Job ID = 1291864 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,621,140 reads read : 22,621,140 reads written : 22,621,140 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:04:20 22621140 reads; of these: 22621140 (100.00%) were unpaired; of these: 262510 (1.16%) aligned 0 times 18791080 (83.07%) aligned exactly 1 time 3567550 (15.77%) aligned >1 times 98.84% overall alignment rate Time searching: 00:04:20 Overall time: 00:04:20 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] 3355269 / 22358630 = 0.1501 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 @ Sun, 02 Jun 2019 17:10:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.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 @ Sun, 02 Jun 2019 17:10:27: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:10:27: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:10:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.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 @ Sun, 02 Jun 2019 17:10:27: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:10:27: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:10:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.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 @ Sun, 02 Jun 2019 17:10:27: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:10:27: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:10:34: 1000000 INFO @ Sun, 02 Jun 2019 17:10:36: 1000000 INFO @ Sun, 02 Jun 2019 17:10:36: 1000000 INFO @ Sun, 02 Jun 2019 17:10:41: 2000000 INFO @ Sun, 02 Jun 2019 17:10:44: 2000000 INFO @ Sun, 02 Jun 2019 17:10:45: 2000000 INFO @ Sun, 02 Jun 2019 17:10:48: 3000000 INFO @ Sun, 02 Jun 2019 17:10:52: 3000000 INFO @ Sun, 02 Jun 2019 17:10:53: 3000000 INFO @ Sun, 02 Jun 2019 17:10:55: 4000000 INFO @ Sun, 02 Jun 2019 17:11:00: 4000000 INFO @ Sun, 02 Jun 2019 17:11:02: 4000000 INFO @ Sun, 02 Jun 2019 17:11:02: 5000000 INFO @ Sun, 02 Jun 2019 17:11:09: 6000000 INFO @ Sun, 02 Jun 2019 17:11:09: 5000000 INFO @ Sun, 02 Jun 2019 17:11:10: 5000000 INFO @ Sun, 02 Jun 2019 17:11:15: 7000000 INFO @ Sun, 02 Jun 2019 17:11:18: 6000000 INFO @ Sun, 02 Jun 2019 17:11:19: 6000000 INFO @ Sun, 02 Jun 2019 17:11:22: 8000000 INFO @ Sun, 02 Jun 2019 17:11:27: 7000000 INFO @ Sun, 02 Jun 2019 17:11:28: 7000000 INFO @ Sun, 02 Jun 2019 17:11:29: 9000000 INFO @ Sun, 02 Jun 2019 17:11:35: 10000000 INFO @ Sun, 02 Jun 2019 17:11:35: 8000000 INFO @ Sun, 02 Jun 2019 17:11:37: 8000000 INFO @ Sun, 02 Jun 2019 17:11:42: 11000000 INFO @ Sun, 02 Jun 2019 17:11:44: 9000000 INFO @ Sun, 02 Jun 2019 17:11:45: 9000000 INFO @ Sun, 02 Jun 2019 17:11:48: 12000000 INFO @ Sun, 02 Jun 2019 17:11:53: 10000000 INFO @ Sun, 02 Jun 2019 17:11:54: 10000000 INFO @ Sun, 02 Jun 2019 17:11:55: 13000000 INFO @ Sun, 02 Jun 2019 17:12:01: 14000000 INFO @ Sun, 02 Jun 2019 17:12:02: 11000000 INFO @ Sun, 02 Jun 2019 17:12:03: 11000000 INFO @ Sun, 02 Jun 2019 17:12:08: 15000000 INFO @ Sun, 02 Jun 2019 17:12:10: 12000000 INFO @ Sun, 02 Jun 2019 17:12:11: 12000000 INFO @ Sun, 02 Jun 2019 17:12:14: 16000000 INFO @ Sun, 02 Jun 2019 17:12:17: 13000000 INFO @ Sun, 02 Jun 2019 17:12:19: 13000000 INFO @ Sun, 02 Jun 2019 17:12:21: 17000000 INFO @ Sun, 02 Jun 2019 17:12:25: 14000000 INFO @ Sun, 02 Jun 2019 17:12:27: 14000000 INFO @ Sun, 02 Jun 2019 17:12:28: 18000000 INFO @ Sun, 02 Jun 2019 17:12:33: 15000000 INFO @ Sun, 02 Jun 2019 17:12:34: 19000000 INFO @ Sun, 02 Jun 2019 17:12:35: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 17:12:35: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 17:12:35: #1 total tags in treatment: 19003361 INFO @ Sun, 02 Jun 2019 17:12:35: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:12:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:12:35: 15000000 INFO @ Sun, 02 Jun 2019 17:12:35: #1 tags after filtering in treatment: 19003361 INFO @ Sun, 02 Jun 2019 17:12:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:12:35: #1 finished! INFO @ Sun, 02 Jun 2019 17:12:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:12:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:12:37: #2 number of paired peaks: 228 WARNING @ Sun, 02 Jun 2019 17:12:37: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Sun, 02 Jun 2019 17:12:37: start model_add_line... INFO @ Sun, 02 Jun 2019 17:12:37: start X-correlation... INFO @ Sun, 02 Jun 2019 17:12:37: end of X-cor INFO @ Sun, 02 Jun 2019 17:12:37: #2 finished! INFO @ Sun, 02 Jun 2019 17:12:37: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 17:12:37: #2 alternative fragment length(s) may be 1,40,580 bps INFO @ Sun, 02 Jun 2019 17:12:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.05_model.r WARNING @ Sun, 02 Jun 2019 17:12:37: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:12:37: #2 You may