Job ID = 2002536 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,524,386 reads read : 28,524,386 reads written : 28,524,386 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR572144.sra.cache’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:05 Time loading mirror index: 00:00:07 Multiseed full-index search: 00:27:06 28524386 reads; of these: 28524386 (100.00%) were unpaired; of these: 516174 (1.81%) aligned 0 times 18914122 (66.31%) aligned exactly 1 time 9094090 (31.88%) aligned >1 times 98.19% overall alignment rate Time searching: 00:27:20 Overall time: 00:27:22 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 818333 / 28008212 = 0.0292 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 @ Fri, 05 Jul 2019 12:27:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 12:27:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:27:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:27:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 12:27:03: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:27:03: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:27:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 12:27:03: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:27:03: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:27:11: 1000000 INFO @ Fri, 05 Jul 2019 12:27:11: 1000000 INFO @ Fri, 05 Jul 2019 12:27:12: 1000000 INFO @ Fri, 05 Jul 2019 12:27:19: 2000000 INFO @ Fri, 05 Jul 2019 12:27:20: 2000000 INFO @ Fri, 05 Jul 2019 12:27:20: 2000000 INFO @ Fri, 05 Jul 2019 12:27:27: 3000000 INFO @ Fri, 05 Jul 2019 12:27:28: 3000000 INFO @ Fri, 05 Jul 2019 12:27:29: 3000000 INFO @ Fri, 05 Jul 2019 12:27:34: 4000000 INFO @ Fri, 05 Jul 2019 12:27:37: 4000000 INFO @ Fri, 05 Jul 2019 12:27:37: 4000000 INFO @ Fri, 05 Jul 2019 12:27:42: 5000000 INFO @ Fri, 05 Jul 2019 12:27:45: 5000000 INFO @ Fri, 05 Jul 2019 12:27:45: 5000000 INFO @ Fri, 05 Jul 2019 12:27:49: 6000000 INFO @ Fri, 05 Jul 2019 12:27:53: 6000000 INFO @ Fri, 05 Jul 2019 12:27:53: 6000000 INFO @ Fri, 05 Jul 2019 12:27:57: 7000000 INFO @ Fri, 05 Jul 2019 12:28:01: 7000000 INFO @ Fri, 05 Jul 2019 12:28:01: 7000000 INFO @ Fri, 05 Jul 2019 12:28:05: 8000000 INFO @ Fri, 05 Jul 2019 12:28:09: 8000000 INFO @ Fri, 05 Jul 2019 12:28:10: 8000000 INFO @ Fri, 05 Jul 2019 12:28:12: 9000000 INFO @ Fri, 05 Jul 2019 12:28:17: 9000000 INFO @ Fri, 05 Jul 2019 12:28:18: 9000000 INFO @ Fri, 05 Jul 2019 12:28:20: 10000000 INFO @ Fri, 05 Jul 2019 12:28:26: 10000000 INFO @ Fri, 05 Jul 2019 12:28:26: 10000000 INFO @ Fri, 05 Jul 2019 12:28:27: 11000000 INFO @ Fri, 05 Jul 2019 12:28:34: 11000000 INFO @ Fri, 05 Jul 2019 12:28:34: 11000000 INFO @ Fri, 05 Jul 2019 12:28:35: 12000000 INFO @ Fri, 05 Jul 2019 12:28:42: 12000000 INFO @ Fri, 05 Jul 2019 12:28:42: 13000000 INFO @ Fri, 05 Jul 2019 12:28:42: 12000000 INFO @ Fri, 05 Jul 2019 12:28:50: 14000000 INFO @ Fri, 05 Jul 2019 12:28:50: 13000000 INFO @ Fri, 05 Jul 2019 12:28:51: 13000000 INFO @ Fri, 05 Jul 2019 12:28:57: 15000000 INFO @ Fri, 05 Jul 2019 12:28:58: 14000000 INFO @ Fri, 05 Jul 2019 12:28:59: 14000000 INFO @ Fri, 05 Jul 2019 12:29:05: 16000000 INFO @ Fri, 05 Jul 2019 12:29:06: 15000000 INFO @ Fri, 05 Jul 2019 12:29:07: 15000000 INFO @ Fri, 05 Jul 2019 12:29:13: 17000000 INFO @ Fri, 05 Jul 2019 12:29:14: 16000000 INFO @ Fri, 05 Jul 2019 12:29:15: 16000000 INFO @ Fri, 05 Jul 2019 12:29:20: 18000000 INFO @ Fri, 05 Jul 2019 12:29:23: 17000000 INFO @ Fri, 05 Jul 2019 12:29:25: 17000000 INFO @ Fri, 05 Jul 2019 12:29:28: 19000000 INFO @ Fri, 05 Jul 2019 12:29:33: 18000000 INFO @ Fri, 05 Jul 2019 12:29:33: 18000000 INFO @ Fri, 05 Jul 2019 12:29:35: 20000000 INFO @ Fri, 05 Jul 2019 12:29:41: 19000000 INFO @ Fri, 05 Jul 2019 12:29:43: 19000000 INFO @ Fri, 05 Jul 2019 12:29:43: 21000000 INFO @ Fri, 05 Jul 2019 12:29:50: 20000000 INFO @ Fri, 05 Jul 2019 12:29:51: 22000000 INFO @ Fri, 05 Jul 2019 12:29:52: 20000000 INFO @ Fri, 05 Jul 2019 12:29:58: 21000000 INFO @ Fri, 05 Jul 2019 12:29:59: 23000000 INFO @ Fri, 05 Jul 2019 12:30:01: 21000000 INFO @ Fri, 05 Jul 2019 12:30:06: 22000000 INFO @ Fri, 05 Jul 2019 12:30:06: 24000000 INFO @ Fri, 05 Jul 2019 12:30:10: 22000000 INFO @ Fri, 05 Jul 2019 12:30:14: 25000000 INFO @ Fri, 05 Jul 2019 12:30:14: 23000000 INFO @ Fri, 05 Jul 2019 12:30:19: 23000000 INFO @ Fri, 05 Jul 2019 12:30:22: 26000000 INFO @ Fri, 05 Jul 2019 12:30:22: 24000000 INFO @ Fri, 05 Jul 2019 12:30:28: 24000000 INFO @ Fri, 05 Jul 2019 12:30:29: 27000000 INFO @ Fri, 05 Jul 2019 12:30:31: 25000000 INFO @ Fri, 05 Jul 2019 12:30:31: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:30:31: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:30:31: #1 total tags in treatment: 27189879 INFO @ Fri, 05 Jul 2019 12:30:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:30:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:30:32: #1 tags after filtering in treatment: 27189787 INFO @ Fri, 05 Jul 2019 12:30:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:30:32: #1 finished! INFO @ Fri, 05 Jul 2019 12:30:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:30:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:30:35: #2 number of paired peaks: 5877 INFO @ Fri, 05 Jul 2019 12:30:35: start model_add_line... INFO @ Fri, 05 Jul 