Job ID = 1292514 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 ‘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 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 171805 (0.56%) aligned 0 times 25273640 (82.09%) aligned exactly 1 time 5342704 (17.35%) aligned >1 times 99.44% 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] 4711378 / 30616344 = 0.1539 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 19:36:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.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 19:36:21: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:36:21: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:36:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.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 19:36:21: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:36:21: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:36:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.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 19:36:21: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:36:21: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:36:28: 1000000 INFO @ Sun, 02 Jun 2019 19:36:29: 1000000 INFO @ Sun, 02 Jun 2019 19:36:29: 1000000 INFO @ Sun, 02 Jun 2019 19:36:36: 2000000 INFO @ Sun, 02 Jun 2019 19:36:37: 2000000 INFO @ Sun, 02 Jun 2019 19:36:37: 2000000 INFO @ Sun, 02 Jun 2019 19:36:43: 3000000 INFO @ Sun, 02 Jun 2019 19:36:44: 3000000 INFO @ Sun, 02 Jun 2019 19:36:44: 3000000 INFO @ Sun, 02 Jun 2019 19:36:50: 4000000 INFO @ Sun, 02 Jun 2019 19:36:52: 4000000 INFO @ Sun, 02 Jun 2019 19:36:53: 4000000 INFO @ Sun, 02 Jun 2019 19:36:58: 5000000 INFO @ Sun, 02 Jun 2019 19:37:00: 5000000 INFO @ Sun, 02 Jun 2019 19:37:01: 5000000 INFO @ Sun, 02 Jun 2019 19:37:05: 6000000 INFO @ Sun, 02 Jun 2019 19:37:08: 6000000 INFO @ Sun, 02 Jun 2019 19:37:08: 6000000 INFO @ Sun, 02 Jun 2019 19:37:12: 7000000 INFO @ Sun, 02 Jun 2019 19:37:16: 7000000 INFO @ Sun, 02 Jun 2019 19:37:16: 7000000 INFO @ Sun, 02 Jun 2019 19:37:20: 8000000 INFO @ Sun, 02 Jun 2019 19:37:24: 8000000 INFO @ Sun, 02 Jun 2019 19:37:25: 8000000 INFO @ Sun, 02 Jun 2019 19:37:27: 9000000 INFO @ Sun, 02 Jun 2019 19:37:32: 9000000 INFO @ Sun, 02 Jun 2019 19:37:33: 9000000 INFO @ Sun, 02 Jun 2019 19:37:34: 10000000 INFO @ Sun, 02 Jun 2019 19:37:40: 10000000 INFO @ Sun, 02 Jun 2019 19:37:41: 10000000 INFO @ Sun, 02 Jun 2019 19:37:42: 11000000 INFO @ Sun, 02 Jun 2019 19:37:48: 11000000 INFO @ Sun, 02 Jun 2019 19:37:49: 11000000 INFO @ Sun, 02 Jun 2019 19:37:49: 12000000 INFO @ Sun, 02 Jun 2019 19:37:57: 12000000 INFO @ Sun, 02 Jun 2019 19:37:57: 13000000 INFO @ Sun, 02 Jun 2019 19:37:57: 12000000 INFO @ Sun, 02 Jun 2019 19:38:04: 14000000 INFO @ Sun, 02 Jun 2019 19:38:05: 13000000 INFO @ Sun, 02 Jun 2019 19:38:05: 13000000 INFO @ Sun, 02 Jun 2019 19:38:11: 15000000 INFO @ Sun, 02 Jun 2019 19:38:13: 14000000 INFO @ Sun, 02 Jun 2019 19:38:13: 14000000 INFO @ Sun, 02 Jun 2019 19:38:19: 16000000 INFO @ Sun, 02 Jun 2019 19:38:21: 15000000 INFO @ Sun, 02 Jun 2019 19:38:21: 15000000 INFO @ Sun, 02 Jun 2019 19:38:26: 17000000 INFO @ Sun, 02 Jun 2019 19:38:29: 16000000 INFO @ Sun, 02 Jun 2019 19:38:29: 16000000 INFO @ Sun, 02 Jun 2019 19:38:34: 18000000 INFO @ Sun, 02 Jun 2019 19:38:37: 17000000 INFO @ Sun, 02 Jun 2019 19:38:37: 17000000 INFO @ Sun, 02 Jun 2019 19:38:41: 19000000 INFO @ Sun, 02 Jun 2019 19:38:45: 18000000 INFO @ Sun, 02 Jun 2019 19:38:45: 18000000 INFO @ Sun, 02 Jun 2019 19:38:48: 20000000 INFO @ Sun, 02 Jun 2019 19:38:53: 19000000 INFO @ Sun, 02 Jun 2019 19:38:53: 19000000 INFO @ Sun, 02 Jun 2019 19:38:56: 21000000 INFO @ Sun, 02 Jun 2019 19:39:01: 20000000 INFO @ Sun, 02 Jun 2019 19:39:01: 20000000 INFO @ Sun, 02 Jun 2019 19:39:03: 22000000 INFO @ Sun, 02 Jun 2019 19:39:09: 21000000 INFO @ Sun, 02 Jun 2019 19:39:09: 21000000 INFO @ Sun, 02 Jun 2019 19:39:10: 23000000 INFO @ Sun, 02 Jun 2019 19:39:17: 22000000 INFO @ Sun, 02 Jun 2019 19:39:17: 22000000 INFO @ Sun, 02 Jun 2019 19:39:17: 24000000 INFO @ Sun, 02 Jun 2019 19:39:25: 25000000 INFO @ Sun, 02 Jun 2019 19:39:25: 23000000 INFO @ Sun, 02 Jun 2019 19:39:25: 23000000 INFO @ Sun, 02 Jun 2019 19:39:31: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:39:31: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:39:31: #1 total tags in treatment: 25904966 INFO @ Sun, 02 Jun 2019 19:39:31: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:39:31: #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 19:39:32: #1 tags after filtering in treatment: 25904966 INFO @ Sun, 02 Jun 2019 19:39:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:39:32: #1 finished! INFO @ Sun, 02 Jun 2019 19:39:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:39:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:39:33: 24000000 INFO @ Sun, 02 Jun 2019 19:39:33: 24000000 INFO @ Sun, 02 Jun 2019 19:39:34: #2 number of paired peaks: 145 WARNING @ Sun, 02 Jun 2019 19:39:34: 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 @ Sun, 02 Jun 2019 19:39:34: start model_add_line... INFO @ Sun, 02 Jun 2019 19:39:34: start X-correlation... INFO @ Sun, 