Job ID = 2001143 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,604,928 reads read : 25,604,928 reads written : 25,604,928 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:29 25604928 reads; of these: 25604928 (100.00%) were unpaired; of these: 655516 (2.56%) aligned 0 times 17830211 (69.64%) aligned exactly 1 time 7119201 (27.80%) aligned >1 times 97.44% overall alignment rate Time searching: 00:11:30 Overall time: 00:11:30 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] 774817 / 24949412 = 0.0311 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 04:11:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.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 04:11:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:11:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:11:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.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 04:11:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:11:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:11:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.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 04:11:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:11:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:11:38: 1000000 INFO @ Fri, 05 Jul 2019 04:11:39: 1000000 INFO @ Fri, 05 Jul 2019 04:11:40: 1000000 INFO @ Fri, 05 Jul 2019 04:11:46: 2000000 INFO @ Fri, 05 Jul 2019 04:11:47: 2000000 INFO @ Fri, 05 Jul 2019 04:11:49: 2000000 INFO @ Fri, 05 Jul 2019 04:11:54: 3000000 INFO @ Fri, 05 Jul 2019 04:11:55: 3000000 INFO @ Fri, 05 Jul 2019 04:11:57: 3000000 INFO @ Fri, 05 Jul 2019 04:12:02: 4000000 INFO @ Fri, 05 Jul 2019 04:12:03: 4000000 INFO @ Fri, 05 Jul 2019 04:12:05: 4000000 INFO @ Fri, 05 Jul 2019 04:12:10: 5000000 INFO @ Fri, 05 Jul 2019 04:12:11: 5000000 INFO @ Fri, 05 Jul 2019 04:12:13: 5000000 INFO @ Fri, 05 Jul 2019 04:12:18: 6000000 INFO @ Fri, 05 Jul 2019 04:12:18: 6000000 INFO @ Fri, 05 Jul 2019 04:12:20: 6000000 INFO @ Fri, 05 Jul 2019 04:12:25: 7000000 INFO @ Fri, 05 Jul 2019 04:12:26: 7000000 INFO @ Fri, 05 Jul 2019 04:12:28: 7000000 INFO @ Fri, 05 Jul 2019 04:12:33: 8000000 INFO @ Fri, 05 Jul 2019 04:12:34: 8000000 INFO @ Fri, 05 Jul 2019 04:12:35: 8000000 INFO @ Fri, 05 Jul 2019 04:12:41: 9000000 INFO @ Fri, 05 Jul 2019 04:12:41: 9000000 INFO @ Fri, 05 Jul 2019 04:12:43: 9000000 INFO @ Fri, 05 Jul 2019 04:12:48: 10000000 INFO @ Fri, 05 Jul 2019 04:12:49: 10000000 INFO @ Fri, 05 Jul 2019 04:12:51: 10000000 INFO @ Fri, 05 Jul 2019 04:12:56: 11000000 INFO @ Fri, 05 Jul 2019 04:12:56: 11000000 INFO @ Fri, 05 Jul 2019 04:12:58: 11000000 INFO @ Fri, 05 Jul 2019 04:13:03: 12000000 INFO @ Fri, 05 Jul 2019 04:13:04: 12000000 INFO @ Fri, 05 Jul 2019 04:13:06: 12000000 INFO @ Fri, 05 Jul 2019 04:13:11: 13000000 INFO @ Fri, 05 Jul 2019 04:13:12: 13000000 INFO @ Fri, 05 Jul 2019 04:13:13: 13000000 INFO @ Fri, 05 Jul 2019 04:13:19: 14000000 INFO @ Fri, 05 Jul 2019 04:13:20: 14000000 INFO @ Fri, 05 Jul 2019 04:13:21: 14000000 INFO @ Fri, 05 Jul 2019 04:13:27: 15000000 INFO @ Fri, 05 Jul 2019 04:13:28: 15000000 INFO @ Fri, 05 Jul 2019 04:13:28: 15000000 INFO @ Fri, 05 Jul 2019 04:13:34: 16000000 INFO @ Fri, 05 Jul 2019 04:13:35: 16000000 INFO @ Fri, 05 Jul 2019 04:13:36: 16000000 INFO @ Fri, 05 Jul 2019 04:13:42: 17000000 INFO @ Fri, 05 Jul 2019 04:13:43: 17000000 INFO @ Fri, 05 Jul 2019 04:13:43: 17000000 INFO @ Fri, 05 Jul 2019 04:13:49: 18000000 INFO @ Fri, 05 Jul 2019 04:13:50: 18000000 INFO @ Fri, 05 Jul 2019 04:13:51: 18000000 INFO @ Fri, 05 Jul 2019 04:13:57: 19000000 INFO @ Fri, 05 Jul 2019 04:13:58: 19000000 INFO @ Fri, 05 Jul 2019 04:13:59: 19000000 INFO @ Fri, 05 Jul 2019 04:14:05: 20000000 INFO @ Fri, 05 Jul 2019 04:14:05: 20000000 INFO @ Fri, 05 Jul 2019 04:14:06: 20000000 INFO @ Fri, 05 Jul 2019 04:14:12: 21000000 INFO @ Fri, 05 Jul 2019 04:14:13: 21000000 INFO @ Fri, 05 Jul 2019 04:14:14: 21000000 INFO @ Fri, 05 Jul 2019 04:14:20: 22000000 INFO @ Fri, 05 Jul 2019 04:14:20: 22000000 INFO @ Fri, 05 Jul 2019 04:14:22: 22000000 INFO @ Fri, 05 Jul 2019 04:14:27: 23000000 INFO @ Fri, 05 Jul 2019 04:14:28: 23000000 INFO @ Fri, 05 Jul 2019 04:14:30: 23000000 INFO @ Fri, 05 Jul 2019 04:14:35: 24000000 INFO @ Fri, 05 Jul 2019 04:14:36: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:14:36: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:14:36: #1 total tags in treatment: 24174595 INFO @ Fri, 05 Jul 2019 04:14:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:14:36: #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 04:14:36: 24000000 INFO @ Fri, 05 Jul 2019 04:14:37: #1 tags after filtering in treatment: 24174469 INFO @ Fri, 05 Jul 2019 