Job ID = 2001636 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,172,426 reads read : 25,172,426 reads written : 25,172,426 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:08:54 25172426 reads; of these: 25172426 (100.00%) were unpaired; of these: 783079 (3.11%) aligned 0 times 18651304 (74.09%) aligned exactly 1 time 5738043 (22.79%) aligned >1 times 96.89% overall alignment rate Time searching: 00:08:57 Overall time: 00:08:57 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] 1765295 / 24389347 = 0.0724 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 07:04:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.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 07:04:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:04:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:04:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.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 07:04:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:04:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:04:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.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 07:04:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:04:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:04:22: 1000000 INFO @ Fri, 05 Jul 2019 07:04:23: 1000000 INFO @ Fri, 05 Jul 2019 07:04:24: 1000000 INFO @ Fri, 05 Jul 2019 07:04:30: 2000000 INFO @ Fri, 05 Jul 2019 07:04:30: 2000000 INFO @ Fri, 05 Jul 2019 07:04:32: 2000000 INFO @ Fri, 05 Jul 2019 07:04:37: 3000000 INFO @ Fri, 05 Jul 2019 07:04:37: 3000000 INFO @ Fri, 05 Jul 2019 07:04:41: 3000000 INFO @ Fri, 05 Jul 2019 07:04:44: 4000000 INFO @ Fri, 05 Jul 2019 07:04:45: 4000000 INFO @ Fri, 05 Jul 2019 07:04:50: 4000000 INFO @ Fri, 05 Jul 2019 07:04:51: 5000000 INFO @ Fri, 05 Jul 2019 07:04:52: 5000000 INFO @ Fri, 05 Jul 2019 07:04:58: 6000000 INFO @ Fri, 05 Jul 2019 07:04:59: 5000000 INFO @ Fri, 05 Jul 2019 07:05:00: 6000000 INFO @ Fri, 05 Jul 2019 07:05:05: 7000000 INFO @ Fri, 05 Jul 2019 07:05:08: 7000000 INFO @ Fri, 05 Jul 2019 07:05:09: 6000000 INFO @ Fri, 05 Jul 2019 07:05:12: 8000000 INFO @ Fri, 05 Jul 2019 07:05:15: 8000000 INFO @ Fri, 05 Jul 2019 07:05:18: 7000000 INFO @ Fri, 05 Jul 2019 07:05:19: 9000000 INFO @ Fri, 05 Jul 2019 07:05:23: 9000000 INFO @ Fri, 05 Jul 2019 07:05:26: 10000000 INFO @ Fri, 05 Jul 2019 07:05:27: 8000000 INFO @ Fri, 05 Jul 2019 07:05:30: 10000000 INFO @ Fri, 05 Jul 2019 07:05:33: 11000000 INFO @ Fri, 05 Jul 2019 07:05:35: 9000000 INFO @ Fri, 05 Jul 2019 07:05:37: 11000000 INFO @ Fri, 05 Jul 2019 07:05:39: 12000000 INFO @ Fri, 05 Jul 2019 07:05:44: 10000000 INFO @ Fri, 05 Jul 2019 07:05:45: 12000000 INFO @ Fri, 05 Jul 2019 07:05:46: 13000000 INFO @ Fri, 05 Jul 2019 07:05:52: 13000000 INFO @ Fri, 05 Jul 2019 07:05:52: 11000000 INFO @ Fri, 05 Jul 2019 07:05:53: 14000000 INFO @ Fri, 05 Jul 2019 07:05:59: 14000000 INFO @ Fri, 05 Jul 2019 07:06:00: 15000000 INFO @ Fri, 05 Jul 2019 07:06:01: 12000000 INFO @ Fri, 05 Jul 2019 07:06:06: 16000000 INFO @ Fri, 05 Jul 2019 07:06:07: 15000000 INFO @ Fri, 05 Jul 2019 07:06:10: 13000000 INFO @ Fri, 05 Jul 2019 07:06:13: 17000000 INFO @ Fri, 05 Jul 2019 07:06:14: 16000000 INFO @ Fri, 05 Jul 2019 07:06:18: 14000000 INFO @ Fri, 05 Jul 2019 07:06:20: 18000000 INFO @ Fri, 05 Jul 2019 07:06:22: 17000000 INFO @ Fri, 05 Jul 2019 07:06:26: 19000000 INFO @ Fri, 05 Jul 2019 07:06:27: 15000000 INFO @ Fri, 05 Jul 2019 07:06:29: 18000000 INFO @ Fri, 05 Jul 2019 07:06:33: 20000000 INFO @ Fri, 05 Jul 2019 07:06:37: 16000000 INFO @ Fri, 05 Jul 2019 07:06:37: 19000000 INFO @ Fri, 05 Jul 2019 07:06:40: 21000000 INFO @ Fri, 05 Jul 2019 07:06:44: 20000000 INFO @ Fri, 05 Jul 2019 07:06:46: 17000000 INFO @ Fri, 05 Jul 2019 07:06:46: 22000000 INFO @ Fri, 05 Jul 2019 07:06:51: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:06:51: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:06:51: #1 total tags in treatment: 22624052 INFO @ Fri, 05 Jul 2019 07:06:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:06:51: #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 07:06:51: 21000000 INFO @ Fri, 05 Jul 2019 07:06:52: #1 tags after filtering in treatment: 22623882 INFO @ Fri, 05 Jul 2019 07:06:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:06:52: #1 finished! INFO @ Fri, 05 Jul 2019 07:06:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:06:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:06:55: 18000000 INFO @ Fri, 05 Jul 2019 07:06:57: #2 number of paired peaks: 66094 INFO @ Fri, 05 Jul 2019 07:06:57: start model_add_line... INFO @ Fri, 05 Jul 2019 07:06:57: start X-correlation... INFO @ Fri, 05 Jul 2019 07:06:57: end of X-cor INFO @ Fri, 05 Jul 2019 07:06:57: #2 finished! INFO @ Fri, 05 Jul 2019 07:06:57: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 07:06:57: #2 alternative fragment length(s) may be 3,135,505 bps INFO @ Fri, 05 Jul 2019 07:06:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.20_model.r INFO @ Fri, 05 Jul 2019 07:06:57: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:06:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:06:59: 22000000 INFO @ Fri, 05 Jul 2019 07:07:04: 19000000 INFO @ Fri, 05 Jul 2019 07:07:04: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:07:04: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:07:04: #1 total tags in treatment: 22624052 INFO @ Fri, 05 Jul 2019 07:07:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:07:04: #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 07:07:04: #1 tags after filtering in treatment: 22623882 INFO @ Fri, 05 Jul 2019 07:07:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:07:04: #1 finished! INFO @ Fri, 05 Jul 2019 07:07:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:07:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:07:09: #2 number of paired peaks: 66094 INFO @ Fri, 05 Jul 2019 07:07:09: start model_add_line... INFO @ Fri, 05 Jul 2019 07:07:10: start X-correlation... INFO @ Fri, 05 Jul 2019 07:07:10: end of X-cor INFO @ Fri, 05 Jul 2019 07:07:10: #2 finished! INFO @ Fri, 05 Jul 2019 07:07:10: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 07:07:10: #2 alternative fragment length(s) may be 3,135,505 bps INFO @ Fri, 05 Jul 2019 07:07:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.10_model.r INFO @ Fri, 05 Jul 2019 07:07:10: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:07:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:07:12: 20000000 INFO @ Fri, 05 Jul 2019 07:07:21: 21000000 INFO @ Fri, 05 Jul 2019 07:07:29: 22000000 INFO @ Fri, 05 Jul 2019 07:07:35: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:07:35: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:07:35: #1 total tags in treatment: 22624052 INFO @ Fri, 05 Jul 2019 07:07:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:07:35: #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 07:07:36: #1 tags after filtering in treatment: 22623882 INFO @ Fri, 05 Jul 2019 07:07:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:07:36: #1 finished! INFO @ Fri, 05 Jul 2019 07:07:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:07:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:07:41: #2 number of paired peaks: 66094 INFO @ Fri, 05 Jul 2019 07:07:41: start model_add_line... INFO @ Fri, 05 Jul 2019 07:07:41: start X-correlation... INFO @ Fri, 05 Jul 2019 07:07:41: end of X-cor INFO @ Fri, 05 Jul 2019 07:07:41: #2 finished! INFO @ Fri, 05 Jul 2019 07:07:41: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 07:07:41: #2 alternative fragment length(s) may be 3,135,505 bps INFO @ Fri, 05 Jul 2019 07:07:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.05_model.r INFO @ Fri, 05 Jul 2019 07:07:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:07:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:08:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:08:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:08:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.20_peaks.xls INFO @ Fri, 05 Jul 2019 07:08:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:08:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.20_summits.bed INFO @ Fri, 05 Jul 2019 07:08:44: Done! pass1 - making usageList (26 chroms): 1 millis pass2 - checking and writing primary data (129 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:08:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:08:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.10_peaks.xls INFO @ Fri, 05 Jul 2019 07:08:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:08:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.10_summits.bed INFO @ Fri, 05 Jul 2019 07:08:59: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (1059 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:09:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.05_peaks.xls INFO @ Fri, 05 Jul 2019 07:09:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:09:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101952/ERX101952.05_summits.bed INFO @ Fri, 05 Jul 2019 07:09:33: Done! pass1 - making usageList (74 chroms): 2 millis pass2 - checking and writing primary data (5019 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。