Job ID = 2001673 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,989,119 reads read : 27,989,119 reads written : 27,989,119 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: 00:10:50 27989119 reads; of these: 27989119 (100.00%) were unpaired; of these: 760939 (2.72%) aligned 0 times 20284356 (72.47%) aligned exactly 1 time 6943824 (24.81%) aligned >1 times 97.28% overall alignment rate Time searching: 00:10:51 Overall time: 00:10:51 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] 1723486 / 27228180 = 0.0633 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 08:24:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.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 08:24:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:24:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:24:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.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 08:24:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:24:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:24:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.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 08:24:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:24:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:24:31: 1000000 INFO @ Fri, 05 Jul 2019 08:24:32: 1000000 INFO @ Fri, 05 Jul 2019 08:24:33: 1000000 INFO @ Fri, 05 Jul 2019 08:24:39: 2000000 INFO @ Fri, 05 Jul 2019 08:24:39: 2000000 INFO @ Fri, 05 Jul 2019 08:24:40: 2000000 INFO @ Fri, 05 Jul 2019 08:24:46: 3000000 INFO @ Fri, 05 Jul 2019 08:24:46: 3000000 INFO @ Fri, 05 Jul 2019 08:24:48: 3000000 INFO @ Fri, 05 Jul 2019 08:24:53: 4000000 INFO @ Fri, 05 Jul 2019 08:24:54: 4000000 INFO @ Fri, 05 Jul 2019 08:24:55: 4000000 INFO @ Fri, 05 Jul 2019 08:25:01: 5000000 INFO @ Fri, 05 Jul 2019 08:25:01: 5000000 INFO @ Fri, 05 Jul 2019 08:25:02: 5000000 INFO @ Fri, 05 Jul 2019 08:25:08: 6000000 INFO @ Fri, 05 Jul 2019 08:25:09: 6000000 INFO @ Fri, 05 Jul 2019 08:25:09: 6000000 INFO @ Fri, 05 Jul 2019 08:25:16: 7000000 INFO @ Fri, 05 Jul 2019 08:25:16: 7000000 INFO @ Fri, 05 Jul 2019 08:25:17: 7000000 INFO @ Fri, 05 Jul 2019 08:25:23: 8000000 INFO @ Fri, 05 Jul 2019 08:25:24: 8000000 INFO @ Fri, 05 Jul 2019 08:25:24: 8000000 INFO @ Fri, 05 Jul 2019 08:25:31: 9000000 INFO @ Fri, 05 Jul 2019 08:25:32: 9000000 INFO @ Fri, 05 Jul 2019 08:25:32: 9000000 INFO @ Fri, 05 Jul 2019 08:25:38: 10000000 INFO @ Fri, 05 Jul 2019 08:25:40: 10000000 INFO @ Fri, 05 Jul 2019 08:25:41: 10000000 INFO @ Fri, 05 Jul 2019 08:25:46: 11000000 INFO @ Fri, 05 Jul 2019 08:25:48: 11000000 INFO @ Fri, 05 Jul 2019 08:25:49: 11000000 INFO @ Fri, 05 Jul 2019 08:25:54: 12000000 INFO @ Fri, 05 Jul 2019 08:25:55: 12000000 INFO @ Fri, 05 Jul 2019 08:25:56: 12000000 INFO @ Fri, 05 Jul 2019 08:26:01: 13000000 INFO @ Fri, 05 Jul 2019 08:26:02: 13000000 INFO @ Fri, 05 Jul 2019 08:26:04: 13000000 INFO @ Fri, 05 Jul 2019 08:26:09: 14000000 INFO @ Fri, 05 Jul 2019 08:26:10: 14000000 INFO @ Fri, 05 Jul 2019 08:26:11: 14000000 INFO @ Fri, 05 Jul 2019 08:26:17: 15000000 INFO @ Fri, 05 Jul 2019 08:26:18: 15000000 INFO @ Fri, 05 Jul 2019 08:26:18: 15000000 INFO @ Fri, 05 Jul 2019 08:26:25: 16000000 INFO @ Fri, 05 Jul 2019 08:26:25: 16000000 INFO @ Fri, 05 Jul 2019 08:26:26: 16000000 INFO @ Fri, 05 Jul 2019 08:26:32: 17000000 INFO @ Fri, 05 Jul 2019 08:26:34: 17000000 INFO @ Fri, 05 Jul 2019 08:26:34: 17000000 INFO @ Fri, 05 Jul 2019 08:26:39: 18000000 INFO @ Fri, 05 Jul 2019 08:26:43: 18000000 INFO @ Fri, 05 Jul 2019 08:26:43: 18000000 INFO @ Fri, 05 Jul 2019 08:26:46: 19000000 INFO @ Fri, 05 Jul 2019 08:26:51: 19000000 INFO @ Fri, 05 Jul 2019 08:26:51: 19000000 INFO @ Fri, 05 Jul 2019 08:26:53: 20000000 INFO @ Fri, 05 Jul 2019 08:26:59: 20000000 INFO @ Fri, 05 Jul 2019 08:27:00: 20000000 INFO @ Fri, 05 Jul 2019 08:27:00: 21000000 INFO @ Fri, 05 Jul 2019 08:27:06: 21000000 INFO @ Fri, 05 Jul 2019 08:27:07: 22000000 INFO @ Fri, 05 Jul 2019 08:27:08: 21000000 INFO @ Fri, 05 Jul 2019 08:27:14: 22000000 INFO @ Fri, 05 Jul 2019 08:27:14: 23000000 INFO @ Fri, 05 Jul 2019 08:27:16: 22000000 INFO @ Fri, 05 Jul 2019 08:27:21: 24000000 INFO @ Fri, 05 Jul 2019 08:27:22: 23000000 INFO @ Fri, 05 Jul 2019 08:27:23: 23000000 INFO @ Fri, 05 Jul 2019 08:27:28: 25000000 INFO @ Fri, 05 Jul 2019 08:27:31: 24000000 INFO @ Fri, 05 Jul 2019 08:27:32: 24000000 INFO @ Fri, 05 Jul 2019 08:27:32: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:27:32: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:27:32: #1 total tags in treatment: 25504694 INFO @ Fri, 05 Jul 2019 08:27:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:27:32: #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 08:27:33: #1 tags after filtering in treatment: 25504551 INFO @ Fri, 05 Jul 2019 08:27:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:27:33: #1 