Job ID = 2590246 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,897,127 reads read : 32,897,127 reads written : 32,897,127 rm: cannot remove ‘[DSE]RR*’: 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: 00:12:18 32897127 reads; of these: 32897127 (100.00%) were unpaired; of these: 233403 (0.71%) aligned 0 times 29498732 (89.67%) aligned exactly 1 time 3164992 (9.62%) aligned >1 times 99.29% overall alignment rate Time searching: 00:12:18 Overall time: 00:12:18 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 16 files... [bam_rmdupse_core] 7428390 / 32663724 = 0.2274 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 @ Mon, 12 Aug 2019 20:57:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.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 @ Mon, 12 Aug 2019 20:57:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:57:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:57:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.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 @ Mon, 12 Aug 2019 20:57:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:57:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:57:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.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 @ Mon, 12 Aug 2019 20:57:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:57:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:57:59: 1000000 INFO @ Mon, 12 Aug 2019 20:58:00: 1000000 INFO @ Mon, 12 Aug 2019 20:58:01: 1000000 INFO @ Mon, 12 Aug 2019 20:58:07: 2000000 INFO @ Mon, 12 Aug 2019 20:58:08: 2000000 INFO @ Mon, 12 Aug 2019 20:58:10: 2000000 INFO @ Mon, 12 Aug 2019 20:58:15: 3000000 INFO @ Mon, 12 Aug 2019 20:58:17: 3000000 INFO @ Mon, 12 Aug 2019 20:58:18: 3000000 INFO @ Mon, 12 Aug 2019 20:58:23: 4000000 INFO @ Mon, 12 Aug 2019 20:58:25: 4000000 INFO @ Mon, 12 Aug 2019 20:58:26: 4000000 INFO @ Mon, 12 Aug 2019 20:58:32: 5000000 INFO @ Mon, 12 Aug 2019 20:58:33: 5000000 INFO @ Mon, 12 Aug 2019 20:58:35: 5000000 INFO @ Mon, 12 Aug 2019 20:58:40: 6000000 INFO @ Mon, 12 Aug 2019 20:58:40: 6000000 INFO @ Mon, 12 Aug 2019 20:58:43: 6000000 INFO @ Mon, 12 Aug 2019 20:58:48: 7000000 INFO @ Mon, 12 Aug 2019 20:58:48: 7000000 INFO @ Mon, 12 Aug 2019 20:58:51: 7000000 INFO @ Mon, 12 Aug 2019 20:58:56: 8000000 INFO @ Mon, 12 Aug 2019 20:58:57: 8000000 INFO @ Mon, 12 Aug 2019 20:59:00: 8000000 INFO @ Mon, 12 Aug 2019 20:59:03: 9000000 INFO @ Mon, 12 Aug 2019 20:59:05: 9000000 INFO @ Mon, 12 Aug 2019 20:59:08: 9000000 INFO @ Mon, 12 Aug 2019 20:59:10: 10000000 INFO @ Mon, 12 Aug 2019 20:59:13: 10000000 INFO @ Mon, 12 Aug 2019 20:59:16: 10000000 INFO @ Mon, 12 Aug 2019 20:59:18: 11000000 INFO @ Mon, 12 Aug 2019 20:59:22: 11000000 INFO @ Mon, 12 Aug 2019 20:59:25: 11000000 INFO @ Mon, 12 Aug 2019 20:59:25: 12000000 INFO @ Mon, 12 Aug 2019 20:59:30: 12000000 INFO @ Mon, 12 Aug 2019 20:59:32: 13000000 INFO @ Mon, 12 Aug 2019 20:59:33: 12000000 INFO @ Mon, 12 Aug 2019 20:59:38: 13000000 INFO @ Mon, 12 Aug 2019 20:59:39: 14000000 INFO @ Mon, 12 Aug 2019 20:59:41: 13000000 INFO @ Mon, 12 Aug 2019 20:59:47: 14000000 INFO @ Mon, 12 Aug 2019 20:59:47: 15000000 INFO @ Mon, 12 Aug 2019 20:59:49: 14000000 INFO @ Mon, 12 Aug 2019 20:59:54: 16000000 INFO @ Mon, 12 Aug 2019 20:59:55: 15000000 INFO @ Mon, 12 Aug 2019 20:59:58: 15000000 INFO @ Mon, 12 Aug 2019 21:00:02: 17000000 INFO @ Mon, 12 Aug 2019 21:00:03: 16000000 INFO @ Mon, 12 Aug 2019 21:00:06: 16000000 INFO @ Mon, 12 Aug 2019 21:00:09: 18000000 INFO @ Mon, 12 Aug 2019 21:00:12: 17000000 INFO @ Mon, 12 Aug 2019 21:00:15: 17000000 INFO @ Mon, 12 Aug 2019 21:00:17: 19000000 INFO @ Mon, 12 Aug 2019 21:00:20: 18000000 INFO @ Mon, 12 Aug 2019 21:00:24: 18000000 INFO @ Mon, 12 Aug 2019 21:00:24: 20000000 INFO @ Mon, 12 Aug 2019 21:00:29: 19000000 INFO @ Mon, 12 Aug 2019 21:00:31: 21000000 INFO @ Mon, 12 Aug 2019 21:00:32: 19000000 INFO @ Mon, 12 Aug 2019 21:00:37: 20000000 INFO @ Mon, 12 Aug 2019 21:00:39: 22000000 INFO @ Mon, 12 Aug 2019 21:00:40: 20000000 INFO @ Mon, 12 Aug 2019 21:00:46: 21000000 INFO @ Mon, 12 Aug 2019 21:00:46: 23000000 INFO @ Mon, 12 Aug 2019 21:00:49: 21000000 INFO @ Mon, 12 Aug 2019 21:00:53: 24000000 INFO @ Mon, 12 Aug 2019 21:00:54: 22000000 INFO @ Mon, 12 Aug 2019 21:00:57: 22000000 INFO @ Mon, 12 Aug 2019 21:01:01: 25000000 INFO @ Mon, 12 Aug 2019 21:01:03: 23000000 INFO @ Mon, 12 Aug 2019 21:01:03: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 21:01:03: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 21:01:03: #1 total tags in treatment: 25235334 INFO @ Mon, 12 Aug 2019 21:01:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:01:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:01:03: #1 tags after filtering in treatment: 25235334 INFO @ Mon, 12 Aug 2019 21:01:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:01:03: #1 finished! INFO @ Mon, 12 Aug 2019 21:01:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:01:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:01:05: #2 number of paired peaks: 124 WARNING @ Mon, 12 Aug 2019 21:01:05: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Mon, 12 Aug 2019 21:01:05: start model_add_line... INFO @ Mon, 12 Aug 2019 21:01:05: 23000000 INFO @ Mon, 12 Aug 2019 21:01:06: start X-correlation... INFO @ Mon, 12 Aug 2019 21:01:06: end of X-cor INFO @ Mon, 12 Aug 2019 21:01:06: #2 finished! INFO @ Mon, 