Job ID = 2002172 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,433,011 reads read : 29,433,011 reads written : 29,433,011 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:11:07 29433011 reads; of these: 29433011 (100.00%) were unpaired; of these: 729667 (2.48%) aligned 0 times 20191634 (68.60%) aligned exactly 1 time 8511710 (28.92%) aligned >1 times 97.52% overall alignment rate Time searching: 00:11:10 Overall time: 00:11:10 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 8 files... [bam_rmdupse_core] 1483147 / 28703344 = 0.0517 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 11:33:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.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 11:33:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:33:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:33:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.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 11:33:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:33:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:33:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.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 11:33:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:33:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:33:12: 1000000 INFO @ Fri, 05 Jul 2019 11:33:13: 1000000 INFO @ Fri, 05 Jul 2019 11:33:13: 1000000 INFO @ Fri, 05 Jul 2019 11:33:20: 2000000 INFO @ Fri, 05 Jul 2019 11:33:20: 2000000 INFO @ Fri, 05 Jul 2019 11:33:21: 2000000 INFO @ Fri, 05 Jul 2019 11:33:27: 3000000 INFO @ Fri, 05 Jul 2019 11:33:27: 3000000 INFO @ Fri, 05 Jul 2019 11:33:28: 3000000 INFO @ Fri, 05 Jul 2019 11:33:34: 4000000 INFO @ Fri, 05 Jul 2019 11:33:35: 4000000 INFO @ Fri, 05 Jul 2019 11:33:36: 4000000 INFO @ Fri, 05 Jul 2019 11:33:41: 5000000 INFO @ Fri, 05 Jul 2019 11:33:42: 5000000 INFO @ Fri, 05 Jul 2019 11:33:44: 5000000 INFO @ Fri, 05 Jul 2019 11:33:48: 6000000 INFO @ Fri, 05 Jul 2019 11:33:50: 6000000 INFO @ Fri, 05 Jul 2019 11:33:51: 6000000 INFO @ Fri, 05 Jul 2019 11:33:55: 7000000 INFO @ Fri, 05 Jul 2019 11:33:58: 7000000 INFO @ Fri, 05 Jul 2019 11:33:59: 7000000 INFO @ Fri, 05 Jul 2019 11:34:01: 8000000 INFO @ Fri, 05 Jul 2019 11:34:05: 8000000 INFO @ Fri, 05 Jul 2019 11:34:06: 8000000 INFO @ Fri, 05 Jul 2019 11:34:08: 9000000 INFO @ Fri, 05 Jul 2019 11:34:12: 9000000 INFO @ Fri, 05 Jul 2019 11:34:13: 9000000 INFO @ Fri, 05 Jul 2019 11:34:15: 10000000 INFO @ Fri, 05 Jul 2019 11:34:20: 10000000 INFO @ Fri, 05 Jul 2019 11:34:20: 10000000 INFO @ Fri, 05 Jul 2019 11:34:21: 11000000 INFO @ Fri, 05 Jul 2019 11:34:27: 11000000 INFO @ Fri, 05 Jul 2019 11:34:28: 11000000 INFO @ Fri, 05 Jul 2019 11:34:28: 12000000 INFO @ Fri, 05 Jul 2019 11:34:35: 12000000 INFO @ Fri, 05 Jul 2019 11:34:35: 13000000 INFO @ Fri, 05 Jul 2019 11:34:35: 12000000 INFO @ Fri, 05 Jul 2019 11:34:42: 14000000 INFO @ Fri, 05 Jul 2019 11:34:42: 13000000 INFO @ Fri, 05 Jul 2019 11:34:43: 13000000 INFO @ Fri, 05 Jul 2019 11:34:49: 15000000 INFO @ Fri, 05 Jul 2019 11:34:49: 14000000 INFO @ Fri, 05 Jul 2019 11:34:50: 14000000 INFO @ Fri, 05 Jul 2019 11:34:56: 16000000 INFO @ Fri, 05 Jul 2019 11:34:57: 15000000 INFO @ Fri, 05 Jul 2019 11:34:58: 15000000 INFO @ Fri, 05 Jul 2019 11:35:02: 17000000 INFO @ Fri, 05 Jul 2019 11:35:04: 16000000 INFO @ Fri, 05 Jul 2019 11:35:05: 16000000 INFO @ Fri, 05 Jul 2019 11:35:11: 18000000 INFO @ Fri, 05 Jul 2019 11:35:12: 17000000 INFO @ Fri, 05 Jul 2019 11:35:13: 17000000 INFO @ Fri, 05 Jul 2019 11:35:19: 19000000 INFO @ Fri, 05 