Job ID = 2590245 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 51,680,402 reads read : 51,680,402 reads written : 51,680,402 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: 00:10:50 51680402 reads; of these: 51680402 (100.00%) were unpaired; of these: 32055181 (62.03%) aligned 0 times 16512975 (31.95%) aligned exactly 1 time 3112246 (6.02%) aligned >1 times 37.97% overall alignment rate Time searching: 00:10:50 Overall time: 00:10:50 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] 1801938 / 19625221 = 0.0918 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 @ Mon, 12 Aug 2019 21:10:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.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 @ Mon, 12 Aug 2019 21:10:39: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:10:39: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:10:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.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 @ Mon, 12 Aug 2019 21:10:40: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:10:40: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:10:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.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 @ Mon, 12 Aug 2019 21:10:41: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:10:41: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:10:49: 1000000 INFO @ Mon, 12 Aug 2019 21:10:50: 1000000 INFO @ Mon, 12 Aug 2019 21:10:50: 1000000 INFO @ Mon, 12 Aug 2019 21:10:58: 2000000 INFO @ Mon, 12 Aug 2019 21:10:58: 2000000 INFO @ Mon, 12 Aug 2019 21:11:00: 2000000 INFO @ Mon, 12 Aug 2019 21:11:07: 3000000 INFO @ Mon, 12 Aug 2019 21:11:08: 3000000 INFO @ Mon, 12 Aug 2019 21:11:10: 3000000 INFO @ Mon, 12 Aug 2019 21:11:15: 4000000 INFO @ Mon, 12 Aug 2019 21:11:17: 4000000 INFO @ Mon, 12 Aug 2019 21:11:20: 4000000 INFO @ Mon, 12 Aug 2019 21:11:23: 5000000 INFO @ Mon, 12 Aug 2019 21:11:26: 5000000 INFO @ Mon, 12 Aug 2019 21:11:29: 5000000 INFO @ Mon, 12 Aug 2019 21:11:31: 6000000 INFO @ Mon, 12 Aug 2019 21:11:36: 6000000 INFO @ Mon, 12 Aug 2019 21:11:39: 6000000 INFO @ Mon, 12 Aug 2019 21:11:39: 7000000 INFO @ Mon, 12 Aug 2019 21:11:45: 7000000 INFO @ Mon, 12 Aug 2019 21:11:48: 8000000 INFO @ Mon, 12 Aug 2019 21:11:48: 7000000 INFO @ Mon, 12 Aug 2019 21:11:54: 8000000 INFO @ Mon, 12 Aug 2019 21:11:56: 9000000 INFO @ Mon, 12 Aug 2019 21:11:58: 8000000 INFO @ Mon, 12 Aug 2019 21:12:04: 9000000 INFO @ Mon, 12 Aug 2019 21:12:04: 10000000 INFO @ Mon, 12 Aug 2019 21:12:08: 9000000 INFO @ Mon, 12 Aug 2019 21:12:12: 11000000 INFO @ Mon, 12 Aug 2019 21:12:13: 10000000 INFO @ Mon, 12 Aug 2019 21:12:17: 10000000 INFO @ Mon, 12 Aug 2019 21:12:20: 12000000 INFO @ Mon, 12 Aug 2019 21:12:22: 11000000 INFO @ Mon, 12 Aug 2019 21:12:27: 11000000 INFO @ Mon, 12 Aug 2019 21:12:29: 13000000 INFO @ Mon, 12 Aug 2019 21:12:31: 12000000 INFO @ Mon, 12 Aug 2019 21:12:36: 12000000 INFO @ Mon, 12 Aug 2019 21:12:37: 14000000 INFO @ Mon, 12 Aug 2019 21:12:41: 13000000 INFO @ Mon, 12 Aug 2019 21:12:46: 15000000 INFO @ Mon, 12 Aug 2019 21:12:47: 13000000 INFO @ Mon, 12 Aug 2019 21:12:51: 14000000 INFO @ Mon, 12 Aug 2019 21:12:54: 16000000 INFO @ Mon, 12 Aug 2019 21:12:57: 14000000 INFO @ Mon, 12 Aug 2019 21:13:00: 15000000 INFO @ Mon, 12 Aug 2019 21:13:02: 17000000 INFO @ Mon, 12 Aug 2019 21:13:06: 15000000 INFO @ Mon, 12 Aug 2019 21:13:09: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 21:13:09: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 21:13:09: #1 total tags in treatment: 17823283 INFO @ Mon, 12 Aug 2019 21:13:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:13:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:13:09: #1 tags after filtering in treatment: 17823283 INFO @ Mon, 12 Aug 2019 21:13:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:13:09: #1 finished! INFO @ Mon, 12 Aug 2019 21:13:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:13:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:13:09: 16000000 INFO @ Mon, 12 Aug 2019 21:13:11: #2 number of paired peaks: 193 WARNING @ Mon, 12 Aug 2019 21:13:11: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Mon, 12 Aug 2019 21:13:11: start model_add_line... INFO @ Mon, 12 Aug 2019 21:13:11: start X-correlation... INFO @ Mon, 12 Aug 2019 21:13:11: end of X-cor INFO @ Mon, 12 Aug 2019 21:13:11: #2 finished! INFO @ Mon, 12 Aug 2019 21:13:11: #2 predicted fragment length is 72 bps INFO @ Mon, 12 Aug 2019 21:13:11: #2 alternative fragment length(s) may be 2,72,541 bps INFO @ Mon, 12 Aug 2019 21:13:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.20_model.r WARNING @ Mon, 12 Aug 2019 21:13:11: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:13:11: #2 You may need