Job ID = 1291653 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,992,486 reads read : 23,992,486 reads written : 23,992,486 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: 00:06:13 23992486 reads; of these: 23992486 (100.00%) were unpaired; of these: 2093725 (8.73%) aligned 0 times 17555339 (73.17%) aligned exactly 1 time 4343422 (18.10%) aligned >1 times 91.27% overall alignment rate Time searching: 00:06:13 Overall time: 00:06:13 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 12 files... [bam_rmdupse_core] 7735764 / 21898761 = 0.3533 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 16:35:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.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 16:35:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:35:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:35:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.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 16:35:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:35:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:35:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.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 16:35:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:35:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:36:02: 1000000 INFO @ Sun, 02 Jun 2019 16:36:02: 1000000 INFO @ Sun, 02 Jun 2019 16:36:02: 1000000 INFO @ Sun, 02 Jun 2019 16:36:11: 2000000 INFO @ Sun, 02 Jun 2019 16:36:11: 2000000 INFO @ Sun, 02 Jun 2019 16:36:11: 2000000 INFO @ Sun, 02 Jun 2019 16:36:21: 3000000 INFO @ Sun, 02 Jun 2019 16:36:21: 3000000 INFO @ Sun, 02 Jun 2019 16:36:21: 3000000 INFO @ Sun, 02 Jun 2019 16:36:30: 4000000 INFO @ Sun, 02 Jun 2019 16:36:30: 4000000 INFO @ Sun, 02 Jun 2019 16:36:30: 4000000 INFO @ Sun, 02 Jun 2019 16:36:39: 5000000 INFO @ Sun, 02 Jun 2019 16:36:39: 5000000 INFO @ Sun, 02 Jun 2019 16:36:40: 5000000 INFO @ Sun, 02 Jun 2019 16:36:48: 6000000 INFO @ Sun, 02 Jun 2019 16:36:48: 6000000 INFO @ Sun, 02 Jun 2019 16:36:49: 6000000 INFO @ Sun, 02 Jun 2019 16:36:56: 7000000 INFO @ Sun, 02 Jun 2019 16:36:57: 7000000 INFO @ Sun, 02 Jun 2019 16:36:57: 7000000 INFO @ Sun, 02 Jun 2019 16:37:04: 8000000 INFO @ Sun, 02 Jun 2019 16:37:06: 8000000 INFO @ Sun, 02 Jun 2019 16:37:06: 8000000 INFO @ Sun, 02 Jun 2019 16:37:14: 9000000 INFO @ Sun, 02 Jun 2019 16:37:16: 9000000 INFO @ Sun, 02 Jun 2019 16:37:16: 9000000 INFO @ Sun, 02 Jun 2019 16:37:23: 10000000 INFO @ Sun, 02 Jun 2019 16:37:25: 10000000 INFO @ Sun, 02 Jun 2019 16:37:26: 10000000 INFO @ Sun, 02 Jun 2019 16:37:32: 11000000 INFO @ Sun, 02 Jun 2019 16:37:35: 11000000 INFO @ Sun, 02 Jun 2019 16:37:35: 11000000 INFO @ Sun, 02 Jun 2019 16:37:41: 12000000 INFO @ Sun, 02 Jun 2019 16:37:44: 12000000 INFO @ Sun, 02 Jun 2019 16:37:45: 12000000 INFO @ Sun, 02 Jun 2019 16:37:50: 13000000 INFO @ Sun, 02 Jun 2019 16:37:54: 13000000 INFO @ Sun, 02 Jun 2019 16:37:55: 13000000 INFO @ Sun, 02 Jun 2019 16:37:59: 14000000 INFO @ Sun, 02 Jun 2019 16:38:01: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:38:01: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:38:01: #1 total tags in treatment: 14162997 INFO @ Sun, 02 Jun 2019 16:38:01: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:38:01: #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 16:38:01: #1 tags after filtering in treatment: 14162997 INFO @ Sun, 02 Jun 2019 16:38:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:38:01: #1 finished! INFO @ Sun, 02 Jun 2019 16:38:01: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:38:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:38:03: #2 number of paired peaks: 386 WARNING @ Sun, 02 Jun 2019 16:38:03: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Sun, 02 Jun 2019 16:38:03: start model_add_line... INFO @ Sun, 02 Jun 2019 16:38:03: start X-correlation... INFO @ Sun, 02 Jun 2019 16:38:03: end of X-cor INFO @ Sun, 02 Jun 2019 16:38:03: #2 finished! INFO @ Sun, 02 Jun 2019 16:38:03: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 16:38:03: #2 alternative fragment length(s) may be 2,29 bps INFO @ Sun, 02 Jun 2019 16:38:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.20_model.r WARNING @ Sun, 02 Jun 2019 16:38:03: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:38:03: #2 You may need to consider one of the other alternative d(s): 2,29 WARNING @ Sun, 02 Jun 2019 16:38:03: #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 16:38:03: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:38:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:38:03: 14000000 INFO @ Sun, 02 Jun 2019 16:38:04: 14000000 INFO @ Sun, 02 Jun 2019 16:38:05: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:38:05: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:38:05: #1 total tags in treatment: 14162997 INFO @ Sun, 02 Jun 2019 16:38:05: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:38:05: #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 16:38:05: #1 tags after filtering in treatment: 14162997 INFO @ Sun, 02 Jun 2019 16:38:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:38:05: #1 finished! INFO @ Sun, 02 Jun 2019 16:38:05: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:38:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:38:05: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:38:05: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:38:05: #1 total tags in treatment: 14162997 INFO @ Sun, 02 Jun 2019 16:38:05: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:38:05: #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 16:38:06: #1 tags after filtering in treatment: 14162997 INFO @ Sun, 02 Jun 2019 16:38:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:38:06: #1 finished! INFO @ Sun, 02 Jun 2019 16:38:06: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:38:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:38:06: #2 number of paired peaks: 386 WARNING @ Sun, 02 Jun 2019 16:38:06: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Sun, 02 Jun 2019 16:38:06: start model_add_line... INFO @ Sun, 02 Jun 2019 16:38:07: start X-correlation... INFO @ Sun, 02 Jun 2019 16:38:07: end of X-cor INFO @ Sun, 02 Jun 2019 16:38:07: #2 finished! INFO @ Sun, 02 Jun 2019 16:38:07: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 16:38:07: #2 alternative fragment length(s) may be 2,29 bps INFO @ Sun, 02 Jun 2019 16:38:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.10_model.r WARNING @ Sun, 02 Jun 2019 16:38:07: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:38:07: #2 You may need to consider one of the other alternative d(s): 2,29 WARNING @ Sun, 02 Jun 2019 16:38:07: #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 16:38:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:38:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:38:07: #2 number of paired peaks: 386 WARNING @ Sun, 02 Jun 2019 16:38:07: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Sun, 02 Jun 2019 16:38:07: start model_add_line... INFO @ Sun, 02 Jun 2019 16:38:07: start X-correlation... INFO @ Sun, 02 Jun 2019 16:38:07: end of X-cor INFO @ Sun, 02 Jun 2019 16:38:07: #2 finished! INFO @ Sun, 02 Jun 2019 16:38:07: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 16:38:07: #2 alternative fragment length(s) may be 2,29 bps INFO @ Sun, 02 Jun 2019 16:38:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.05_model.r WARNING @ Sun, 02 Jun 2019 16:38:07: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:38:07: #2 You may need to consider one of the other alternative d(s): 2,29 WARNING @ Sun, 02 Jun 2019 16:38:07: #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 16:38:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:38:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:38:37: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:38:40: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:38:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:38:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:38:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:38:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.20_summits.bed INFO @ Sun, 02 Jun 2019 16:38:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:38:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:38:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:38:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.10_summits.bed INFO @ Sun, 02 Jun 2019 16:38:56: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:38:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:38:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:38:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX172527/SRX172527.05_summits.bed INFO @ Sun, 02 Jun 2019 16:38:57: 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。