2019 12:30:36: start X-correlation... INFO @ Fri, 05 Jul 2019 12:30:36: end of X-cor INFO @ Fri, 05 Jul 2019 12:30:36: #2 finished! INFO @ Fri, 05 Jul 2019 12:30:36: #2 predicted fragment length is 50 bps INFO @ Fri, 05 Jul 2019 12:30:36: #2 alternative fragment length(s) may be 50,507 bps INFO @ Fri, 05 Jul 2019 12:30:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.20_model.r WARNING @ Fri, 05 Jul 2019 12:30:36: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 12:30:36: #2 You may need to consider one of the other alternative d(s): 50,507 WARNING @ Fri, 05 Jul 2019 12:30:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 12:30:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:30:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:30:37: 25000000 INFO @ Fri, 05 Jul 2019 12:30:39: 26000000 INFO @ Fri, 05 Jul 2019 12:30:46: 26000000 INFO @ Fri, 05 Jul 2019 12:30:47: 27000000 INFO @ Fri, 05 Jul 2019 12:30:49: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:30:49: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:30:49: #1 total tags in treatment: 27189879 INFO @ Fri, 05 Jul 2019 12:30:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:30:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:30:50: #1 tags after filtering in treatment: 27189787 INFO @ Fri, 05 Jul 2019 12:30:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:30:50: #1 finished! INFO @ Fri, 05 Jul 2019 12:30:50: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:30:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:30:53: #2 number of paired peaks: 5877 INFO @ Fri, 05 Jul 2019 12:30:53: start model_add_line... INFO @ Fri, 05 Jul 2019 12:30:54: start X-correlation... INFO @ Fri, 05 Jul 2019 12:30:54: end of X-cor INFO @ Fri, 05 Jul 2019 12:30:54: #2 finished! INFO @ Fri, 05 Jul 2019 12:30:54: #2 predicted fragment length is 50 bps INFO @ Fri, 05 Jul 2019 12:30:54: #2 alternative fragment length(s) may be 50,507 bps INFO @ Fri, 05 Jul 2019 12:30:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.10_model.r WARNING @ Fri, 05 Jul 2019 12:30:54: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 12:30:54: #2 You may need to consider one of the other alternative d(s): 50,507 WARNING @ Fri, 05 Jul 2019 12:30:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 12:30:54: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:30:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:30:56: 27000000 INFO @ Fri, 05 Jul 2019 12:30:58: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:30:58: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:30:58: #1 total tags in treatment: 27189879 INFO @ Fri, 05 Jul 2019 12:30:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:30:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:30:59: #1 tags after filtering in treatment: 27189787 INFO @ Fri, 05 Jul 2019 12:30:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:30:59: #1 finished! INFO @ Fri, 05 Jul 2019 12:30:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:30:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:31:02: #2 number of paired peaks: 5877 INFO @ Fri, 05 Jul 2019 12:31:02: start model_add_line... INFO @ Fri, 05 Jul 2019 12:31:02: start X-correlation... INFO @ Fri, 05 Jul 2019 12:31:02: end of X-cor INFO @ Fri, 05 Jul 2019 12:31:02: #2 finished! INFO @ Fri, 05 Jul 2019 12:31:02: #2 predicted fragment length is 50 bps INFO @ Fri, 05 Jul 2019 12:31:02: #2 alternative fragment length(s) may be 50,507 bps INFO @ Fri, 05 Jul 2019 12:31:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.05_model.r WARNING @ Fri, 05 Jul 2019 12:31:02: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 12:31:02: #2 You may need to consider one of the other alternative d(s): 50,507 WARNING @ Fri, 05 Jul 2019 12:31:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 12:31:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:31:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:32:05: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:32:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:32:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:32:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:32:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:32:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.20_summits.bed INFO @ Fri, 05 Jul 2019 12:32:51: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (488 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:33:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:33:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:33:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.10_summits.bed INFO @ Fri, 05 Jul 2019 12:33:08: Done! pass1 - making usageList (44 chroms): 2 millis pass2 - checking and writing primary data (967 records, 4 fields): 6 millis INFO @ Fri, 05 Jul 2019 12:33:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:33:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:33:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX531062/ERX531062.05_summits.bed INFO @ Fri, 05 Jul 2019 12:33:10: Done! pass1 - making usageList (53 chroms): 1 millis pass2 - checking and writing primary data (1667 records, 4 fields): 11 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。