Job ID = 2002181 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,322,423 reads read : 20,322,423 reads written : 20,322,423 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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:13 20322423 reads; of these: 20322423 (100.00%) were unpaired; of these: 5125183 (25.22%) aligned 0 times 11903990 (58.58%) aligned exactly 1 time 3293250 (16.21%) aligned >1 times 74.78% overall alignment rate Time searching: 00:08:17 Overall time: 00:08:17 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] 2388639 / 15197240 = 0.1572 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 11:26:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.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 11:26:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:26:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:26:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.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 11:26:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:26:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:26:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.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 11:26:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:26:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:26:33: 1000000 INFO @ Fri, 05 Jul 2019 11:26:34: 1000000 INFO @ Fri, 05 Jul 2019 11:26:35: 1000000 INFO @ Fri, 05 Jul 2019 11:26:41: 2000000 INFO @ Fri, 05 Jul 2019 11:26:41: 2000000 INFO @ Fri, 05 Jul 2019 11:26:43: 2000000 INFO @ Fri, 05 Jul 2019 11:26:47: 3000000 INFO @ Fri, 05 Jul 2019 11:26:49: 3000000 INFO @ Fri, 05 Jul 2019 11:26:51: 3000000 INFO @ Fri, 05 Jul 2019 11:26:54: 4000000 INFO @ Fri, 05 Jul 2019 11:26:57: 4000000 INFO @ Fri, 05 Jul 2019 11:26:58: 4000000 INFO @ Fri, 05 Jul 2019 11:27:00: 5000000 INFO @ Fri, 05 Jul 2019 11:27:04: 5000000 INFO @ Fri, 05 Jul 2019 11:27:06: 5000000 INFO @ Fri, 05 Jul 2019 11:27:06: 6000000 INFO @ Fri, 05 Jul 2019 11:27:12: 6000000 INFO @ Fri, 05 Jul 2019 11:27:13: 7000000 INFO @ Fri, 05 Jul 2019 11:27:14: 6000000 INFO @ Fri, 05 Jul 2019 11:27:19: 8000000 INFO @ Fri, 05 Jul 2019 11:27:20: 7000000 INFO @ Fri, 05 Jul 2019 11:27:22: 7000000 INFO @ Fri, 05 Jul 2019 11:27:26: 9000000 INFO @ Fri, 05 Jul 2019 11:27:28: 8000000 INFO @ Fri, 05 Jul 2019 11:27:29: 8000000 INFO @ Fri, 05 Jul 2019 11:27:32: 10000000 INFO @ Fri, 05 Jul 2019 11:27:35: 9000000 INFO @ Fri, 05 Jul 2019 11:27:37: 9000000 INFO @ Fri, 05 Jul 2019 11:27:39: 11000000 INFO @ Fri, 05 Jul 2019 11:27:43: 10000000 INFO @ Fri, 05 Jul 2019 11:27:45: 12000000 INFO @ Fri, 05 Jul 2019 11:27:46: 10000000 INFO @ Fri, 05 Jul 2019 11:27:51: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 11:27:51: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 11:27:51: #1 total tags in treatment: 12808601 INFO @ Fri, 05 Jul 2019 11:27:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:27:51: #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 11:27:51: #1 tags after filtering in treatment: 12808394 INFO @ Fri, 05 Jul 2019 11:27:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:27:51: #1 finished! INFO @ Fri, 05 Jul 2019 11:27:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:27:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:27:52: 11000000 INFO @ Fri, 05 Jul 2019 11:27:54: 11000000 INFO @ Fri, 05 Jul 2019 11:27:54: #2 number of paired peaks: 54550 INFO @ Fri, 05 Jul 2019 11:27:54: start model_add_line... INFO @ Fri, 05 Jul 2019 11:27:54: start X-correlation... INFO @ Fri, 05 Jul 2019 11:27:54: end of X-cor INFO @ Fri, 05 Jul 2019 11:27:54: #2 finished! INFO @ Fri, 05 Jul 2019 11:27:54: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 11:27:54: #2 alternative fragment length(s) may be 131 bps INFO @ Fri, 05 Jul 2019 11:27:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.20_model.r INFO @ Fri, 05 Jul 2019 11:27:54: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:27:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:28:00: 12000000 INFO @ Fri, 05 Jul 2019 11:28:02: 12000000 INFO @ Fri, 05 Jul 2019 11:28:07: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 11:28:07: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 11:28:07: #1 total tags in treatment: 12808601 INFO @ Fri, 05 Jul 2019 11:28:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:28:07: #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 11:28:07: #1 tags after filtering in treatment: 12808394 INFO @ Fri, 05 Jul 2019 11:28:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:28:07: #1 finished! INFO @ Fri, 05 Jul 2019 11:28:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:28:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:28:09: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 11:28:09: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 11:28:09: #1 total tags in treatment: 12808601 INFO @ Fri, 05 Jul 2019 11:28:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:28:09: #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 11:28:09: #1 tags after filtering in treatment: 12808394 INFO @ Fri, 05 Jul 2019 11:28:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:28:09: #1 finished! INFO @ Fri, 05 Jul 2019 11:28:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:28:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:28:11: #2 number of paired peaks: 54550 INFO @ Fri, 05 Jul 2019 11:28:11: start model_add_line... INFO @ Fri, 05 Jul 2019 11:28:11: start X-correlation... INFO @ Fri, 05 Jul 2019 11:28:11: end of X-cor INFO @ Fri, 05 Jul 2019 11:28:11: #2 finished! INFO @ Fri, 05 Jul 2019 11:28:11: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 11:28:11: #2 alternative fragment length(s) may be 131 bps INFO @ Fri, 05 Jul 2019 11:28:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.05_model.r INFO @ Fri, 05 Jul 2019 11:28:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:28:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:28:13: #2 number of paired peaks: 54550 INFO @ Fri, 05 Jul 2019 11:28:13: start model_add_line... INFO @ Fri, 05 Jul 2019 11:28:13: start X-correlation... INFO @ Fri, 05 Jul 2019 11:28:13: end of X-cor INFO @ Fri, 05 Jul 2019 11:28:13: #2 finished! INFO @ Fri, 05 Jul 2019 11:28:13: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 11:28:13: #2 alternative fragment length(s) may be 131 bps INFO @ Fri, 05 Jul 2019 11:28:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.10_model.r INFO @ Fri, 05 Jul 2019 11:28:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:28:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:28:35: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:28:52: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:28:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:28:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:28:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:28:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.20_summits.bed INFO @ Fri, 05 Jul 2019 11:28:57: Done! pass1 - making usageList (95 chroms): 5 millis pass2 - checking and writing primary data (16957 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:29:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:29:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:29:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.05_summits.bed INFO @ Fri, 05 Jul 2019 11:29:16: Done! INFO @ Fri, 05 Jul 2019 11:29:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.10_peaks.xls INFO @ Fri, 05 Jul 2019 11:29:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:29:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210290/ERX210290.10_summits.bed INFO @ Fri, 05 Jul 2019 11:29:17: Done! pass1 - making usageList (150 chroms): 11 millis pass2 - checking and writing primary data (42025 records, 4 fields): 65 millis pass1 - making usageList (120 chroms): 11 millis pass2 - checking and writing primary data (28566 records, 4 fields): 286 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。