Job ID = 1293069 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,411,962 reads read : 48,823,924 reads written : 24,411,962 reads 0-length : 24,411,962 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: 00:06:23 24411962 reads; of these: 24411962 (100.00%) were unpaired; of these: 642934 (2.63%) aligned 0 times 19812680 (81.16%) aligned exactly 1 time 3956348 (16.21%) aligned >1 times 97.37% overall alignment rate Time searching: 00:06:23 Overall time: 00:06:23 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] 2696066 / 23769028 = 0.1134 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 22:01:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.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 22:01:11: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:01:11: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:01:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.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 22:01:11: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:01:11: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:01:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.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 22:01:11: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:01:11: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:01:22: 1000000 INFO @ Sun, 02 Jun 2019 22:01:22: 1000000 INFO @ Sun, 02 Jun 2019 22:01:22: 1000000 INFO @ Sun, 02 Jun 2019 22:01:31: 2000000 INFO @ Sun, 02 Jun 2019 22:01:31: 2000000 INFO @ Sun, 02 Jun 2019 22:01:32: 2000000 INFO @ Sun, 02 Jun 2019 22:01:40: 3000000 INFO @ Sun, 02 Jun 2019 22:01:41: 3000000 INFO @ Sun, 02 Jun 2019 22:01:41: 3000000 INFO @ Sun, 02 Jun 2019 22:01:49: 4000000 INFO @ Sun, 02 Jun 2019 22:01:51: 4000000 INFO @ Sun, 02 Jun 2019 22:01:51: 4000000 INFO @ Sun, 02 Jun 2019 22:01:58: 5000000 INFO @ Sun, 02 Jun 2019 22:02:01: 5000000 INFO @ Sun, 02 Jun 2019 22:02:01: 5000000 INFO @ Sun, 02 Jun 2019 22:02:07: 6000000 INFO @ Sun, 02 Jun 2019 22:02:11: 6000000 INFO @ Sun, 02 Jun 2019 22:02:11: 6000000 INFO @ Sun, 02 Jun 2019 22:02:16: 7000000 INFO @ Sun, 02 Jun 2019 22:02:20: 7000000 INFO @ Sun, 02 Jun 2019 22:02:20: 7000000 INFO @ Sun, 02 Jun 2019 22:02:25: 8000000 INFO @ Sun, 02 Jun 2019 22:02:30: 8000000 INFO @ Sun, 02 Jun 2019 22:02:30: 8000000 INFO @ Sun, 02 Jun 2019 22:02:34: 9000000 INFO @ Sun, 02 Jun 2019 22:02:40: 9000000 INFO @ Sun, 02 Jun 2019 22:02:40: 9000000 INFO @ Sun, 02 Jun 2019 22:02:43: 10000000 INFO @ Sun, 02 Jun 2019 22:02:50: 10000000 INFO @ Sun, 02 Jun 2019 22:02:50: 10000000 INFO @ Sun, 02 Jun 2019 22:02:53: 11000000 INFO @ Sun, 02 Jun 2019 22:03:00: 11000000 INFO @ Sun, 02 Jun 2019 22:03:00: 11000000 INFO @ Sun, 02 Jun 2019 22:03:03: 12000000 INFO @ Sun, 02 Jun 2019 22:03:10: 12000000 INFO @ Sun, 02 Jun 2019 22:03:10: 12000000 INFO @ Sun, 02 Jun 2019 22:03:12: 13000000 INFO @ Sun, 02 Jun 2019 22:03:20: 13000000 INFO @ Sun, 02 Jun 2019 22:03:21: 13000000 INFO @ Sun, 02 Jun 2019 22:03:21: 14000000 INFO @ Sun, 02 Jun 2019 22:03:31: 15000000 INFO @ Sun, 02 Jun 2019 22:03:31: 14000000 INFO @ Sun, 02 Jun 2019 22:03:31: 14000000 INFO @ Sun, 02 Jun 2019 22:03:40: 16000000 INFO @ Sun, 02 Jun 2019 22:03:41: 15000000 INFO @ Sun, 02 Jun 2019 22:03:41: 15000000 INFO @ Sun, 02 Jun 2019 22:03:49: 17000000 INFO @ Sun, 02 Jun 2019 22:03:51: 16000000 INFO @ Sun, 02 Jun 2019 22:03:52: 16000000 INFO @ Sun, 02 Jun 2019 22:03:58: 18000000 INFO @ Sun, 02 Jun 2019 22:04:01: 17000000 INFO @ Sun, 02 Jun 2019 22:04:02: 17000000 INFO @ Sun, 02 Jun 2019 22:04:07: 19000000 INFO @ Sun, 02 Jun 2019 22:04:11: 18000000 INFO @ Sun, 02 Jun 2019 22:04:11: 18000000 INFO @ Sun, 02 Jun 2019 22:04:16: 20000000 INFO @ Sun, 02 Jun 2019 22:04:20: 19000000 INFO @ Sun, 02 Jun 2019 22:04:21: 19000000 INFO @ Sun, 02 Jun 2019 22:04:25: 21000000 INFO @ Sun, 02 Jun 2019 22:04:26: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:04:26: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:04:26: #1 total tags in treatment: 21072962 INFO @ Sun, 02 Jun 2019 22:04:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:04:26: #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 22:04:26: #1 tags after filtering in treatment: 21072962 INFO @ Sun, 02 Jun 2019 22:04:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:04:26: #1 finished! INFO @ Sun, 02 Jun 2019 22:04:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:04:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:04:28: #2 number of paired peaks: 179 WARNING @ Sun, 02 Jun 2019 22:04:28: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Sun, 02 Jun 2019 22:04:28: start model_add_line... INFO @ Sun, 02 Jun 2019 22:04:28: start X-correlation... INFO @ Sun, 02 Jun 2019 22:04:28: end of X-cor INFO @ Sun, 02 Jun 2019 22:04:28: #2 finished! INFO @ Sun, 02 Jun 2019 22:04:28: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:04:28: #2 alternative fragment length(s) may