02 Jun 2019 19:39:34: end of X-cor INFO @ Sun, 02 Jun 2019 19:39:34: #2 finished! INFO @ Sun, 02 Jun 2019 19:39:34: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:39:34: #2 alternative fragment length(s) may be 1,18,34,495,559,575,577,598 bps INFO @ Sun, 02 Jun 2019 19:39:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.10_model.r WARNING @ Sun, 02 Jun 2019 19:39:34: #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 19:39:34: #2 You may need to consider one of the other alternative d(s): 1,18,34,495,559,575,577,598 WARNING @ Sun, 02 Jun 2019 19:39:34: #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 19:39:34: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:39:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:39:40: 25000000 INFO @ Sun, 02 Jun 2019 19:39:40: 25000000 INFO @ Sun, 02 Jun 2019 19:39:47: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:39:47: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:39:47: #1 total tags in treatment: 25904966 INFO @ Sun, 02 Jun 2019 19:39:47: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:39:47: #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 19:39:47: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:39:47: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:39:47: #1 total tags in treatment: 25904966 INFO @ Sun, 02 Jun 2019 19:39:47: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:39:47: #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 19:39:48: #1 tags after filtering in treatment: 25904966 INFO @ Sun, 02 Jun 2019 19:39:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:39:48: #1 finished! INFO @ Sun, 02 Jun 2019 19:39:48: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:39:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:39:48: #1 tags after filtering in treatment: 25904966 INFO @ Sun, 02 Jun 2019 19:39:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:39:48: #1 finished! INFO @ Sun, 02 Jun 2019 19:39:48: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:39:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:39:50: #2 number of paired peaks: 145 WARNING @ Sun, 02 Jun 2019 19:39:50: 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 @ Sun, 02 Jun 2019 19:39:50: start model_add_line... INFO @ Sun, 02 Jun 2019 19:39:50: #2 number of paired peaks: 145 WARNING @ Sun, 02 Jun 2019 19:39:50: 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 @ Sun, 02 Jun 2019 19:39:50: start model_add_line... INFO @ Sun, 02 Jun 2019 19:39:50: start X-correlation... INFO @ Sun, 02 Jun 2019 19:39:50: end of X-cor INFO @ Sun, 02 Jun 2019 19:39:50: #2 finished! INFO @ Sun, 02 Jun 2019 19:39:50: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:39:50: #2 alternative fragment length(s) may be 1,18,34,495,559,575,577,598 bps INFO @ Sun, 02 Jun 2019 19:39:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.20_model.r WARNING @ Sun, 02 Jun 2019 19:39:50: #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 19:39:50: #2 You may need to consider one of the other alternative d(s): 1,18,34,495,559,575,577,598 WARNING @ Sun, 02 Jun 2019 19:39:50: #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 19:39:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:39:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:39:50: start X-correlation... INFO @ Sun, 02 Jun 2019 19:39:50: end of X-cor INFO @ Sun, 02 Jun 2019 19:39:50: #2 finished! INFO @ Sun, 02 Jun 2019 19:39:50: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:39:50: #2 alternative fragment length(s) may be 1,18,34,495,559,575,577,598 bps INFO @ Sun, 02 Jun 2019 19:39:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.05_model.r WARNING @ Sun, 02 Jun 2019 19:39:50: #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 19:39:50: #2 You may need to consider one of the other alternative d(s): 1,18,34,495,559,575,577,598 WARNING @ Sun, 02 Jun 2019 19:39:50: #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 19:39:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:39:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:40:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:40:42: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:40:42: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:40:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:40:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:40:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.10_summits.bed INFO @ Sun, 02 Jun 2019 19:40:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:41:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:41:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:41:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.20_summits.bed INFO @ Sun, 02 Jun 2019 19:41:05: Done! INFO @ Sun, 02 Jun 2019 19:41:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:41:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:41:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466527/SRX466527.05_summits.bed INFO @ Sun, 02 Jun 2019 19:41:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling 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。