Job ID = 1292606 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,509,609 reads read : 21,509,609 reads written : 21,509,609 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: 00:04:22 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 256446 (1.19%) aligned 0 times 17820654 (82.85%) aligned exactly 1 time 3432509 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:04:22 Overall time: 00:04:22 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] 3667295 / 21253163 = 0.1726 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 20:06:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.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 20:06:40: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:06:40: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:06:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.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 20:06:40: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:06:40: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:06:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.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 20:06:40: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:06:40: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:06:47: 1000000 INFO @ Sun, 02 Jun 2019 20:06:48: 1000000 INFO @ Sun, 02 Jun 2019 20:06:49: 1000000 INFO @ Sun, 02 Jun 2019 20:06:53: 2000000 INFO @ Sun, 02 Jun 2019 20:06:55: 2000000 INFO @ Sun, 02 Jun 2019 20:06:56: 2000000 INFO @ Sun, 02 Jun 2019 20:06:59: 3000000 INFO @ Sun, 02 Jun 2019 20:07:03: 3000000 INFO @ Sun, 02 Jun 2019 20:07:03: 3000000 INFO @ Sun, 02 Jun 2019 20:07:05: 4000000 INFO @ Sun, 02 Jun 2019 20:07:10: 4000000 INFO @ Sun, 02 Jun 2019 20:07:11: 4000000 INFO @ Sun, 02 Jun 2019 20:07:11: 5000000 INFO @ Sun, 02 Jun 2019 20:07:17: 6000000 INFO @ Sun, 02 Jun 2019 20:07:17: 5000000 INFO @ Sun, 02 Jun 2019 20:07:18: 5000000 INFO @ Sun, 02 Jun 2019 20:07:23: 7000000 INFO @ Sun, 02 Jun 2019 20:07:25: 6000000 INFO @ Sun, 02 Jun 2019 20:07:26: 6000000 INFO @ Sun, 02 Jun 2019 20:07:29: 8000000 INFO @ Sun, 02 Jun 2019 20:07:32: 7000000 INFO @ Sun, 02 Jun 2019 20:07:33: 7000000 INFO @ Sun, 02 Jun 2019 20:07:35: 9000000 INFO @ Sun, 02 Jun 2019 20:07:39: 8000000 INFO @ Sun, 02 Jun 2019 20:07:41: 8000000 INFO @ Sun, 02 Jun 2019 20:07:41: 10000000 INFO @ Sun, 02 Jun 2019 20:07:46: 9000000 INFO @ Sun, 02 Jun 2019 20:07:48: 11000000 INFO @ Sun, 02 Jun 2019 20:07:48: 9000000 INFO @ Sun, 02 Jun 2019 20:07:53: 10000000 INFO @ Sun, 02 Jun 2019 20:07:54: 12000000 INFO @ Sun, 02 Jun 2019 20:07:56: 10000000 INFO @ Sun, 02 Jun 2019 20:08:00: 13000000 INFO @ Sun, 02 Jun 2019 20:08:01: 11000000 INFO @ Sun, 02 Jun 2019 20:08:03: 11000000 INFO @ Sun, 02 Jun 2019 20:08:06: 14000000 INFO @ Sun, 02 Jun 2019 20:08:08: 12000000 INFO @ Sun, 02 Jun 2019 20:08:11: 12000000 INFO @ Sun, 02 Jun 2019 20:08:12: 15000000 INFO @ Sun, 02 Jun 2019 20:08:15: 13000000 INFO @ Sun, 02 Jun 2019 20:08:18: 13000000 INFO @ Sun, 02 Jun 2019 20:08:18: 16000000 INFO @ Sun, 02 Jun 2019 20:08:22: 14000000 INFO @ Sun, 02 Jun 2019 20:08:24: 17000000 INFO @ Sun, 02 Jun 2019 20:08:25: 14000000 INFO @ Sun, 02 Jun 2019 20:08:28: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:08:28: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:08:28: #1 total tags in treatment: 17585868 INFO @ Sun, 02 Jun 2019 20:08:28: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:08:28: #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 20:08:28: #1 tags after filtering in treatment: 17585868 INFO @ Sun, 02 Jun 2019 20:08:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:08:28: #1 finished! INFO @ Sun, 02 Jun 2019 20:08:28: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:08:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:08:30: 15000000 INFO @ Sun, 02 Jun 2019 20:08:30: #2 number of paired peaks: 207 WARNING @ Sun, 02 Jun 2019 20:08:30: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sun, 02 Jun 2019 20:08:30: start model_add_line... INFO @ Sun, 02 Jun 2019 20:08:30: start X-correlation... INFO @ Sun, 02 Jun 2019 20:08:30: end of X-cor INFO @ Sun, 02 Jun 2019 20:08:30: #2 finished! INFO @ Sun, 02 Jun 2019 20:08:30: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 20:08:30: #2 alternative fragment length(s) may be 1,18,36 bps INFO @ Sun, 02 Jun 2019 20:08:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.05_model.r WARNING @ Sun, 02 Jun 2019 20:08:30: #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 20:08:30: #2 You may need to consider one of the other alternative d(s): 1,18,36 WARNING @ Sun, 02 Jun 2019 20:08:30: #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 