Job ID = 1291766 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,225,540 reads read : 28,225,540 reads written : 28,225,540 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: 00:05:36 28225540 reads; of these: 28225540 (100.00%) were unpaired; of these: 1618608 (5.73%) aligned 0 times 22165031 (78.53%) aligned exactly 1 time 4441901 (15.74%) aligned >1 times 94.27% overall alignment rate Time searching: 00:05:36 Overall time: 00:05:36 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] 2683609 / 26606932 = 0.1009 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 16:48:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.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 16:48:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.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 16:48:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:48:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:48:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:48:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:48:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.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 16:48:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:48:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:48:13: 1000000 INFO @ Sun, 02 Jun 2019 16:48:13: 1000000 INFO @ Sun, 02 Jun 2019 16:48:14: 1000000 INFO @ Sun, 02 Jun 2019 16:48:21: 2000000 INFO @ Sun, 02 Jun 2019 16:48:21: 2000000 INFO @ Sun, 02 Jun 2019 16:48:21: 2000000 INFO @ Sun, 02 Jun 2019 16:48:28: 3000000 INFO @ Sun, 02 Jun 2019 16:48:28: 3000000 INFO @ Sun, 02 Jun 2019 16:48:28: 3000000 INFO @ Sun, 02 Jun 2019 16:48:35: 4000000 INFO @ Sun, 02 Jun 2019 16:48:35: 4000000 INFO @ Sun, 02 Jun 2019 16:48:35: 4000000 INFO @ Sun, 02 Jun 2019 16:48:42: 5000000 INFO @ Sun, 02 Jun 2019 16:48:42: 5000000 INFO @ Sun, 02 Jun 2019 16:48:43: 5000000 INFO @ Sun, 02 Jun 2019 16:48:50: 6000000 INFO @ Sun, 02 Jun 2019 16:48:50: 6000000 INFO @ Sun, 02 Jun 2019 16:48:50: 6000000 INFO @ Sun, 02 Jun 2019 16:48:57: 7000000 INFO @ Sun, 02 Jun 2019 16:48:57: 7000000 INFO @ Sun, 02 Jun 2019 16:48:57: 7000000 INFO @ Sun, 02 Jun 2019 16:49:04: 8000000 INFO @ Sun, 02 Jun 2019 16:49:04: 8000000 INFO @ Sun, 02 Jun 2019 16:49:04: 8000000 INFO @ Sun, 02 Jun 2019 16:49:11: 9000000 INFO @ Sun, 02 Jun 2019 16:49:11: 9000000 INFO @ Sun, 02 Jun 2019 16:49:12: 9000000 INFO @ Sun, 02 Jun 2019 16:49:18: 10000000 INFO @ Sun, 02 Jun 2019 16:49:18: 10000000 INFO @ Sun, 02 Jun 2019 16:49:19: 10000000 INFO @ Sun, 02 Jun 2019 16:49:26: 11000000 INFO @ Sun, 02 Jun 2019 16:49:26: 11000000 INFO @ Sun, 02 Jun 2019 16:49:26: 11000000 INFO @ Sun, 02 Jun 2019 16:49:33: 12000000 INFO @ Sun, 02 Jun 2019 16:49:33: 12000000 INFO @ Sun, 02 Jun 2019 16:49:33: 12000000 INFO @ Sun, 02 Jun 2019 16:49:40: 13000000 INFO @ Sun, 02 Jun 2019 16:49:40: 13000000 INFO @ Sun, 02 Jun 2019 16:49:40: 13000000 INFO @ Sun, 02 Jun 2019 16:49:47: 14000000 INFO @ Sun, 02 Jun 2019 16:49:47: 14000000 INFO @ Sun, 02 Jun 2019 16:49:48: 14000000 INFO @ Sun, 02 Jun 2019 16:49:54: 15000000 INFO @ Sun, 02 Jun 2019 16:49:54: 15000000 INFO @ Sun, 02 Jun 2019 16:49:55: 15000000 INFO @ Sun, 02 Jun 2019 16:50:00: 16000000 INFO @ Sun, 02 Jun 2019 16:50:02: 16000000 INFO @ Sun, 02 Jun 2019 16:50:02: 16000000 INFO @ Sun, 02 Jun 2019 16:50:07: 17000000 INFO @ Sun, 02 Jun 2019 16:50:09: 17000000 INFO @ Sun, 02 Jun 2019 16:50:10: 17000000 INFO @ Sun, 02 Jun 2019 16:50:13: 18000000 INFO @ Sun, 02 Jun 2019 16:50:16: 18000000 INFO @ Sun, 02 Jun 2019 16:50:18: 18000000 INFO @ Sun, 02 Jun 2019 16:50:19: 19000000 INFO @ Sun, 02 Jun 2019 16:50:23: 19000000 INFO @ Sun, 02 Jun 2019 16:50:26: 20000000 INFO @ Sun, 02 Jun 2019 16:50:26: 19000000 INFO @ Sun, 02 Jun 2019 16:50:30: 20000000 INFO @ Sun, 02 Jun 2019 16:50:32: 21000000 INFO @ Sun, 02 Jun 2019 16:50:34: 20000000 INFO @ Sun, 02 Jun 2019 16:50:37: 21000000 INFO @ Sun, 02 Jun 2019 16:50:38: 22000000 INFO @ Sun, 02 Jun 2019 16:50:42: 21000000 INFO @ Sun, 02 Jun 2019 16:50:44: 22000000 INFO @ Sun, 02 Jun 2019 16:50:45: 23000000 INFO @ Sun, 02 Jun 2019 16:50:50: 22000000 INFO @ Sun, 02 Jun 2019 16:50:51: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:50:51: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:50:51: #1 total tags in treatment: 23923323 INFO @ Sun, 02 Jun 2019 16:50:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:50:51: #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 16:50:51: #1 tags after filtering in treatment: 23923323 INFO @ Sun, 02 Jun 2019 16:50:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:50:51: #1 finished! INFO @ Sun, 02 Jun 2019 16:50:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:50:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:50:52: 23000000 INFO @ Sun, 02 Jun 2019 16:50:53: #2 number of paired peaks: 167 WARNING @ Sun, 02 Jun 2019 16:50:53: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Sun, 02 Jun 2019 16:50:53: start model_add_line... INFO @ Sun, 02 Jun 2019 16:50:53: start