Job ID = 2003737 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,829,438 reads read : 55,658,876 reads written : 27,829,438 reads 0-length : 27,829,438 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: 00:26:07 27829438 reads; of these: 27829438 (100.00%) were unpaired; of these: 3364353 (12.09%) aligned 0 times 15533002 (55.82%) aligned exactly 1 time 8932083 (32.10%) aligned >1 times 87.91% overall alignment rate Time searching: 00:26:08 Overall time: 00:26:08 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 12 files... [bam_rmdupse_core] 13666806 / 24465085 = 0.5586 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 14:36:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.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 14:36:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:36:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:36:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.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 14:36:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:36:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:36:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.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 14:36:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:36:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:36:37: 1000000 INFO @ Fri, 05 Jul 2019 14:36:40: 1000000 INFO @ Fri, 05 Jul 2019 14:36:40: 1000000 INFO @ Fri, 05 Jul 2019 14:36:46: 2000000 INFO @ Fri, 05 Jul 2019 14:36:49: 2000000 INFO @ Fri, 05 Jul 2019 14:36:50: 2000000 INFO @ Fri, 05 Jul 2019 14:36:55: 3000000 INFO @ Fri, 05 Jul 2019 14:36:58: 3000000 INFO @ Fri, 05 Jul 2019 14:37:01: 3000000 INFO @ Fri, 05 Jul 2019 14:37:04: 4000000 INFO @ Fri, 05 Jul 2019 14:37:07: 4000000 INFO @ Fri, 05 Jul 2019 14:37:11: 4000000 INFO @ Fri, 05 Jul 2019 14:37:13: 5000000 INFO @ Fri, 05 Jul 2019 14:37:16: 5000000 INFO @ Fri, 05 Jul 2019 14:37:21: 5000000 INFO @ Fri, 05 Jul 2019 14:37:23: 6000000 INFO @ Fri, 05 Jul 2019 14:37:25: 6000000 INFO @ Fri, 05 Jul 2019 14:37:31: 6000000 INFO @ Fri, 05 Jul 2019 14:37:32: 7000000 INFO @ Fri, 05 Jul 2019 14:37:34: 7000000 INFO @ Fri, 05 Jul 2019 14:37:41: 8000000 INFO @ Fri, 05 Jul 2019 14:37:41: 7000000 INFO @ Fri, 05 Jul 2019 14:37:43: 8000000 INFO @ Fri, 05 Jul 2019 14:37:50: 9000000 INFO @ Fri, 05 Jul 2019 14:37:52: 8000000 INFO @ Fri, 05 Jul 2019 14:37:52: 9000000 INFO @ Fri, 05 Jul 2019 14:38:00: 10000000 INFO @ Fri, 05 Jul 2019 14:38:01: 10000000 INFO @ Fri, 05 Jul 2019 14:38:02: 9000000 INFO @ Fri, 05 Jul 2019 14:38:08: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 14:38:08: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 14:38:08: #1 total tags in treatment: 10798279 INFO @ Fri, 05 Jul 2019 14:38:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:38:08: #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 14:38:09: #1 tags after filtering in treatment: 10798149 INFO @ Fri, 05 Jul 2019 14:38:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:38:09: #1 finished! INFO @ Fri, 05 Jul 2019 14:38:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:38:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:38:09: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 14:38:09: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 14:38:09: #1 total tags in treatment: 10798279 INFO @ Fri, 05 Jul 2019 14:38:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:38:09: #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 14:38:09: #1 tags after filtering in treatment: 10798149 INFO @ Fri, 05 Jul 2019 14:38:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:38:09: #1 finished! INFO @ Fri, 05 Jul 2019 14:38:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:38:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:38:11: #2 number of paired peaks: 34232 INFO @ Fri, 05 Jul 2019 14:38:11: start model_add_line... INFO @ Fri, 05 Jul 2019 14:38:11: start X-correlation... INFO @ Fri, 05 Jul 2019 14:38:11: end of X-cor INFO @ Fri, 05 Jul 2019 14:38:11: #2 finished! INFO @ Fri, 05 Jul 2019 14:38:11: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 14:38:11: #2 alternative fragment length(s) may be 52,135 bps INFO @ Fri, 05 Jul 2019 14:38:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.05_model.r INFO @ Fri, 05 Jul 2019 14:38:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:38:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:38:12: #2 number of paired peaks: 34232 INFO @ Fri, 05 Jul 2019 14:38:12: start model_add_line... INFO @ Fri, 05 Jul 2019 14:38:12: start X-correlation... INFO @ Fri, 05 Jul 2019 14:38:12: end of X-cor INFO @ Fri, 05 Jul 2019 14:38:12: #2 finished! INFO @ Fri, 05 Jul 2019 14:38:12: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 14:38:12: #2 alternative fragment length(s) may be 52,135 bps INFO @ Fri, 05 Jul 2019 14:38:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.20_model.r INFO @ Fri, 05 Jul 2019 14:38:12: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:38:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:38:12: 10000000 INFO @ Fri, 05 Jul 2019 14:38:20: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 14:38:20: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 14:38:20: #1 total tags in treatment: 10798279 INFO @ Fri, 05 Jul 2019 14:38:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:38:20: #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 14:38:20: #1 tags after filtering in treatment: 10798149 INFO @ Fri, 05 Jul 2019 14:38:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:38:20: #1 finished! INFO @ Fri, 05 Jul 2019 14:38:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:38:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:38:23: #2 number of paired peaks: 34232 INFO @ Fri, 05 Jul 2019 14:38:24: start model_add_line... INFO @ Fri, 05 Jul 2019 14:38:24: start X-correlation... INFO @ Fri, 05 Jul 2019 14:38:24: end of X-cor INFO @ Fri, 05 Jul 2019 14:38:24: #2 finished! INFO @ Fri, 05 Jul 2019 14:38:24: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 14:38:24: #2 alternative fragment length(s) may be 52,135 bps INFO @ Fri, 05 Jul 2019 14:38:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.10_model.r INFO @ Fri, 05 Jul 2019 14:38:24: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:38:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:38:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:38:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:38:59: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:39:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.05_peaks.xls INFO @ Fri, 05 Jul 2019 14:39:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.20_peaks.xls INFO @ Fri, 05 Jul 2019 14:39:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:39:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.20_summits.bed INFO @ Fri, 05 Jul 2019 14:39:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:39:04: Done! INFO @ Fri, 05 Jul 2019 14:39:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.05_summits.bed INFO @ Fri, 05 Jul 2019 14:39:04: Done! pass1 - making usageList (50 chroms): 1 millis pass2 - checking and writing primary data (496 records, 4 fields): 8 millis pass1 - making usageList (67 chroms): 2 millis pass2 - checking and writing primary data (1547 records, 4 fields): 11 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 14:39:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.10_peaks.xls INFO @ Fri, 05 Jul 2019 14:39:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:39:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5333729/SRX5333729.10_summits.bed INFO @ Fri, 05 Jul 2019 14:39:16: Done! pass1 - making usageList (55 chroms): 2 millis pass2 - checking and writing primary data (833 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。