20:08:30: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:08:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:08:33: 15000000 INFO @ Sun, 02 Jun 2019 20:08:37: 16000000 INFO @ Sun, 02 Jun 2019 20:08:41: 16000000 INFO @ Sun, 02 Jun 2019 20:08:44: 17000000 INFO @ Sun, 02 Jun 2019 20:08:48: 17000000 INFO @ Sun, 02 Jun 2019 20:08:49: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:08:49: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:08:49: #1 total tags in treatment: 17585868 INFO @ Sun, 02 Jun 2019 20:08:49: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:08:49: #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 20:08:49: #1 tags after filtering in treatment: 17585868 INFO @ Sun, 02 Jun 2019 20:08:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:08:49: #1 finished! INFO @ Sun, 02 Jun 2019 20:08:49: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:08:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:08:51: #2 number of paired peaks: 207 WARNING @ Sun, 02 Jun 2019 20:08:51: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sun, 02 Jun 2019 20:08:51: start model_add_line... INFO @ Sun, 02 Jun 2019 20:08:51: start X-correlation... INFO @ Sun, 02 Jun 2019 20:08:51: end of X-cor INFO @ Sun, 02 Jun 2019 20:08:51: #2 finished! INFO @ Sun, 02 Jun 2019 20:08:51: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 20:08:51: #2 alternative fragment length(s) may be 1,18,36 bps INFO @ Sun, 02 Jun 2019 20:08:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.20_model.r WARNING @ Sun, 02 Jun 2019 20:08:51: #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 20:08:51: #2 You may need to consider one of the other alternative d(s): 1,18,36 WARNING @ Sun, 02 Jun 2019 20:08:51: #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 20:08:51: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:08:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:08:53: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:08:53: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:08:53: #1 total tags in treatment: 17585868 INFO @ Sun, 02 Jun 2019 20:08:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:08:53: #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 20:08:53: #1 tags after filtering in treatment: 17585868 INFO @ Sun, 02 Jun 2019 20:08:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:08:53: #1 finished! INFO @ Sun, 02 Jun 2019 20:08:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:08:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:08:55: #2 number of paired peaks: 207 WARNING @ Sun, 02 Jun 2019 20:08:55: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sun, 02 Jun 2019 20:08:55: start model_add_line... INFO @ Sun, 02 Jun 2019 20:08:55: start X-correlation... INFO @ Sun, 02 Jun 2019 20:08:55: end of X-cor INFO @ Sun, 02 Jun 2019 20:08:55: #2 finished! INFO @ Sun, 02 Jun 2019 20:08:55: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 20:08:55: #2 alternative fragment length(s) may be 1,18,36 bps INFO @ Sun, 02 Jun 2019 20:08:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.10_model.r WARNING @ Sun, 02 Jun 2019 20:08:55: #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 20:08:55: #2 You may need to consider one of the other alternative d(s): 1,18,36 WARNING @ Sun, 02 Jun 2019 20:08:55: #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 20:08:55: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:08:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:09:09: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:09:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.05_peaks.xls INFO @ Sun, 02 Jun 2019 20:09:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:09:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.05_summits.bed INFO @ Sun, 02 Jun 2019 20:09:28: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:09:30: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:09:34: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:09:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.20_peaks.xls INFO @ Sun, 02 Jun 2019 20:09:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:09:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.20_summits.bed INFO @ Sun, 02 Jun 2019 20:09:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:09:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.10_peaks.xls INFO @ Sun, 02 Jun 2019 20:09:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:09:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494853/SRX494853.10_summits.bed INFO @ Sun, 02 Jun 2019 20:09:54: Done! pass1 - making usageList (0 chroms): 2 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。