Job ID = 1293202 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,239,844 reads read : 29,239,844 reads written : 29,239,844 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:46 29239844 reads; of these: 29239844 (100.00%) were unpaired; of these: 2503032 (8.56%) aligned 0 times 21333242 (72.96%) aligned exactly 1 time 5403570 (18.48%) aligned >1 times 91.44% overall alignment rate Time searching: 00:06:47 Overall time: 00:06:47 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] 3580998 / 26736812 = 0.1339 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 22:38:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.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 22:38:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:38:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:38:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.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 22:38:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:38:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:38:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.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 22:38:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:38:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:38:33: 1000000 INFO @ Sun, 02 Jun 2019 22:38:34: 1000000 INFO @ Sun, 02 Jun 2019 22:38:35: 1000000 INFO @ Sun, 02 Jun 2019 22:38:41: 2000000 INFO @ Sun, 02 Jun 2019 22:38:42: 2000000 INFO @ Sun, 02 Jun 2019 22:38:44: 2000000 INFO @ Sun, 02 Jun 2019 22:38:49: 3000000 INFO @ Sun, 02 Jun 2019 22:38:50: 3000000 INFO @ Sun, 02 Jun 2019 22:38:54: 3000000 INFO @ Sun, 02 Jun 2019 22:38:58: 4000000 INFO @ Sun, 02 Jun 2019 22:38:58: 4000000 INFO @ Sun, 02 Jun 2019 22:39:03: 4000000 INFO @ Sun, 02 Jun 2019 22:39:06: 5000000 INFO @ Sun, 02 Jun 2019 22:39:06: 5000000 INFO @ Sun, 02 Jun 2019 22:39:12: 5000000 INFO @ Sun, 02 Jun 2019 22:39:14: 6000000 INFO @ Sun, 02 Jun 2019 22:39:14: 6000000 INFO @ Sun, 02 Jun 2019 22:39:22: 6000000 INFO @ Sun, 02 Jun 2019 22:39:22: 7000000 INFO @ Sun, 02 Jun 2019 22:39:22: 7000000 INFO @ Sun, 02 Jun 2019 22:39:29: 8000000 INFO @ Sun, 02 Jun 2019 22:39:30: 8000000 INFO @ Sun, 02 Jun 2019 22:39:31: 7000000 INFO @ Sun, 02 Jun 2019 22:39:37: 9000000 INFO @ Sun, 02 Jun 2019 22:39:37: 9000000 INFO @ Sun, 02 Jun 2019 22:39:41: 8000000 INFO @ Sun, 02 Jun 2019 22:39:44: 10000000 INFO @ Sun, 02 Jun 2019 22:39:44: 10000000 INFO @ Sun, 02 Jun 2019 22:39:51: 9000000 INFO @ Sun, 02 Jun 2019 22:39:51: 11000000 INFO @ Sun, 02 Jun 2019 22:39:52: 11000000 INFO @ Sun, 02 Jun 2019 22:39:59: 12000000 INFO @ Sun, 02 Jun 2019 22:39:59: 12000000 INFO @ Sun, 02 Jun 2019 22:40:01: 10000000 INFO @ Sun, 02 Jun 2019 22:40:06: 13000000 INFO @ Sun, 02 Jun 2019 22:40:06: 13000000 INFO @ Sun, 02 Jun 2019 22:40:10: 11000000 INFO @ Sun, 02 Jun 2019 22:40:13: 14000000 INFO @ Sun, 02 Jun 2019 22:40:13: 14000000 INFO @ Sun, 02 Jun 2019 22:40:19: 12000000 INFO @ Sun, 02 Jun 2019 22:40:20: 15000000 INFO @ Sun, 02 Jun 2019 22:40:21: 15000000 INFO @ Sun, 02 Jun 2019 22:40:28: 16000000 INFO @ Sun, 02 Jun 2019 22:40:28: 16000000 INFO @ Sun, 02 Jun 2019 22:40:28: 13000000 INFO @ Sun, 02 Jun 2019 22:40:35: 17000000 INFO @ Sun, 02 Jun 2019 22:40:36: 17000000 INFO @ Sun, 02 Jun 2019 22:40:37: 14000000 INFO @ Sun, 02 Jun 2019 22:40:43: 18000000 INFO @ Sun, 02 Jun 2019 22:40:43: 18000000 INFO @ Sun, 02 Jun 2019 22:40:46: 15000000 INFO @ Sun, 02 Jun 2019 22:40:50: 19000000 INFO @ Sun, 02 Jun 2019 22:40:50: 19000000 INFO @ Sun, 02 Jun 2019 22:40:55: 16000000 INFO @ Sun, 02 Jun 2019 22:40:58: 20000000 INFO @ Sun, 02 Jun 2019 22:40:58: 20000000 INFO @ Sun, 02 Jun 2019 22:41:04: 17000000 INFO @ Sun, 02 Jun 2019 22:41:05: 21000000 INFO @ Sun, 02 Jun 2019 22:41:05: 21000000 INFO @ Sun, 02 Jun 2019 22:41:12: 22000000 INFO @ Sun, 02 Jun 2019 22:41:12: 22000000 INFO @ Sun, 02 Jun 2019 22:41:13: 18000000 INFO @ Sun, 02 Jun 2019 22:41:19: 23000000 INFO @ Sun, 02 Jun 2019 22:41:19: 23000000 INFO @ Sun, 02 Jun 2019 22:41:21: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:41:21: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:41:21: #1 total tags in treatment: 23155814 INFO @ Sun, 02 Jun 2019 22:41:21: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:41:21: #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 22:41:21: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:41:21: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:41:21: #1 total tags in treatment: 23155814 INFO @ Sun, 02 Jun 2019 22:41:21: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:41:21: #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 22:41:21: #1 tags after filtering in treatment: 23155814 INFO @ Sun, 02 Jun 2019 22:41:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:41:21: #1 finished! INFO @ Sun, 02 Jun 2019 22:41:21: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:41:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:41:21: #1 tags after filtering in treatment: 23155814 INFO @ Sun, 02 Jun 2019 