Job ID = 4288947 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,440,768 reads read : 36,881,536 reads written : 18,440,768 reads 0-length : 18,440,768 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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:18:47 18440768 reads; of these: 18440768 (100.00%) were unpaired; of these: 1763931 (9.57%) aligned 0 times 13373185 (72.52%) aligned exactly 1 time 3303652 (17.91%) aligned >1 times 90.43% overall alignment rate Time searching: 00:18:49 Overall time: 00:18:49 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4788205 / 16676837 = 0.2871 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:19:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.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 @ Tue, 10 Dec 2019 13:19:13: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:19:13: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:19:22: 1000000 INFO @ Tue, 10 Dec 2019 13:19:31: 2000000 INFO @ Tue, 10 Dec 2019 13:19:41: 3000000 INFO @ Tue, 10 Dec 2019 13:19:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.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 @ Tue, 10 Dec 2019 13:19:42: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:19:42: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:19:50: 4000000 INFO @ Tue, 10 Dec 2019 13:19:51: 1000000 INFO @ Tue, 10 Dec 2019 13:19:59: 5000000 INFO @ Tue, 10 Dec 2019 13:20:00: 2000000 INFO @ Tue, 10 Dec 2019 13:20:09: 6000000 INFO @ Tue, 10 Dec 2019 13:20:09: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:20:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.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 @ Tue, 10 Dec 2019 13:20:12: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:20:12: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:20:17: 4000000 INFO @ Tue, 10 Dec 2019 13:20:18: 7000000 INFO @ Tue, 10 Dec 2019 13:20:23: 1000000 INFO @ Tue, 10 Dec 2019 13:20:26: 5000000 INFO @ Tue, 10 Dec 2019 13:20:28: 8000000 INFO @ Tue, 10 Dec 2019 13:20:32: 2000000 INFO @ Tue, 10 Dec 2019 13:20:34: 6000000 INFO @ Tue, 10 Dec 2019 13:20:37: 9000000 INFO @ Tue, 10 Dec 2019 13:20:42: 3000000 INFO @ Tue, 10 Dec 2019 13:20:43: 7000000 INFO @ Tue, 10 Dec 2019 13:20:46: 10000000 INFO @ Tue, 10 Dec 2019 13:20:52: 4000000 INFO @ Tue, 10 Dec 2019 13:20:52: 8000000 INFO @ Tue, 10 Dec 2019 13:20:56: 11000000 INFO @ Tue, 10 Dec 2019 13:21:00: 9000000 INFO @ Tue, 10 Dec 2019 13:21:01: 5000000 INFO @ Tue, 10 Dec 2019 13:21:06: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:21:06: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:21:06: #1 total tags in treatment: 11888632 INFO @ Tue, 10 Dec 2019 13:21:06: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:21:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:21:06: #1 tags after filtering in treatment: 11888433 INFO @ Tue, 10 Dec 2019 13:21:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:21:06: #1 finished! INFO @ Tue, 10 Dec 2019 13:21:06: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:21:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:21:09: 10000000 INFO @ Tue, 10 Dec 2019 13:21:09: #2 number of paired peaks: 44796 INFO @ Tue, 10 Dec 2019 13:21:09: start model_add_line... INFO @ Tue, 10 Dec 2019 13:21:09: start X-correlation... INFO @ Tue, 10 Dec 2019 13:21:09: end of X-cor INFO @ Tue, 10 Dec 2019 13:21:09: #2 finished! INFO @ Tue, 10 Dec 2019 13:21:09: #2 predicted fragment length is 158 bps INFO @ Tue, 10 Dec 2019 13:21:09: #2 alternative fragment length(s) may be 158 bps INFO @ Tue, 10 Dec 2019 13:21:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.05_model.r WARNING @ Tue, 10 Dec 2019 13:21:09: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:21:09: #2 You may need to consider one of the other alternative d(s): 158 WARNING @ Tue, 10 Dec 2019 13:21:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:21:09: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:21:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:21:10: 6000000 INFO @ Tue, 10 Dec 2019 13:21:17: 11000000 INFO @ Tue, 10 Dec 2019 13:21:20: 7000000 INFO @ Tue, 10 Dec 2019 13:21:26: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:21:26: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:21:26: #1 total tags in treatment: 