04:14:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:14:37: #1 finished! INFO @ Fri, 05 Jul 2019 04:14:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:14:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:14:38: 24000000 INFO @ Fri, 05 Jul 2019 04:14:38: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:14:38: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:14:38: #1 total tags in treatment: 24174595 INFO @ Fri, 05 Jul 2019 04:14:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:14:38: #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 04:14:39: #1 tags after filtering in treatment: 24174469 INFO @ Fri, 05 Jul 2019 04:14:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:14:39: #1 finished! INFO @ Fri, 05 Jul 2019 04:14:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:14:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:14:39: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:14:39: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:14:39: #1 total tags in treatment: 24174595 INFO @ Fri, 05 Jul 2019 04:14:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:14:39: #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 04:14:40: #1 tags after filtering in treatment: 24174469 INFO @ Fri, 05 Jul 2019 04:14:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:14:40: #1 finished! INFO @ Fri, 05 Jul 2019 04:14:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:14:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:14:40: #2 number of paired peaks: 20168 INFO @ Fri, 05 Jul 2019 04:14:40: start model_add_line... INFO @ Fri, 05 Jul 2019 04:14:41: start X-correlation... INFO @ Fri, 05 Jul 2019 04:14:41: end of X-cor INFO @ Fri, 05 Jul 2019 04:14:41: #2 finished! INFO @ Fri, 05 Jul 2019 04:14:41: #2 predicted fragment length is 124 bps INFO @ Fri, 05 Jul 2019 04:14:41: #2 alternative fragment length(s) may be 4,124 bps INFO @ Fri, 05 Jul 2019 04:14:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.20_model.r INFO @ Fri, 05 Jul 2019 04:14:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:14:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:14:42: #2 number of paired peaks: 20168 INFO @ Fri, 05 Jul 2019 04:14:42: start model_add_line... INFO @ Fri, 05 Jul 2019 04:14:43: start X-correlation... INFO @ Fri, 05 Jul 2019 04:14:43: end of X-cor INFO @ Fri, 05 Jul 2019 04:14:43: #2 finished! INFO @ Fri, 05 Jul 2019 04:14:43: #2 predicted fragment length is 124 bps INFO @ Fri, 05 Jul 2019 04:14:43: #2 alternative fragment length(s) may be 4,124 bps INFO @ Fri, 05 Jul 2019 04:14:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.05_model.r INFO @ Fri, 05 Jul 2019 04:14:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:14:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:14:44: #2 number of paired peaks: 20168 INFO @ Fri, 05 Jul 2019 04:14:44: start model_add_line... INFO @ Fri, 05 Jul 2019 04:14:44: start X-correlation... INFO @ Fri, 05 Jul 2019 04:14:44: end of X-cor INFO @ Fri, 05 Jul 2019 04:14:44: #2 finished! INFO @ Fri, 05 Jul 2019 04:14:44: #2 predicted fragment length is 124 bps INFO @ Fri, 05 Jul 2019 04:14:44: #2 alternative fragment length(s) may be 4,124 bps INFO @ Fri, 05 Jul 2019 04:14:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.10_model.r INFO @ Fri, 05 Jul 2019 04:14:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:14:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:16:01: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:16:02: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:16:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:16:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:16:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:16:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.20_summits.bed INFO @ Fri, 05 Jul 2019 04:16:41: Done! pass1 - making usageList (21 chroms): 1 millis pass2 - checking and writing primary data (82 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:16:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:16:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:16:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.05_summits.bed INFO @ Fri, 05 Jul 2019 04:16:42: Done! pass1 - making usageList (44 chroms): 1 millis pass2 - checking and writing primary data (1257 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:16:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:16:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:16:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101833/ERX101833.10_summits.bed INFO @ Fri, 05 Jul 2019 04:16:45: Done! pass1 - making usageList (31 chroms): 2 millis pass2 - checking and writing primary data (319 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。