finished! INFO @ Fri, 05 Jul 2019 08:27:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:27:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:27:37: #2 number of paired peaks: 46254 INFO @ Fri, 05 Jul 2019 08:27:37: start model_add_line... INFO @ Fri, 05 Jul 2019 08:27:38: start X-correlation... INFO @ Fri, 05 Jul 2019 08:27:38: end of X-cor INFO @ Fri, 05 Jul 2019 08:27:38: #2 finished! INFO @ Fri, 05 Jul 2019 08:27:38: #2 predicted fragment length is 137 bps INFO @ Fri, 05 Jul 2019 08:27:38: #2 alternative fragment length(s) may be 137,304,511 bps INFO @ Fri, 05 Jul 2019 08:27:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.10_model.r INFO @ Fri, 05 Jul 2019 08:27:38: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:27:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:27:39: 25000000 INFO @ Fri, 05 Jul 2019 08:27:40: 25000000 INFO @ Fri, 05 Jul 2019 08:27:44: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:27:44: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:27:44: #1 total tags in treatment: 25504694 INFO @ Fri, 05 Jul 2019 08:27:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:27:44: #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 08:27:44: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:27:44: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:27:44: #1 total tags in treatment: 25504694 INFO @ Fri, 05 Jul 2019 08:27:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:27:44: #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 08:27:44: #1 tags after filtering in treatment: 25504551 INFO @ Fri, 05 Jul 2019 08:27:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:27:44: #1 finished! INFO @ Fri, 05 Jul 2019 08:27:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:27:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:27:45: #1 tags after filtering in treatment: 25504551 INFO @ Fri, 05 Jul 2019 08:27:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:27:45: #1 finished! INFO @ Fri, 05 Jul 2019 08:27:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:27:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:27:49: #2 number of paired peaks: 46254 INFO @ Fri, 05 Jul 2019 08:27:49: start model_add_line... INFO @ Fri, 05 Jul 2019 08:27:49: start X-correlation... INFO @ Fri, 05 Jul 2019 08:27:49: end of X-cor INFO @ Fri, 05 Jul 2019 08:27:49: #2 finished! INFO @ Fri, 05 Jul 2019 08:27:49: #2 predicted fragment length is 137 bps INFO @ Fri, 05 Jul 2019 08:27:49: #2 alternative fragment length(s) may be 137,304,511 bps INFO @ Fri, 05 Jul 2019 08:27:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.20_model.r INFO @ Fri, 05 Jul 2019 08:27:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:27:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:27:49: #2 number of paired peaks: 46254 INFO @ Fri, 05 Jul 2019 08:27:49: start model_add_line... INFO @ Fri, 05 Jul 2019 08:27:50: start X-correlation... INFO @ Fri, 05 Jul 2019 08:27:50: end of X-cor INFO @ Fri, 05 Jul 2019 08:27:50: #2 finished! INFO @ Fri, 05 Jul 2019 08:27:50: #2 predicted fragment length is 137 bps INFO @ Fri, 05 Jul 2019 08:27:50: #2 alternative fragment length(s) may be 137,304,511 bps INFO @ Fri, 05 Jul 2019 08:27:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.05_model.r INFO @ Fri, 05 Jul 2019 08:27:50: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:27:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:28:59: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:29:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:29:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:29:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.10_peaks.xls INFO @ Fri, 05 Jul 2019 08:29:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:29:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.10_summits.bed INFO @ Fri, 05 Jul 2019 08:29:40: Done! pass1 - making usageList (37 chroms): 2 millis pass2 - checking and writing primary data (467 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:29:53: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.05_peaks.xls INFO @ Fri, 05 Jul 2019 08:29:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:29:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.05_summits.bed INFO @ Fri, 05 Jul 2019 08:29:53: Done! pass1 - making usageList (56 chroms): 2 millis pass2 - checking and writing primary data (2307 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:29:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.20_peaks.xls INFO @ Fri, 05 Jul 2019 08:29:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:29:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101988/ERX101988.20_summits.bed INFO @ Fri, 05 Jul 2019 08:29:57: Done! pass1 - making usageList (27 chroms): 2 millis pass2 - checking and writing primary data (78 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。