11888632 INFO @ Tue, 10 Dec 2019 13:21:26: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:21:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:21:26: #1 tags after filtering in treatment: 11888433 INFO @ Tue, 10 Dec 2019 13:21:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:21:26: #1 finished! INFO @ Tue, 10 Dec 2019 13:21:26: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:21:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:21:29: 8000000 INFO @ Tue, 10 Dec 2019 13:21:29: #2 number of paired peaks: 44796 INFO @ Tue, 10 Dec 2019 13:21:29: start model_add_line... INFO @ Tue, 10 Dec 2019 13:21:29: start X-correlation... INFO @ Tue, 10 Dec 2019 13:21:29: end of X-cor INFO @ Tue, 10 Dec 2019 13:21:29: #2 finished! INFO @ Tue, 10 Dec 2019 13:21:29: #2 predicted fragment length is 158 bps INFO @ Tue, 10 Dec 2019 13:21:29: #2 alternative fragment length(s) may be 158 bps INFO @ Tue, 10 Dec 2019 13:21:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.10_model.r WARNING @ Tue, 10 Dec 2019 13:21:29: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:21:29: #2 You may need to consider one of the other alternative d(s): 158 WARNING @ Tue, 10 Dec 2019 13:21:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:21:29: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:21:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:21:38: 9000000 INFO @ Tue, 10 Dec 2019 13:21:47: 10000000 INFO @ Tue, 10 Dec 2019 13:21:47: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:21:57: 11000000 INFO @ Tue, 10 Dec 2019 13:22:05: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:22:05: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:22:05: #1 total tags in treatment: 11888632 INFO @ Tue, 10 Dec 2019 13:22:05: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:22:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:22:05: #1 tags after filtering in treatment: 11888433 INFO @ Tue, 10 Dec 2019 13:22:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:22:05: #1 finished! INFO @ Tue, 10 Dec 2019 13:22:05: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:22:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:22:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:22:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:22:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.05_summits.bed INFO @ Tue, 10 Dec 2019 13:22:08: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:22:08: Done! INFO @ Tue, 10 Dec 2019 13:22:08: #2 number of paired peaks: 44796 INFO @ Tue, 10 Dec 2019 13:22:08: start model_add_line... INFO @ Tue, 10 Dec 2019 13:22:08: start X-correlation... INFO @ Tue, 10 Dec 2019 13:22:08: end of X-cor INFO @ Tue, 10 Dec 2019 13:22:08: #2 finished! INFO @ Tue, 10 Dec 2019 13:22:08: #2 predicted fragment length is 158 bps INFO @ Tue, 10 Dec 2019 13:22:08: #2 alternative fragment length(s) may be 158 bps INFO @ Tue, 10 Dec 2019 13:22:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.20_model.r WARNING @ Tue, 10 Dec 2019 13:22:08: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:22:08: #2 You may need to consider one of the other alternative d(s): 158 WARNING @ Tue, 10 Dec 2019 13:22:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:22:08: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:22:08: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (77 chroms): 6 millis pass2 - checking and writing primary data (23205 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:22:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:22:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:22:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.10_summits.bed INFO @ Tue, 10 Dec 2019 13:22:28: Done! pass1 - making usageList (55 chroms): 3 millis pass2 - checking and writing primary data (11957 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:22:46: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:23:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:23:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:23:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460575/SRX5460575.20_summits.bed INFO @ Tue, 10 Dec 2019 13:23:06: Done! pass1 - making usageList (43 chroms): 3 millis pass2 - checking and writing primary data (4564 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。