be 1,22,531,547,562,591 bps INFO @ Sun, 02 Jun 2019 22:04:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.05_model.r WARNING @ Sun, 02 Jun 2019 22:04:28: #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 22:04:28: #2 You may need to consider one of the other alternative d(s): 1,22,531,547,562,591 WARNING @ Sun, 02 Jun 2019 22:04:28: #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 22:04:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:04:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:04:30: 20000000 INFO @ Sun, 02 Jun 2019 22:04:30: 20000000 INFO @ Sun, 02 Jun 2019 22:04:39: 21000000 INFO @ Sun, 02 Jun 2019 22:04:40: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:04:40: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:04:40: #1 total tags in treatment: 21072962 INFO @ Sun, 02 Jun 2019 22:04:40: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:04:40: #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 22:04:40: 21000000 INFO @ Sun, 02 Jun 2019 22:04:40: #1 tags after filtering in treatment: 21072962 INFO @ Sun, 02 Jun 2019 22:04:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:04:40: #1 finished! INFO @ Sun, 02 Jun 2019 22:04:40: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:04:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:04:41: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:04:41: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:04:41: #1 total tags in treatment: 21072962 INFO @ Sun, 02 Jun 2019 22:04:41: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:04:41: #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 22:04:41: #1 tags after filtering in treatment: 21072962 INFO @ Sun, 02 Jun 2019 22:04:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:04:41: #1 finished! INFO @ Sun, 02 Jun 2019 22:04:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:04:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:04:42: #2 number of paired peaks: 179 WARNING @ Sun, 02 Jun 2019 22:04:42: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Sun, 02 Jun 2019 22:04:42: start model_add_line... INFO @ Sun, 02 Jun 2019 22:04:42: start X-correlation... INFO @ Sun, 02 Jun 2019 22:04:42: end of X-cor INFO @ Sun, 02 Jun 2019 22:04:42: #2 finished! INFO @ Sun, 02 Jun 2019 22:04:42: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:04:42: #2 alternative fragment length(s) may be 1,22,531,547,562,591 bps INFO @ Sun, 02 Jun 2019 22:04:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.20_model.r WARNING @ Sun, 02 Jun 2019 22:04:42: #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 22:04:42: #2 You may need to consider one of the other alternative d(s): 1,22,531,547,562,591 WARNING @ Sun, 02 Jun 2019 22:04:42: #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 22:04:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:04:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:04:43: #2 number of paired peaks: 179 WARNING @ Sun, 02 Jun 2019 22:04:43: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Sun, 02 Jun 2019 22:04:43: start model_add_line... INFO @ Sun, 02 Jun 2019 22:04:43: start X-correlation... INFO @ Sun, 02 Jun 2019 22:04:43: end of X-cor INFO @ Sun, 02 Jun 2019 22:04:43: #2 finished! INFO @ Sun, 02 Jun 2019 22:04:43: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:04:43: #2 alternative fragment length(s) may be 1,22,531,547,562,591 bps INFO @ Sun, 02 Jun 2019 22:04:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.10_model.r WARNING @ Sun, 02 Jun 2019 22:04:43: #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 22:04:43: #2 You may need to consider one of the other alternative d(s): 1,22,531,547,562,591 WARNING @ Sun, 02 Jun 2019 22:04:43: #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 22:04:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:04:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:05:14: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:05:28: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:05:29: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:05:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:05:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:05:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.05_summits.bed INFO @ Sun, 02 Jun 2019 22:05:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:05:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:05:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:05:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.20_summits.bed INFO @ Sun, 02 Jun 2019 22:05:48: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:05:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:05:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:05:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020831/SRX5020831.10_summits.bed INFO @ Sun, 02 Jun 2019 22:05:50: 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。