model.r WARNING @ Sat, 24 Aug 2019 18:12:16: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:12:16: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 24 Aug 2019 18:12:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 18:12:16: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:12:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:12:16: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:12:16: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:12:16: #1 total tags in treatment: 27851292 INFO @ Sat, 24 Aug 2019 18:12:16: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:12:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:12:17: #1 tags after filtering in treatment: 27851180 INFO @ Sat, 24 Aug 2019 18:12:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:12:17: #1 finished! INFO @ Sat, 24 Aug 2019 18:12:17: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:12:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:12:20: #2 number of paired peaks: 5814 INFO @ Sat, 24 Aug 2019 18:12:20: start model_add_line... INFO @ Sat, 24 Aug 2019 18:12:20: start X-correlation... INFO @ Sat, 24 Aug 2019 18:12:20: end of X-cor INFO @ Sat, 24 Aug 2019 18:12:20: #2 finished! INFO @ Sat, 24 Aug 2019 18:12:20: #2 predicted fragment length is 52 bps INFO @ Sat, 24 Aug 2019 18:12:20: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 24 Aug 2019 18:12:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.20_model.r WARNING @ Sat, 24 Aug 2019 18:12:20: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:12:20: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 24 Aug 2019 18:12:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 18:12:20: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:12:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:12:49: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:13:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:13:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:13:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.05_summits.bed INFO @ Sat, 24 Aug 2019 18:13:34: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (2042 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:13:44: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:13:48: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:14:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:14:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:14:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.10_summits.bed INFO @ Sat, 24 Aug 2019 18:14:29: Done! pass1 - making usageList (39 chroms): 2 millis pass2 - checking and writing primary data (1203 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:14:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:14:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:14:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374998/SRX5374998.20_summits.bed INFO @ Sat, 24 Aug 2019 18:14:33: Done! pass1 - making usageList (30 chroms): 62 millis pass2 - checking and writing primary data (533 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。