X-correlation... INFO @ Sun, 02 Jun 2019 16:50:53: end of X-cor INFO @ Sun, 02 Jun 2019 16:50:53: #2 finished! INFO @ Sun, 02 Jun 2019 16:50:53: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:50:53: #2 alternative fragment length(s) may be 1,420,479,528,561,598 bps INFO @ Sun, 02 Jun 2019 16:50:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.05_model.r WARNING @ Sun, 02 Jun 2019 16:50:53: #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 16:50:53: #2 You may need to consider one of the other alternative d(s): 1,420,479,528,561,598 WARNING @ Sun, 02 Jun 2019 16:50:53: #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 16:50:53: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:50:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:50:58: 23000000 INFO @ Sun, 02 Jun 2019 16:50:58: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:50:58: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:50:58: #1 total tags in treatment: 23923323 INFO @ Sun, 02 Jun 2019 16:50:58: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:50:58: #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 16:50:59: #1 tags after filtering in treatment: 23923323 INFO @ Sun, 02 Jun 2019 16:50:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:50:59: #1 finished! INFO @ Sun, 02 Jun 2019 16:50:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:50:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:51:01: #2 number of paired peaks: 167 WARNING @ Sun, 02 Jun 2019 16:51:01: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Sun, 02 Jun 2019 16:51:01: start model_add_line... INFO @ Sun, 02 Jun 2019 16:51:01: start X-correlation... INFO @ Sun, 02 Jun 2019 16:51:01: end of X-cor INFO @ Sun, 02 Jun 2019 16:51:01: #2 finished! INFO @ Sun, 02 Jun 2019 16:51:01: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:51:01: #2 alternative fragment length(s) may be 1,420,479,528,561,598 bps INFO @ Sun, 02 Jun 2019 16:51:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.20_model.r WARNING @ Sun, 02 Jun 2019 16:51:01: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:51:01: #2 You may need to consider one of the other alternative d(s): 1,420,479,528,561,598 WARNING @ Sun, 02 Jun 2019 16:51:01: #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 16:51:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:51:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:51:06: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:51:06: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:51:06: #1 total tags in treatment: 23923323 INFO @ Sun, 02 Jun 2019 16:51:06: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:51:06: #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 16:51:06: #1 tags after filtering in treatment: 23923323 INFO @ Sun, 02 Jun 2019 16:51:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:51:06: #1 finished! INFO @ Sun, 02 Jun 2019 16:51:06: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:51:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:51:08: #2 number of paired peaks: 167 WARNING @ Sun, 02 Jun 2019 16:51:08: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Sun, 02 Jun 2019 16:51:08: start model_add_line... INFO @ Sun, 02 Jun 2019 16:51:08: start X-correlation... INFO @ Sun, 02 Jun 2019 16:51:08: end of X-cor INFO @ Sun, 02 Jun 2019 16:51:08: #2 finished! INFO @ Sun, 02 Jun 2019 16:51:08: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:51:08: #2 alternative fragment length(s) may be 1,420,479,528,561,598 bps INFO @ Sun, 02 Jun 2019 16:51:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.10_model.r WARNING @ Sun, 02 Jun 2019 16:51:08: #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 16:51:08: #2 You may need to consider one of the other alternative d(s): 1,420,479,528,561,598 WARNING @ Sun, 02 Jun 2019 16:51:08: #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 16:51:08: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:51:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:51:42: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:51:50: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:51:57: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:52:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:52:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:52:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.05_summits.bed INFO @ Sun, 02 Jun 2019 16:52:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:52:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:52:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:52:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.20_summits.bed INFO @ Sun, 02 Jun 2019 16:52:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:52:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:52:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:52:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX245915/SRX245915.10_summits.bed INFO @ Sun, 02 Jun 2019 16:52:19: 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。