Jul 2019 11:35:20: 18000000 INFO @ Fri, 05 Jul 2019 11:35:20: 18000000 INFO @ Fri, 05 Jul 2019 11:35:27: 19000000 INFO @ Fri, 05 Jul 2019 11:35:27: 20000000 INFO @ Fri, 05 Jul 2019 11:35:28: 19000000 INFO @ Fri, 05 Jul 2019 11:35:35: 20000000 INFO @ Fri, 05 Jul 2019 11:35:35: 20000000 INFO @ Fri, 05 Jul 2019 11:35:36: 21000000 INFO @ Fri, 05 Jul 2019 11:35:42: 21000000 INFO @ Fri, 05 Jul 2019 11:35:43: 21000000 INFO @ Fri, 05 Jul 2019 11:35:44: 22000000 INFO @ Fri, 05 Jul 2019 11:35:49: 22000000 INFO @ Fri, 05 Jul 2019 11:35:50: 22000000 INFO @ Fri, 05 Jul 2019 11:35:53: 23000000 INFO @ Fri, 05 Jul 2019 11:35:57: 23000000 INFO @ Fri, 05 Jul 2019 11:35:58: 23000000 INFO @ Fri, 05 Jul 2019 11:36:01: 24000000 INFO @ Fri, 05 Jul 2019 11:36:05: 24000000 INFO @ Fri, 05 Jul 2019 11:36:06: 24000000 INFO @ Fri, 05 Jul 2019 11:36:10: 25000000 INFO @ Fri, 05 Jul 2019 11:36:13: 25000000 INFO @ Fri, 05 Jul 2019 11:36:14: 25000000 INFO @ Fri, 05 Jul 2019 11:36:19: 26000000 INFO @ Fri, 05 Jul 2019 11:36:21: 26000000 INFO @ Fri, 05 Jul 2019 11:36:21: 26000000 INFO @ Fri, 05 Jul 2019 11:36:29: 27000000 INFO @ Fri, 05 Jul 2019 11:36:29: 27000000 INFO @ Fri, 05 Jul 2019 11:36:29: 27000000 INFO @ Fri, 05 Jul 2019 11:36:31: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:36:31: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:36:31: #1 total tags in treatment: 27220197 INFO @ Fri, 05 Jul 2019 11:36:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:36:31: #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 11:36:31: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:36:31: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:36:31: #1 total tags in treatment: 27220197 INFO @ Fri, 05 Jul 2019 11:36:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:36:31: #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 11:36:31: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:36:31: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:36:31: #1 total tags in treatment: 27220197 INFO @ Fri, 05 Jul 2019 11:36:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:36:31: #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 11:36:31: #1 tags after filtering in treatment: 27220080 INFO @ Fri, 05 Jul 2019 11:36:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:36:31: #1 finished! INFO @ Fri, 05 Jul 2019 11:36:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:36:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:36:32: #1 tags after filtering in treatment: 27220080 INFO @ Fri, 05 Jul 2019 11:36:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:36:32: #1 finished! INFO @ Fri, 05 Jul 2019 11:36:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:36:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:36:32: #1 tags after filtering in treatment: 27220080 INFO @ Fri, 05 Jul 2019 11:36:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:36:32: #1 finished! INFO @ Fri, 05 Jul 2019 11:36:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:36:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:36:35: #2 number of paired peaks: 7957 INFO @ Fri, 05 Jul 2019 11:36:35: start model_add_line... INFO @ Fri, 05 Jul 2019 11:36:35: start X-correlation... INFO @ Fri, 05 Jul 2019 11:36:35: end of X-cor INFO @ Fri, 05 Jul 2019 11:36:35: #2 finished! INFO @ Fri, 05 Jul 2019 11:36:35: #2 predicted fragment length is 42 bps INFO @ Fri, 05 Jul 2019 11:36:35: #2 alternative fragment length(s) may be 42,82 bps INFO @ Fri, 05 Jul 2019 11:36:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.05_model.r