22:41:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:41:21: #1 finished! INFO @ Sun, 02 Jun 2019 22:41:21: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:41:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:41:23: 19000000 INFO @ Sun, 02 Jun 2019 22:41:23: #2 number of paired peaks: 176 WARNING @ Sun, 02 Jun 2019 22:41:23: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sun, 02 Jun 2019 22:41:23: start model_add_line... INFO @ Sun, 02 Jun 2019 22:41:23: #2 number of paired peaks: 176 WARNING @ Sun, 02 Jun 2019 22:41:23: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sun, 02 Jun 2019 22:41:23: start model_add_line... INFO @ Sun, 02 Jun 2019 22:41:23: start X-correlation... INFO @ Sun, 02 Jun 2019 22:41:23: start X-correlation... INFO @ Sun, 02 Jun 2019 22:41:23: end of X-cor INFO @ Sun, 02 Jun 2019 22:41:23: #2 finished! INFO @ Sun, 02 Jun 2019 22:41:23: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:41:23: #2 alternative fragment length(s) may be 1,35,533,550,572,597 bps INFO @ Sun, 02 Jun 2019 22:41:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.05_model.r WARNING @ Sun, 02 Jun 2019 22:41:23: #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 22:41:23: #2 You may need to consider one of the other alternative d(s): 1,35,533,550,572,597 WARNING @ Sun, 02 Jun 2019 22:41:23: #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 22:41:23: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:41:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:41:23: end of X-cor INFO @ Sun, 02 Jun 2019 22:41:23: #2 finished! INFO @ Sun, 02 Jun 2019 22:41:23: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:41:23: #2 alternative fragment length(s) may be 1,35,533,550,572,597 bps INFO @ Sun, 02 Jun 2019 22:41:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.10_model.r WARNING @ Sun, 02 Jun 2019 22:41:23: #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 22:41:23: #2 You may need to consider one of the other alternative d(s): 1,35,533,550,572,597 WARNING @ Sun, 02 Jun 2019 22:41:23: #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 22:41:23: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:41:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:41:32: 20000000 INFO @ Sun, 02 Jun 2019 22:41:41: 21000000 INFO @ Sun, 02 Jun 2019 22:41:50: 22000000 INFO @ Sun, 02 Jun 2019 22:41:59: 23000000 INFO @ Sun, 02 Jun 2019 22:42:00: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:42:00: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:42:00: #1 total tags in treatment: 23155814 INFO @ Sun, 02 Jun 2019 22:42:00: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:42:00: #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 22:42:01: #1 tags after filtering in treatment: 23155814 INFO @ Sun, 02 Jun 2019 22:42:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:42:01: #1 finished! INFO @ Sun, 02 Jun 2019 22:42:01: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:42:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:42:03: #2 number of paired peaks: 176 WARNING @ Sun, 02 Jun 2019 22:42:03: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sun, 02 Jun 2019 22:42:03: start model_add_line... INFO @ Sun, 02 Jun 2019 22:42:03: start X-correlation... INFO @ Sun, 02 Jun 2019 22:42:03: end of X-cor INFO @ Sun, 02 Jun 2019 22:42:03: #2 finished! INFO @ Sun, 02 Jun 2019 22:42:03: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:42:03: #2 alternative fragment length(s) may be 1,35,533,550,572,597 bps INFO @ Sun, 02 Jun 2019 22:42:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.20_model.r WARNING @ Sun, 02 Jun 2019 22:42:03: #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 22:42:03: #2 You may need to consider one of the other alternative d(s): 1,35,533,550,572,597 WARNING @ Sun, 02 Jun 2019 22:42:03: #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 22:42:03: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:42:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:42:11: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:42:11: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:42:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:42:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:42:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.05_summits.bed INFO @ Sun, 02 Jun 2019 22:42:33: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:42:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:42:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:42:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.10_summits.bed INFO @ Sun, 02 Jun 2019 22:42:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:42:51: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:43:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:43:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:43:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402755/SRX5402755.20_summits.bed INFO @ Sun, 02 Jun 2019 22:43:13: 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。