Job ID = 4303043 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 44,266,107 reads read : 44,266,107 reads written : 44,266,107 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1198440.sra.cache’: 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:48 44266107 reads; of these: 44266107 (100.00%) were unpaired; of these: 4760503 (10.75%) aligned 0 times 29035304 (65.59%) aligned exactly 1 time 10470300 (23.65%) aligned >1 times 89.25% overall alignment rate Time searching: 00:11:48 Overall time: 00:11:48 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 31220582 / 39505604 = 0.7903 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:56:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 12 Dec 2019 00:56:58: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:56:58: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:57:06: 1000000 INFO @ Thu, 12 Dec 2019 00:57:13: 2000000 INFO @ Thu, 12 Dec 2019 00:57:20: 3000000 INFO @ Thu, 12 Dec 2019 00:57:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 12 Dec 2019 00:57:27: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:57:27: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:57:27: 4000000 INFO @ Thu, 12 Dec 2019 00:57:35: 5000000 INFO @ Thu, 12 Dec 2019 00:57:36: 1000000 INFO @ Thu, 12 Dec 2019 00:57:42: 6000000 INFO @ Thu, 12 Dec 2019 00:57:45: 2000000 INFO @ Thu, 12 Dec 2019 00:57:50: 7000000 INFO @ Thu, 12 Dec 2019 00:57:53: 3000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:57:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 12 Dec 2019 00:57:57: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:57:57: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:57:57: 8000000 INFO @ Thu, 12 Dec 2019 00:58:00: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:58:00: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:58:00: #1 total tags in treatment: 8285022 INFO @ Thu, 12 Dec 2019 00:58:00: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:58:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:58:00: #1 tags after filtering in treatment: 8285022 INFO @ Thu, 12 Dec 2019 00:58:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:58:00: #1 finished! INFO @ Thu, 12 Dec 2019 00:58:00: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:58:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:58:01: #2 number of paired peaks: 1437 INFO @ Thu, 12 Dec 2019 00:58:01: start model_add_line... INFO @ Thu, 12 Dec 2019 00:58:01: start X-correlation... INFO @ Thu, 12 Dec 2019 00:58:01: end of X-cor INFO @ Thu, 12 Dec 2019 00:58:01: #2 finished! INFO @ Thu, 12 Dec 2019 00:58:01: #2 predicted fragment length is 129 bps INFO @ Thu, 12 Dec 2019 00:58:01: #2 alternative fragment length(s) may be 129 bps INFO @ Thu, 12 Dec 2019 00:58:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.05_model.r INFO @ Thu, 12 Dec 2019 00:58:01: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:58:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:58:02: 4000000 INFO @ Thu, 12 Dec 2019 00:58:06: 1000000 INFO @ Thu, 12 Dec 2019 00:58:10: 5000000 INFO @ Thu, 12 Dec 2019 00:58:15: 2000000 INFO @ Thu, 12 Dec 2019 00:58:19: 6000000 INFO @ Thu, 12 Dec 2019 00:58:23: 3000000 INFO @ Thu, 12 Dec 2019 00:58:27: 7000000 INFO @ Thu, 12 Dec 2019 00:58:27: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:58:32: 4000000 INFO @ Thu, 12 Dec 2019 00:58:36: 8000000 INFO @ Thu, 12 Dec 2019 00:58:38: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:58:38: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:58:38: #1 total tags in treatment: 8285022 INFO @ Thu, 12 Dec 2019 00:58:38: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:58:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:58:39: #1 tags after filtering in treatment: 8285022 INFO @ Thu, 12 Dec 2019 00:58:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:58:39: #1 finished! INFO @ Thu, 12 Dec 2019 00:58:39: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:58:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:58:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:58:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:58:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.05_summits.bed INFO @ Thu, 12 Dec 2019 00:58:39: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4128 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:58:39: #2 number of paired peaks: 1437 INFO @ Thu, 12 Dec 2019 00:58:39: start model_add_line... INFO @ Thu, 12 Dec 2019 00:58:40: start X-correlation... INFO @ Thu, 12 Dec 2019 00:58:40: end of X-cor INFO @ Thu, 12 Dec 2019 00:58:40: #2 finished! INFO @ Thu, 12 Dec 2019 00:58:40: #2 predicted fragment length is 129 bps INFO @ Thu, 12 Dec 2019 00:58:40: #2 alternative fragment length(s) may be 129 bps INFO @ Thu, 12 Dec 2019 00:58:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.10_model.r INFO @ Thu, 12 Dec 2019 00:58:40: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:58:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:58:41: 5000000 INFO @ Thu, 12 Dec 2019 00:58:49: 6000000 INFO @ Thu, 12 Dec 2019 00:58:57: 7000000 INFO @ Thu, 12 Dec 2019 00:59:06: 8000000 INFO @ Thu, 12 Dec 2019 00:59:06: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:59:08: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:59:08: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:59:08: #1 total tags in treatment: 8285022 INFO @ Thu, 12 Dec 2019 00:59:08: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:59:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:59:08: #1 tags after filtering in treatment: 8285022 INFO @ Thu, 12 Dec 2019 00:59:08: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:59:08: #1 finished! INFO @ Thu, 12 Dec 2019 00:59:08: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:59:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:59:09: #2 number of paired peaks: 1437 INFO @ Thu, 12 Dec 2019 00:59:09: start model_add_line... INFO @ Thu, 12 Dec 2019 00:59:09: start X-correlation... INFO @ Thu, 12 Dec 2019 00:59:09: end of X-cor INFO @ Thu, 12 Dec 2019 00:59:09: #2 finished! INFO @ Thu, 12 Dec 2019 00:59:09: #2 predicted fragment length is 129 bps INFO @ Thu, 12 Dec 2019 00:59:09: #2 alternative fragment length(s) may be 129 bps INFO @ Thu, 12 Dec 2019 00:59:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.20_model.r INFO @ Thu, 12 Dec 2019 00:59:09: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:59:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:59:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:59:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:59:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.10_summits.bed INFO @ Thu, 12 Dec 2019 00:59:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2355 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:59:36: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:59:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:59:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:59:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494908/SRX494908.20_summits.bed INFO @ Thu, 12 Dec 2019 00:59:48: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1295 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。