Job ID = 1292771 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,812,743 reads read : 18,812,743 reads written : 18,812,743 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: 00:05:09 18812743 reads; of these: 18812743 (100.00%) were unpaired; of these: 150178 (0.80%) aligned 0 times 15590827 (82.87%) aligned exactly 1 time 3071738 (16.33%) aligned >1 times 99.20% overall alignment rate Time searching: 00:05:09 Overall time: 00:05:09 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] 8433160 / 18662565 = 0.4519 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 20:28:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.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 20:28:34: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:28:34: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:28:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.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 20:28:34: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:28:34: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:28:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.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 20:28:34: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:28:34: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:28:45: 1000000 INFO @ Sun, 02 Jun 2019 20:28:45: 1000000 INFO @ Sun, 02 Jun 2019 20:28:45: 1000000 INFO @ Sun, 02 Jun 2019 20:28:53: 2000000 INFO @ Sun, 02 Jun 2019 20:28:55: 2000000 INFO @ Sun, 02 Jun 2019 20:28:55: 2000000 INFO @ Sun, 02 Jun 2019 20:29:00: 3000000 INFO @ Sun, 02 Jun 2019 20:29:05: 3000000 INFO @ Sun, 02 Jun 2019 20:29:05: 3000000 INFO @ Sun, 02 Jun 2019 20:29:07: 4000000 INFO @ Sun, 02 Jun 2019 20:29:14: 5000000 INFO @ Sun, 02 Jun 2019 20:29:15: 4000000 INFO @ Sun, 02 Jun 2019 20:29:15: 4000000 INFO @ Sun, 02 Jun 2019 20:29:22: 6000000 INFO @ Sun, 02 Jun 2019 20:29:25: 5000000 INFO @ Sun, 02 Jun 2019 20:29:25: 5000000 INFO @ Sun, 02 Jun 2019 20:29:29: 7000000 INFO @ Sun, 02 Jun 2019 20:29:34: 6000000 INFO @ Sun, 02 Jun 2019 20:29:34: 6000000 INFO @ Sun, 02 Jun 2019 20:29:36: 8000000 INFO @ Sun, 02 Jun 2019 20:29:43: 9000000 INFO @ Sun, 02 Jun 2019 20:29:44: 7000000 INFO @ Sun, 02 Jun 2019 20:29:44: 7000000 INFO @ Sun, 02 Jun 2019 20:29:50: 10000000 INFO @ Sun, 02 Jun 2019 20:29:52: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 20:29:52: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 20:29:52: #1 total tags in treatment: 10229405 INFO @ Sun, 02 Jun 2019 20:29:52: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:29:52: #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 20:29:52: #1 tags after filtering in treatment: 10229405 INFO @ Sun, 02 Jun 2019 20:29:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:29:52: #1 finished! INFO @ Sun, 02 Jun 2019 20:29:52: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:29:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:29:53: #2 number of paired peaks: 429 WARNING @ Sun, 02 Jun 2019 20:29:53: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Sun, 02 Jun 2019 20:29:53: start model_add_line... INFO @ Sun, 02 Jun 2019 20:29:53: start X-correlation... INFO @ Sun, 02 Jun 2019 20:29:53: end of X-cor INFO @ Sun, 02 Jun 2019 20:29:53: #2 finished! INFO @ Sun, 02 Jun 2019 20:29:53: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 20:29:53: #2 alternative fragment length(s) may be 2,47,580 bps INFO @ Sun, 02 Jun 2019 20:29:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.10_model.r WARNING @ Sun, 02 Jun 2019 20:29:53: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:29:53: #2 You may need to consider one of the other alternative d(s): 2,47,580 WARNING @ Sun, 02 Jun 2019 20:29:53: #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 20:29:53: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:29:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:29:54: 8000000 INFO @ Sun, 02 Jun 2019 20:29:54: 8000000 INFO @ Sun, 02 Jun 2019 20:30:03: 9000000 INFO @ Sun, 02 Jun 2019 20:30:03: 9000000 INFO @ Sun, 02 Jun 2019 20:30:12: 10000000 INFO @ Sun, 02 Jun 2019 20:30:12: 10000000 INFO @ Sun, 02 Jun 2019 20:30:14: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 20:30:14: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 20:30:14: #1 total tags in treatment: 10229405 INFO @ Sun, 02 Jun 2019 20:30:14: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:30:14: #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 20:30:14: #1 tags after filtering in treatment: 10229405 INFO @ Sun, 02 Jun 2019 20:30:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:30:14: #1 finished! INFO @ Sun, 02 Jun 2019 20:30:14: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:30:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:30:14: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 20:30:14: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 20:30:14: #1 total tags in treatment: 10229405 INFO @ Sun, 02 Jun 2019 20:30:14: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:30:14: #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 20:30:14: #1 tags after filtering in treatment: 10229405 INFO @ Sun, 02 Jun 2019 20:30:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:30:14: #1 finished! INFO @ Sun, 02 Jun 2019 20:30:14: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:30:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:30:15: #2 number of paired peaks: 429 WARNING @ Sun, 02 Jun 2019 20:30:15: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Sun, 02 Jun 2019 20:30:15: start model_add_line... INFO @ Sun, 02 Jun 2019 20:30:15: start X-correlation... INFO @ Sun, 02 Jun 2019 20:30:15: end of X-cor INFO @ Sun, 02 Jun 2019 20:30:15: #2 finished! INFO @ Sun, 02 Jun 2019 20:30:15: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 20:30:15: #2 alternative fragment length(s) may be 2,47,580 bps INFO @ Sun, 02 Jun 2019 20:30:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.20_model.r WARNING @ Sun, 02 Jun 2019 20:30:15: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:30:15: #2 You may need to consider one of the other alternative d(s): 2,47,580 WARNING @ Sun, 02 Jun 2019 20:30:15: #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 20:30:15: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:30:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:30:15: #2 number of paired peaks: 429 WARNING @ Sun, 02 Jun 2019 20:30:15: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Sun, 02 Jun 2019 20:30:15: start model_add_line... INFO @ Sun, 02 Jun 2019 20:30:16: start X-correlation... INFO @ Sun, 02 Jun 2019 20:30:16: end of X-cor INFO @ Sun, 02 Jun 2019 20:30:16: #2 finished! INFO @ Sun, 02 Jun 2019 20:30:16: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 20:30:16: #2 alternative fragment length(s) may be 2,47,580 bps INFO @ Sun, 02 Jun 2019 20:30:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.05_model.r WARNING @ Sun, 02 Jun 2019 20:30:16: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:30:16: #2 You may need to consider one of the other alternative d(s): 2,47,580 WARNING @ Sun, 02 Jun 2019 20:30:16: #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 20:30:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:30:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:30:21: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:30:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.10_peaks.xls INFO @ Sun, 02 Jun 2019 20:30:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:30:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.10_summits.bed INFO @ Sun, 02 Jun 2019 20:30:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (560 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:30:42: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:30:43: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:30:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.20_peaks.xls INFO @ Sun, 02 Jun 2019 20:30:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:30:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.20_summits.bed INFO @ Sun, 02 Jun 2019 20:30:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (216 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:30:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.05_peaks.xls INFO @ Sun, 02 Jun 2019 20:30:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:30:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494995/SRX494995.05_summits.bed INFO @ Sun, 02 Jun 2019 20:30:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (770 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。