12 Aug 2019 21:01:06: #2 predicted fragment length is 119 bps INFO @ Mon, 12 Aug 2019 21:01:06: #2 alternative fragment length(s) may be 2,37,87,119,141,158,197,264,267,270,272,279,300,334 bps INFO @ Mon, 12 Aug 2019 21:01:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.05_model.r WARNING @ Mon, 12 Aug 2019 21:01:06: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:01:06: #2 You may need to consider one of the other alternative d(s): 2,37,87,119,141,158,197,264,267,270,272,279,300,334 WARNING @ Mon, 12 Aug 2019 21:01:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 21:01:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:01:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:01:11: 24000000 INFO @ Mon, 12 Aug 2019 21:01:14: 24000000 INFO @ Mon, 12 Aug 2019 21:01:18: 25000000 INFO @ Mon, 12 Aug 2019 21:01:20: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 21:01:20: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 21:01:20: #1 total tags in treatment: 25235334 INFO @ Mon, 12 Aug 2019 21:01:20: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:01:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:01:21: #1 tags after filtering in treatment: 25235334 INFO @ Mon, 12 Aug 2019 21:01:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:01:21: #1 finished! INFO @ Mon, 12 Aug 2019 21:01:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:01:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:01:22: 25000000 INFO @ Mon, 12 Aug 2019 21:01:23: #2 number of paired peaks: 124 WARNING @ Mon, 12 Aug 2019 21:01:23: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Mon, 12 Aug 2019 21:01:23: start model_add_line... INFO @ Mon, 12 Aug 2019 21:01:23: start X-correlation... INFO @ Mon, 12 Aug 2019 21:01:23: end of X-cor INFO @ Mon, 12 Aug 2019 21:01:23: #2 finished! INFO @ Mon, 12 Aug 2019 21:01:23: #2 predicted fragment length is 119 bps INFO @ Mon, 12 Aug 2019 21:01:23: #2 alternative fragment length(s) may be 2,37,87,119,141,158,197,264,267,270,272,279,300,334 bps INFO @ Mon, 12 Aug 2019 21:01:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.10_model.r WARNING @ Mon, 12 Aug 2019 21:01:23: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:01:23: #2 You may need to consider one of the other alternative d(s): 2,37,87,119,141,158,197,264,267,270,272,279,300,334 WARNING @ Mon, 12 Aug 2019 21:01:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 21:01:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:01:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:01:24: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 21:01:24: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 21:01:24: #1 total tags in treatment: 25235334 INFO @ Mon, 12 Aug 2019 21:01:24: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:01:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:01:25: #1 tags after filtering in treatment: 25235334 INFO @ Mon, 12 Aug 2019 21:01:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:01:25: #1 finished! INFO @ Mon, 12 Aug 2019 21:01:25: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:01:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:01:27: #2 number of paired peaks: 124 WARNING @ Mon, 12 Aug 2019 21:01:27: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Mon, 12 Aug 2019 21:01:27: start model_add_line... INFO @ Mon, 12 Aug 2019 21:01:27: start X-correlation... INFO @ Mon, 12 Aug 2019 21:01:27: end of X-cor INFO @ Mon, 12 Aug 2019 21:01:27: #2 finished! INFO @ Mon, 12 Aug 2019 21:01:27: #2 predicted fragment length is 119 bps INFO @ Mon, 12 Aug 2019 21:01:27: #2 alternative fragment length(s) may be 2,37,87,119,141,158,197,264,267,270,272,279,300,334 bps INFO @ Mon, 12 Aug 2019 21:01:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.20_model.r WARNING @ Mon, 12 Aug 2019 21:01:27: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:01:27: #2 You may need to consider one of the other alternative d(s): 2,37,87,119,141,158,197,264,267,270,272,279,300,334 WARNING @ Mon, 12 Aug 2019 21:01:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 21:01:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:01:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:02:04: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:02:21: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:02:25: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:02:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:02:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:02:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.05_summits.bed INFO @ Mon, 12 Aug 2019 21:02:29: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (9759 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:02:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:02:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:02:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.10_summits.bed INFO @ Mon, 12 Aug 2019 21:02:45: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (5303 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:02:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:02:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:02:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985678/SRX5985678.20_summits.bed INFO @ Mon, 12 Aug 2019 21:02:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1512 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。