Job ID = 2001667 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,178,575 reads read : 24,178,575 reads written : 24,178,575 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:52 24178575 reads; of these: 24178575 (100.00%) were unpaired; of these: 585159 (2.42%) aligned 0 times 17489672 (72.34%) aligned exactly 1 time 6103744 (25.24%) aligned >1 times 97.58% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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] 1331927 / 23593416 = 0.0565 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 08:04:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.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 08:04:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:04:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:04:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.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 08:04:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:04:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:04:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.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 08:04:03: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:04:03: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:04:09: 1000000 INFO @ Fri, 05 Jul 2019 08:04:09: 1000000 INFO @ Fri, 05 Jul 2019 08:04:10: 1000000 INFO @ Fri, 05 Jul 2019 08:04:15: 2000000 INFO @ Fri, 05 Jul 2019 08:04:15: 2000000 INFO @ Fri, 05 Jul 2019 08:04:17: 2000000 INFO @ Fri, 05 Jul 2019 08:04:21: 3000000 INFO @ Fri, 05 Jul 2019 08:04:22: 3000000 INFO @ Fri, 05 Jul 2019 08:04:24: 3000000 INFO @ Fri, 05 Jul 2019 08:04:27: 4000000 INFO @ Fri, 05 Jul 2019 08:04:28: 4000000 INFO @ Fri, 05 Jul 2019 08:04:31: 4000000 INFO @ Fri, 05 Jul 2019 08:04:33: 5000000 INFO @ Fri, 05 Jul 2019 08:04:35: 5000000 INFO @ Fri, 05 Jul 2019 08:04:38: 5000000 INFO @ Fri, 05 Jul 2019 08:04:39: 6000000 INFO @ Fri, 05 Jul 2019 08:04:41: 6000000 INFO @ Fri, 05 Jul 2019 08:04:44: 6000000 INFO @ Fri, 05 Jul 2019 08:04:46: 7000000 INFO @ Fri, 05 Jul 2019 08:04:48: 7000000 INFO @ Fri, 05 Jul 2019 08:04:51: 7000000 INFO @ Fri, 05 Jul 2019 08:04:52: 8000000 INFO @ Fri, 05 Jul 2019 08:04:54: 8000000 INFO @ Fri, 05 Jul 2019 08:04:58: 9000000 INFO @ Fri, 05 Jul 2019 08:04:58: 8000000 INFO @ Fri, 05 Jul 2019 08:05:01: 9000000 INFO @ Fri, 05 Jul 2019 08:05:04: 10000000 INFO @ Fri, 05 Jul 2019 08:05:05: 9000000 INFO @ Fri, 05 Jul 2019 08:05:08: 10000000 INFO @ Fri, 05 Jul 2019 08:05:11: 11000000 INFO @ Fri, 05 Jul 2019 08:05:12: 10000000 INFO @ Fri, 05 Jul 2019 08:05:14: 11000000 INFO @ Fri, 05 Jul 2019 08:05:17: 12000000 INFO @ Fri, 05 Jul 2019 08:05:19: 11000000 INFO @ Fri, 05 Jul 2019 08:05:21: 12000000 INFO @ Fri, 05 Jul 2019 08:05:24: 13000000 INFO @ Fri, 05 Jul 2019 08:05:26: 12000000 INFO @ Fri, 05 Jul 2019 08:05:27: 13000000 INFO @ Fri, 05 Jul 2019 08:05:30: 14000000 INFO @ Fri, 05 Jul 2019 08:05:33: 13000000 INFO @ Fri, 05 Jul 2019 08:05:34: 14000000 INFO @ Fri, 05 Jul 2019 08:05:37: 15000000 INFO @ Fri, 05 Jul 2019 08:05:40: 14000000 INFO @ Fri, 05 Jul 2019 08:05:40: 15000000 INFO @ Fri, 05 Jul 2019 08:05:44: 16000000 INFO @ Fri, 05 Jul 2019 08:05:47: 15000000 INFO @ Fri, 05 Jul 2019 08:05:47: 16000000 INFO @ Fri, 05 Jul 2019 08:05:50: 17000000 INFO @ Fri, 05 Jul 2019 08:05:53: 16000000 INFO @ Fri, 05 Jul 2019 08:05:54: 17000000 INFO @ Fri, 05 Jul 2019 08:05:57: 18000000 INFO @ Fri, 05 Jul 2019 08:06:00: 18000000 INFO @ Fri, 05 Jul 2019 08:06:00: 17000000 INFO @ Fri, 05 Jul 2019 08:06:03: 19000000 INFO @ Fri, 05 Jul 2019 08:06:07: 19000000 INFO @ Fri, 05 Jul 2019 08:06:07: 18000000 INFO @ Fri, 05 Jul 2019 08:06:10: 20000000 INFO @ Fri, 05 Jul 2019 08:06:13: 20000000 INFO @ Fri, 05 Jul 2019 08:06:14: 19000000 INFO @ Fri, 05 Jul 2019 08:06:16: 21000000 INFO @ Fri, 05 Jul 2019 08:06:20: 21000000 INFO @ Fri, 05 Jul 2019 08:06:21: 20000000 INFO @ Fri, 05 Jul 2019 08:06:23: 22000000 INFO @ Fri, 05 Jul 2019 08:06:25: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:06:25: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:06:25: #1 total tags in treatment: 22261489 INFO @ Fri, 05 Jul 2019 08:06:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:06:25: #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 08:06:26: #1 tags after filtering in treatment: 22261349 INFO @ Fri, 05 Jul 2019 08:06:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:06:26: #1 finished! INFO @ Fri, 05 Jul 2019 08:06:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:06:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:06:27: 22000000 INFO @ Fri, 05 Jul 2019 08:06:28: 