WARNING @ Fri, 05 Jul 2019 11:36:35: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 11:36:35: #2 You may need to consider one of the other alternative d(s): 42,82 WARNING @ Fri, 05 Jul 2019 11:36:35: #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 11:36:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:36:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:36:35: #2 number of paired peaks: 7957 INFO @ Fri, 05 Jul 2019 11:36:35: start model_add_line... INFO @ Fri, 05 Jul 2019 11:36:35: #2 number of paired peaks: 7957 INFO @ Fri, 05 Jul 2019 11:36:35: start model_add_line... INFO @ Fri, 05 Jul 2019 11:36:36: start X-correlation... INFO @ Fri, 05 Jul 2019 11:36:36: start X-correlation... INFO @ Fri, 05 Jul 2019 11:36:36: end of X-cor INFO @ Fri, 05 Jul 2019 11:36:36: #2 finished! INFO @ Fri, 05 Jul 2019 11:36:36: #2 predicted fragment length is 42 bps INFO @ Fri, 05 Jul 2019 11:36:36: #2 alternative fragment length(s) may be 42,82 bps INFO @ Fri, 05 Jul 2019 11:36:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.10_model.r INFO @ Fri, 05 Jul 2019 11:36:36: end of X-cor INFO @ Fri, 05 Jul 2019 11:36:36: #2 finished! INFO @ Fri, 05 Jul 2019 11:36:36: #2 predicted fragment length is 42 bps INFO @ Fri, 05 Jul 2019 11:36:36: #2 alternative fragment length(s) may be 42,82 bps INFO @ Fri, 05 Jul 2019 11:36:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.20_model.r WARNING @ Fri, 05 Jul 2019 11:36:36: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 11:36:36: #2 You may need to consider one of the other alternative d(s): 42,82 WARNING @ Fri, 05 Jul 2019 11:36:36: #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 11:36:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:36:36: #3 Pre-compute pvalue-qvalue table... WARNING @ Fri, 05 Jul 2019 11:36:36: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 11:36:36: #2 You may need to consider one of the other alternative d(s): 42,82 WARNING @ Fri, 05 Jul 2019 11:36:36: #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 11:36:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:36:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:37:59: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:38:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:38:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:38:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:38:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:38:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.05_summits.bed INFO @ Fri, 05 Jul 2019 11:38:43: Done! pass1 - making usageList (74 chroms): 2 millis pass2 - checking and writing primary data (2648 records, 4 fields): 10 millis INFO @ Fri, 05 Jul 2019 11:38:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:38:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:38:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.20_summits.bed INFO @ Fri, 05 Jul 2019 11:38:44: Done! CompletedMACS2peakCalling pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (478 records, 4 fields): 6 millis INFO @ Fri, 05 Jul 2019 11:38:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.10_peaks.xls INFO @ Fri, 05 Jul 2019 11:38:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:38:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210232/ERX210232.10_summits.bed INFO @ Fri, 05 Jul 2019 11:38:44: Done! pass1 - making usageList (45 chroms): 2 millis pass2 - checking and writing primary data (1144 records, 4 fields): 9 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。