Job ID = 4303034 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,788,149 reads read : 30,788,149 reads written : 30,788,149 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1163597.sra.cache’: 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: 00:00:00 Multiseed full-index search: 00:07:08 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 171815 (0.56%) aligned 0 times 25273606 (82.09%) aligned exactly 1 time 5342728 (17.35%) aligned >1 times 99.44% overall alignment rate Time searching: 00:07:09 Overall time: 00:07:09 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] 4711154 / 30616334 = 0.1539 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:48:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.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, 12 Dec 2019 00:48:19: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:48:19: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:48:28: 1000000 INFO @ Thu, 12 Dec 2019 00:48:36: 2000000 INFO @ Thu, 12 Dec 2019 00:48:45: 3000000 INFO @ Thu, 12 Dec 2019 00:48:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.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, 12 Dec 2019 00:48:48: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:48:48: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:48:53: 4000000 INFO @ Thu, 12 Dec 2019 00:48:57: 1000000 INFO @ Thu, 12 Dec 2019 00:49:01: 5000000 INFO @ Thu, 12 Dec 2019 00:49:07: 2000000 INFO @ Thu, 12 Dec 2019 00:49:10: 6000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:49:16: 3000000 INFO @ Thu, 12 Dec 2019 00:49:18: 7000000 INFO @ Thu, 12 Dec 2019 00:49:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.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, 12 Dec 2019 00:49:18: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:49:18: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:49:25: 4000000 INFO @ Thu, 12 Dec 2019 00:49:25: 1000000 INFO @ Thu, 12 Dec 2019 00:49:26: 8000000 INFO @ Thu, 12 Dec 2019 00:49:32: 2000000 INFO @ Thu, 12 Dec 2019 00:49:34: 5000000 INFO @ Thu, 12 Dec 2019 00:49:35: 9000000 INFO @ Thu, 12 Dec 2019 00:49:39: 3000000 INFO @ Thu, 12 Dec 2019 00:49:43: 10000000 INFO @ Thu, 12 Dec 2019 00:49:43: 6000000 INFO @ Thu, 12 Dec 2019 00:49:46: 4000000 INFO @ Thu, 12 Dec 2019 00:49:52: 11000000 INFO @ Thu, 12 Dec 2019 00:49:52: 5000000 INFO @ Thu, 12 Dec 2019 00:49:53: 7000000 INFO @ Thu, 12 Dec 2019 00:49:59: 6000000 INFO @ Thu, 12 Dec 2019 00:50:00: 12000000 INFO @ Thu, 12 Dec 2019 00:50:02: 8000000 INFO @ Thu, 12 Dec 2019 00:50:05: 7000000 INFO @ Thu, 12 Dec 2019 00:50:09: 13000000 INFO @ Thu, 12 Dec 2019 00:50:11: 9000000 INFO @ Thu, 12 Dec 2019 00:50:12: 8000000 INFO @ Thu, 12 Dec 2019 00:50:17: 14000000 INFO @ Thu, 12 Dec 2019 00:50:19: 9000000 INFO @ Thu, 12 Dec 2019 00:50:20: 10000000 INFO @ Thu, 12 Dec 2019 00:50:25: 10000000 INFO @ Thu, 12 Dec 2019 00:50:25: 15000000 INFO @ Thu, 12 Dec 2019 00:50:29: 11000000 INFO @ Thu, 12 Dec 2019 00:50:32: 11000000 INFO @ Thu, 12 Dec 2019 00:50:34: 16000000 INFO @ Thu, 12 Dec 2019 00:50:38: 12000000 INFO @ Thu, 12 Dec 2019 00:50:39: 12000000 INFO @ Thu, 12 Dec 2019 00:50:43: 17000000 INFO @ Thu, 12 Dec 2019 00:50:45: 13000000 INFO @ Thu, 12 Dec 2019 00:50:47: 13000000 INFO @ Thu, 12 Dec 2019 00:50:51: 18000000 INFO @ Thu, 12 Dec 2019 00:50:52: 14000000 INFO @ Thu, 12 Dec 2019 00:50:56: 14000000 INFO @ Thu, 12 Dec 2019 00:50:59: 15000000 INFO @ Thu, 12 Dec 2019 00:50:59: 19000000 INFO @ Thu, 12 Dec 2019 00:51:05: 15000000 INFO @ Thu, 12 Dec 2019 00:51:06: 16000000 INFO @ Thu, 12 Dec 2019 00:51:08: 20000000 INFO @ Thu, 12 Dec 2019 00:51:12: 17000000 INFO @ Thu, 12 Dec 2019 00:51:15: 16000000 INFO @ Thu, 12 Dec 2019 00:51:16: 21000000 INFO @ Thu, 12 Dec 2019 00:51:19: 18000000 INFO @ Thu, 12 Dec 2019 00:51:24: 17000000 INFO @ Thu, 12 Dec 2019 00:51:25: 22000000 INFO @ Thu, 12 Dec 2019 00:51:25: 19000000 INFO @ Thu, 12 Dec 2019 00:51:32: 20000000 INFO @ Thu, 12 Dec 2019 00:51:33: 23000000 INFO @ Thu, 12 Dec 2019 00:51:33: 18000000 INFO @ Thu, 12 Dec 2019 00:51:39: 21000000 INFO @ Thu, 12 Dec 2019 00:51:42: 24000000 INFO @ Thu, 12 Dec 2019 00:51:42: 19000000 INFO @ Thu, 12 Dec 2019 00:51:45: 22000000 INFO @ Thu, 12 Dec 2019 00:51:50: 25000000 INFO @ Thu, 12 Dec 2019 00:51:51: 20000000 INFO @ Thu, 12 Dec 2019 00:51:52: 23000000 INFO @ Thu, 12 Dec 2019 00:51:58: #1 tag size is determined as 36 bps INFO @ Thu, 12 Dec 2019 00:51:58: #1 tag size = 36 INFO @ Thu, 12 Dec 2019 00:51:58: #1 total tags in treatment: 25905180 INFO @ Thu, 12 Dec 2019 00:51:58: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:51:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:51:59: #1 tags after filtering in treatment: 25905180 INFO @ Thu, 12 Dec 2019 00:51:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:51:59: #1 finished! INFO @ Thu, 12 Dec 2019 00:51:59: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:51:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:51:59: 24000000 INFO @ Thu, 12 Dec 2019 00:52:01: #2 number of paired peaks: 145 WARNING @ Thu, 12 Dec 2019 00:52:01: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Thu, 12 Dec 2019 00:52:01: start model_add_line... INFO @ Thu, 12 Dec 