21000000 INFO @ Fri, 05 Jul 2019 08:06:29: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:06:29: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:06:29: #1 total tags in treatment: 22261489 INFO @ Fri, 05 Jul 2019 08:06:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:06:29: #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 08:06:29: #1 tags after filtering in treatment: 22261349 INFO @ Fri, 05 Jul 2019 08:06:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:06:29: #1 finished! INFO @ Fri, 05 Jul 2019 08:06:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:06:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:06:30: #2 number of paired peaks: 45212 INFO @ Fri, 05 Jul 2019 08:06:30: start model_add_line... INFO @ Fri, 05 Jul 2019 08:06:30: start X-correlation... INFO @ Fri, 05 Jul 2019 08:06:30: end of X-cor INFO @ Fri, 05 Jul 2019 08:06:30: #2 finished! INFO @ Fri, 05 Jul 2019 08:06:30: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 08:06:30: #2 alternative fragment length(s) may be 136,303,504 bps INFO @ Fri, 05 Jul 2019 08:06:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.10_model.r INFO @ Fri, 05 Jul 2019 08:06:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:06:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:06:33: #2 number of paired peaks: 45212 INFO @ Fri, 05 Jul 2019 08:06:33: start model_add_line... INFO @ Fri, 05 Jul 2019 08:06:34: start X-correlation... INFO @ Fri, 05 Jul 2019 08:06:34: end of X-cor INFO @ Fri, 05 Jul 2019 08:06:34: #2 finished! INFO @ Fri, 05 Jul 2019 08:06:34: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 08:06:34: #2 alternative fragment length(s) may be 136,303,504 bps INFO @ Fri, 05 Jul 2019 08:06:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.05_model.r INFO @ Fri, 05 Jul 2019 08:06:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:06:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:06:35: 22000000 INFO @ Fri, 05 Jul 2019 08:06:37: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:06:37: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:06:37: #1 total tags in treatment: 22261489 INFO @ Fri, 05 Jul 2019 08:06:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:06:37: #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 08:06:38: #1 tags after filtering in treatment: 22261349 INFO @ Fri, 05 Jul 2019 08:06:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:06:38: #1 finished! INFO @ Fri, 05 Jul 2019 08:06:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:06:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:06:42: #2 number of paired peaks: 45212 INFO @ Fri, 05 Jul 2019 08:06:42: start model_add_line... INFO @ Fri, 05 Jul 2019 08:06:42: start X-correlation... INFO @ Fri, 05 Jul 2019 08:06:42: end of X-cor INFO @ Fri, 05 Jul 2019 08:06:42: #2 finished! INFO @ Fri, 05 Jul 2019 08:06:42: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 08:06:42: #2 alternative fragment length(s) may be 136,303,504 bps INFO @ Fri, 05 Jul 2019 08:06:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.20_model.r INFO @ Fri, 05 Jul 2019 08:06:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:06:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:07:42: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:07:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:07:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:08:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.10_peaks.xls INFO @ Fri, 05 Jul 2019 08:08:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.05_peaks.xls INFO @ Fri, 05 Jul 2019 08:08:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:08:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.10_summits.bed INFO @ Fri, 05 Jul 2019 08:08:24: Done! INFO @ Fri, 05 Jul 2019 08:08:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:08:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.05_summits.bed INFO @ Fri, 05 Jul 2019 08:08:24: Done! pass1 - making usageList (37 chroms): 2 millis pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (403 records, 4 fields): 7 millis pass2 - checking and writing primary data (1844 records, 4 fields): 9 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:08:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.20_peaks.xls INFO @ Fri, 05 Jul 2019 08:08:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:08:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101982/ERX101982.20_summits.bed INFO @ Fri, 05 Jul 2019 08:08:31: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (70 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。