Job ID = 1291793 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,095,646 reads read : 34,191,292 reads written : 17,095,646 reads 0-length : 17,095,646 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: 00:06:59 17095646 reads; of these: 17095646 (100.00%) were unpaired; of these: 309684 (1.81%) aligned 0 times 13873665 (81.15%) aligned exactly 1 time 2912297 (17.04%) aligned >1 times 98.19% overall alignment rate Time searching: 00:06:59 Overall time: 00:06:59 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] 2184697 / 16785962 = 0.1302 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 16:46:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.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 16:46:31: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:46:31: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:46:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.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 16:46:31: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:46:31: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:46:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.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 16:46:31: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:46:31: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:46:40: 1000000 INFO @ Sun, 02 Jun 2019 16:46:40: 1000000 INFO @ Sun, 02 Jun 2019 16:46:41: 1000000 INFO @ Sun, 02 Jun 2019 16:46:48: 2000000 INFO @ Sun, 02 Jun 2019 16:46:48: 2000000 INFO @ Sun, 02 Jun 2019 16:46:50: 2000000 INFO @ Sun, 02 Jun 2019 16:46:57: 3000000 INFO @ Sun, 02 Jun 2019 16:46:57: 3000000 INFO @ Sun, 02 Jun 2019 16:46:59: 3000000 INFO @ Sun, 02 Jun 2019 16:47:05: 4000000 INFO @ Sun, 02 Jun 2019 16:47:05: 4000000 INFO @ Sun, 02 Jun 2019 16:47:08: 4000000 INFO @ Sun, 02 Jun 2019 16:47:14: 5000000 INFO @ Sun, 02 Jun 2019 16:47:14: 5000000 INFO @ Sun, 02 Jun 2019 16:47:17: 5000000 INFO @ Sun, 02 Jun 2019 16:47:22: 6000000 INFO @ Sun, 02 Jun 2019 16:47:22: 6000000 INFO @ Sun, 02 Jun 2019 16:47:25: 6000000 INFO @ Sun, 02 Jun 2019 16:47:30: 7000000 INFO @ Sun, 02 Jun 2019 16:47:30: 7000000 INFO @ Sun, 02 Jun 2019 16:47:35: 7000000 INFO @ Sun, 02 Jun 2019 16:47:39: 8000000 INFO @ Sun, 02 Jun 2019 16:47:39: 8000000 INFO @ Sun, 02 Jun 2019 16:47:43: 8000000 INFO @ Sun, 02 Jun 2019 16:47:47: 9000000 INFO @ Sun, 02 Jun 2019 16:47:47: 9000000 INFO @ Sun, 02 Jun 2019 16:47:52: 9000000 INFO @ Sun, 02 Jun 2019 16:47:55: 10000000 INFO @ Sun, 02 Jun 2019 16:47:56: 10000000 INFO @ Sun, 02 Jun 2019 16:48:01: 10000000 INFO @ Sun, 02 Jun 2019 16:48:04: 11000000 INFO @ Sun, 02 Jun 2019 16:48:04: 11000000 INFO @ Sun, 02 Jun 2019 16:48:10: 11000000 INFO @ Sun, 02 Jun 2019 16:48:12: 12000000 INFO @ Sun, 02 Jun 2019 16:48:12: 12000000 INFO @ Sun, 02 Jun 2019 16:48:19: 12000000 INFO @ Sun, 02 Jun 2019 16:48:20: 13000000 INFO @ Sun, 02 Jun 2019 16:48:20: 13000000 INFO @ Sun, 02 Jun 2019 16:48:28: 13000000 INFO @ Sun, 02 Jun 2019 16:48:29: 14000000 INFO @ Sun, 02 Jun 2019 16:48:29: 14000000 INFO @ Sun, 02 Jun 2019 16:48:34: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 16:48:34: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 16:48:34: #1 total tags in treatment: 14601265 INFO @ Sun, 02 Jun 2019 16:48:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:48:34: #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 16:48:34: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 16:48:34: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 16:48:34: #1 total tags in treatment: 14601265 INFO @ Sun, 02 Jun 2019 16:48:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:48:34: #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 16:48:34: #1 tags after filtering in treatment: 14601265 INFO @ Sun, 02 Jun 2019 16:48:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:48:34: #1 finished! INFO @ Sun, 02 Jun 2019 16:48:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:48:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:48:34: #1 tags after filtering in treatment: 14601265 INFO @ Sun, 02 Jun 2019 16:48:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:48:34: #1 finished! INFO @ Sun, 02 Jun 2019 16:48:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:48:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:48:35: #2 number of paired peaks: 243 WARNING @ Sun, 02 Jun 2019 16:48:35: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Sun, 02 Jun 2019 16:48:35: start model_add_line... INFO @ Sun, 02 Jun 2019 16:48:35: #2 number of paired peaks: 243 WARNING @ Sun, 02 Jun 2019 16:48:35: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Sun, 02 Jun 2019 16:48:35: start model_add_line... INFO @ Sun, 02 Jun 2019 16:48:35: start X-correlation... INFO @ Sun, 02 Jun 2019 16:48:35: start X-correlation... INFO @ Sun, 02 Jun 2019 16:48:35: end of X-cor INFO @ Sun, 02 Jun 2019 16:48:35: #2 finished! INFO @ Sun, 02 Jun 2019 16:48:35: #2 predicted fragment length is 74 bps INFO @ Sun, 02 Jun 2019 16:48:35: #2 alternative fragment length(s) may be 2,74 bps INFO @ Sun, 02 Jun 2019 16:48:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.10_model.r WARNING @ Sun, 02 Jun 2019 16:48:35: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:48:35: #2 You may need to consider one of the other alternative d(s): 2,74 WARNING @ Sun, 02 Jun 2019 16:48:35: #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 16:48:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:48:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:48:35: end of X-cor INFO @ Sun, 02 Jun 2019 16:48:35: #2 finished! INFO @ Sun, 02 Jun 2019 16:48:35: #2 predicted fragment length is 74 bps INFO @ Sun, 02 Jun 2019 16:48:35: #2 alternative fragment length(s) may be 2,74 bps INFO @ Sun, 02 Jun 2019 16:48:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.05_model.r WARNING @ Sun, 02 Jun 2019 16:48:35: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:48:35: #2 You may need to consider one of the other alternative d(s): 2,74 WARNING @ Sun, 02 Jun 2019 16:48:35: #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 16:48:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:48:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:48:37: 14000000 INFO @ Sun, 02 Jun 2019 16:48:42: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 16:48:42: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 16:48:42: #1 total tags in treatment: 14601265 INFO @ Sun, 02 Jun 2019 16:48:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:48:42: #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 16:48:42: #1 tags after filtering in treatment: 14601265 INFO @ Sun, 02 Jun 2019 16:48:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:48:42: #1 finished! INFO @ Sun, 02 Jun 2019 16:48:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:48:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:48:44: #2 number of paired peaks: 243 WARNING @ Sun, 02 Jun 2019 16:48:44: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Sun, 02 Jun 2019 16:48:44: start model_add_line... INFO @ Sun, 02 Jun 2019 16:48:44: start X-correlation... INFO @ Sun, 02 Jun 2019 16:48:44: end of X-cor INFO @ Sun, 02 Jun 2019 16:48:44: #2 finished! INFO @ Sun, 02 Jun 2019 16:48:44: #2 predicted fragment length is 74 bps INFO @ Sun, 02 Jun 2019 16:48:44: #2 alternative fragment length(s) may be 2,74 bps INFO @ Sun, 02 Jun 2019 16:48:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.20_model.r WARNING @ Sun, 02 Jun 2019 16:48:44: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:48:44: #2 You may need to consider one of the other alternative d(s): 2,74 WARNING @ Sun, 02 Jun 2019 16:48:44: #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 16:48:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:48:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:49:12: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:49:12: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:49:21: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:49:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:49:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:49:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.05_summits.bed INFO @ Sun, 02 Jun 2019 16:49:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (605 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:49:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:49:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:49:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.10_summits.bed INFO @ Sun, 02 Jun 2019 16:49:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (403 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:49:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:49:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:49:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2543061/SRX2543061.20_summits.bed INFO @ Sun, 02 Jun 2019 16:49:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (216 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。