to consider one of the other alternative d(s): 2,72,541 WARNING @ Mon, 12 Aug 2019 21:13:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 21:13:11: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:13:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:13:16: 16000000 INFO @ Mon, 12 Aug 2019 21:13:19: 17000000 INFO @ Mon, 12 Aug 2019 21:13:25: 17000000 INFO @ Mon, 12 Aug 2019 21:13:26: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 21:13:26: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 21:13:26: #1 total tags in treatment: 17823283 INFO @ Mon, 12 Aug 2019 21:13:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:13:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:13:27: #1 tags after filtering in treatment: 17823283 INFO @ Mon, 12 Aug 2019 21:13:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:13:27: #1 finished! INFO @ Mon, 12 Aug 2019 21:13:27: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:13:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:13:28: #2 number of paired peaks: 193 WARNING @ Mon, 12 Aug 2019 21:13:28: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Mon, 12 Aug 2019 21:13:28: start model_add_line... INFO @ Mon, 12 Aug 2019 21:13:28: start X-correlation... INFO @ Mon, 12 Aug 2019 21:13:28: end of X-cor INFO @ Mon, 12 Aug 2019 21:13:28: #2 finished! INFO @ Mon, 12 Aug 2019 21:13:28: #2 predicted fragment length is 72 bps INFO @ Mon, 12 Aug 2019 21:13:28: #2 alternative fragment length(s) may be 2,72,541 bps INFO @ Mon, 12 Aug 2019 21:13:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.05_model.r WARNING @ Mon, 12 Aug 2019 21:13:28: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:13:28: #2 You may need to consider one of the other alternative d(s): 2,72,541 WARNING @ Mon, 12 Aug 2019 21:13:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 21:13:28: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:13:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:13:33: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 21:13:33: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 21:13:33: #1 total tags in treatment: 17823283 INFO @ Mon, 12 Aug 2019 21:13:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:13:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:13:33: #1 tags after filtering in treatment: 17823283 INFO @ Mon, 12 Aug 2019 21:13:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:13:33: #1 finished! INFO @ Mon, 12 Aug 2019 21:13:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:13:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:13:35: #2 number of paired peaks: 193 WARNING @ Mon, 12 Aug 2019 21:13:35: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Mon, 12 Aug 2019 21:13:35: start model_add_line... INFO @ Mon, 12 Aug 2019 21:13:35: start X-correlation... INFO @ Mon, 12 Aug 2019 21:13:35: end of X-cor INFO @ Mon, 12 Aug 2019 21:13:35: #2 finished! INFO @ Mon, 12 Aug 2019 21:13:35: #2 predicted fragment length is 72 bps INFO @ Mon, 12 Aug 2019 21:13:35: #2 alternative fragment length(s) may be 2,72,541 bps INFO @ Mon, 12 Aug 2019 21:13:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.10_model.r WARNING @ Mon, 12 Aug 2019 21:13:35: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:13:35: #2 You may need to consider one of the other alternative d(s): 2,72,541 WARNING @ Mon, 12 Aug 2019 21:13:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 21:13:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:13:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:13:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:14:10: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:14:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:14:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:14:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.20_summits.bed INFO @ Mon, 12 Aug 2019 21:14:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (224 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:14:17: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:14:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:14:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:14:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.05_summits.bed INFO @ Mon, 12 Aug 2019 21:14:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (595 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:14:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:14:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:14:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985677/SRX5985677.10_summits.bed INFO @ Mon, 12 Aug 2019 21:14:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (433 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。