need to consider one of the other alternative d(s): 1,40,580 WARNING @ Sun, 02 Jun 2019 17:12:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:12:37: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:12:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:12:41: 16000000 INFO @ Sun, 02 Jun 2019 17:12:43: 16000000 INFO @ Sun, 02 Jun 2019 17:12:49: 17000000 INFO @ Sun, 02 Jun 2019 17:12:52: 17000000 INFO @ Sun, 02 Jun 2019 17:12:57: 18000000 INFO @ Sun, 02 Jun 2019 17:13:00: 18000000 INFO @ Sun, 02 Jun 2019 17:13:05: 19000000 INFO @ Sun, 02 Jun 2019 17:13:05: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 17:13:05: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 17:13:05: #1 total tags in treatment: 19003361 INFO @ Sun, 02 Jun 2019 17:13:05: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:13:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:13:06: #1 tags after filtering in treatment: 19003361 INFO @ Sun, 02 Jun 2019 17:13:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:13:06: #1 finished! INFO @ Sun, 02 Jun 2019 17:13:06: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:13:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:13:07: #2 number of paired peaks: 228 WARNING @ Sun, 02 Jun 2019 17:13:07: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Sun, 02 Jun 2019 17:13:07: start model_add_line... INFO @ Sun, 02 Jun 2019 17:13:07: start X-correlation... INFO @ Sun, 02 Jun 2019 17:13:07: end of X-cor INFO @ Sun, 02 Jun 2019 17:13:07: #2 finished! INFO @ Sun, 02 Jun 2019 17:13:07: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 17:13:07: #2 alternative fragment length(s) may be 1,40,580 bps INFO @ Sun, 02 Jun 2019 17:13:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.10_model.r WARNING @ Sun, 02 Jun 2019 17:13:07: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:13:07: #2 You may need to consider one of the other alternative d(s): 1,40,580 WARNING @ Sun, 02 Jun 2019 17:13:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:13:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:13:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:13:08: 19000000 INFO @ Sun, 02 Jun 2019 17:13:08: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 17:13:08: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 17:13:08: #1 total tags in treatment: 19003361 INFO @ Sun, 02 Jun 2019 17:13:08: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:13:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:13:09: #1 tags after filtering in treatment: 19003361 INFO @ Sun, 02 Jun 2019 17:13:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:13:09: #1 finished! INFO @ Sun, 02 Jun 2019 17:13:09: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:13:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:13:10: #2 number of paired peaks: 228 WARNING @ Sun, 02 Jun 2019 17:13:10: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Sun, 02 Jun 2019 17:13:10: start model_add_line... INFO @ Sun, 02 Jun 2019 17:13:10: start X-correlation... INFO @ Sun, 02 Jun 2019 17:13:10: end of X-cor INFO @ Sun, 02 Jun 2019 17:13:10: #2 finished! INFO @ Sun, 02 Jun 2019 17:13:10: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 17:13:10: #2 alternative fragment length(s) may be 1,40,580 bps INFO @ Sun, 02 Jun 2019 17:13:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.20_model.r WARNING @ Sun, 02 Jun 2019 17:13:10: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:13:10: #2 You may need to consider one of the other alternative d(s): 1,40,580 WARNING @ Sun, 02 Jun 2019 17:13:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:13:10: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:13:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:13:19: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:13:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:13:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:13:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.05_summits.bed INFO @ Sun, 02 Jun 2019 17:13:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:13:49: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:13:53: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:14:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:14:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:14:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.10_summits.bed INFO @ Sun, 02 Jun 2019 17:14:09: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:14:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:14:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:14:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257699/SRX257699.20_summits.bed INFO @ Sun, 02 Jun 2019 17:14:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。