2019 00:52:01: 21000000 INFO @ Thu, 12 Dec 2019 00:52:01: start X-correlation... INFO @ Thu, 12 Dec 2019 00:52:01: end of X-cor INFO @ Thu, 12 Dec 2019 00:52:01: #2 finished! INFO @ Thu, 12 Dec 2019 00:52:01: #2 predicted fragment length is 1 bps INFO @ Thu, 12 Dec 2019 00:52:01: #2 alternative fragment length(s) may be 1,32,512,574 bps INFO @ Thu, 12 Dec 2019 00:52:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.05_model.r WARNING @ Thu, 12 Dec 2019 00:52:01: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:52:01: #2 You may need to consider one of the other alternative d(s): 1,32,512,574 WARNING @ Thu, 12 Dec 2019 00:52:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:52:01: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:52:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:52:05: 25000000 INFO @ Thu, 12 Dec 2019 00:52:10: 22000000 INFO @ Thu, 12 Dec 2019 00:52:11: #1 tag size is determined as 36 bps INFO @ Thu, 12 Dec 2019 00:52:11: #1 tag size = 36 INFO @ Thu, 12 Dec 2019 00:52:11: #1 total tags in treatment: 25905180 INFO @ Thu, 12 Dec 2019 00:52:11: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:52:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:52:12: #1 tags after filtering in treatment: 25905180 INFO @ Thu, 12 Dec 2019 00:52:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:52:12: #1 finished! INFO @ Thu, 12 Dec 2019 00:52:12: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:52:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:52:14: #2 number of paired peaks: 145 WARNING @ Thu, 12 Dec 2019 00:52:14: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Thu, 12 Dec 2019 00:52:14: start model_add_line... INFO @ Thu, 12 Dec 2019 00:52:14: start X-correlation... INFO @ Thu, 12 Dec 2019 00:52:14: end of X-cor INFO @ Thu, 12 Dec 2019 00:52:14: #2 finished! INFO @ Thu, 12 Dec 2019 00:52:14: #2 predicted fragment length is 1 bps INFO @ Thu, 12 Dec 2019 00:52:14: #2 alternative fragment length(s) may be 1,32,512,574 bps INFO @ Thu, 12 Dec 2019 00:52:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.20_model.r WARNING @ Thu, 12 Dec 2019 00:52:14: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:52:14: #2 You may need to consider one of the other alternative d(s): 1,32,512,574 WARNING @ Thu, 12 Dec 2019 00:52:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:52:14: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:52:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:52:19: 23000000 INFO @ Thu, 12 Dec 2019 00:52:28: 24000000 INFO @ Thu, 12 Dec 2019 00:52:37: 25000000 INFO @ Thu, 12 Dec 2019 00:52:45: #1 tag size is determined as 36 bps INFO @ Thu, 12 Dec 2019 00:52:45: #1 tag size = 36 INFO @ Thu, 12 Dec 2019 00:52:45: #1 total tags in treatment: 25905180 INFO @ Thu, 12 Dec 2019 00:52:45: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:52:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:52:46: #1 tags after filtering in treatment: 25905180 INFO @ Thu, 12 Dec 2019 00:52:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:52:46: #1 finished! INFO @ Thu, 12 Dec 2019 00:52:46: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:52:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:52:48: #2 number of paired peaks: 145 WARNING @ Thu, 12 Dec 2019 00:52:48: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Thu, 12 Dec 2019 00:52:48: start model_add_line... INFO @ Thu, 12 Dec 2019 00:52:48: start X-correlation... INFO @ Thu, 12 Dec 2019 00:52:48: end of X-cor INFO @ Thu, 12 Dec 2019 00:52:48: #2 finished! INFO @ Thu, 12 Dec 2019 00:52:48: #2 predicted fragment length is 1 bps INFO @ Thu, 12 Dec 2019 00:52:48: #2 alternative fragment length(s) may be 1,32,512,574 bps INFO @ Thu, 12 Dec 2019 00:52:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.10_model.r WARNING @ Thu, 12 Dec 2019 00:52:48: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:52:48: #2 You may need to consider one of the other alternative d(s): 1,32,512,574 WARNING @ Thu, 12 Dec 2019 00:52:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:52:48: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:52:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:52:53: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:53:06: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:53:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:53:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:53:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.05_summits.bed INFO @ Thu, 12 Dec 2019 00:53:16: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:53:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:53:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:53:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.20_summits.bed INFO @ Thu, 12 Dec 2019 00:53:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:53:40: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:54:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:54:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:54:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466531/SRX466531.10_summits.bed INFO @ Thu, 12 Dec 2019 00:54:03: 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。