Job ID = 4303040 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,920,832 reads read : 32,920,832 reads written : 32,920,832 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1198437.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: 00:05:04 32920832 reads; of these: 32920832 (100.00%) were unpaired; of these: 7545015 (22.92%) aligned 0 times 21056297 (63.96%) aligned exactly 1 time 4319520 (13.12%) aligned >1 times 77.08% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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 12 files... [bam_rmdupse_core] 14853055 / 25375817 = 0.5853 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:44:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.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 00:44:41: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:44:41: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:44:46: 1000000 INFO @ Thu, 12 Dec 2019 00:44:50: 2000000 INFO @ Thu, 12 Dec 2019 00:44:55: 3000000 INFO @ Thu, 12 Dec 2019 00:45:00: 4000000 INFO @ Thu, 12 Dec 2019 00:45:04: 5000000 INFO @ Thu, 12 Dec 2019 00:45:09: 6000000 INFO @ Thu, 12 Dec 2019 00:45:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.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 00:45:10: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:45:10: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:45:14: 7000000 INFO @ Thu, 12 Dec 2019 00:45:15: 1000000 INFO @ Thu, 12 Dec 2019 00:45:18: 8000000 INFO @ Thu, 12 Dec 2019 00:45:20: 2000000 INFO @ Thu, 12 Dec 2019 00:45:23: 9000000 INFO @ Thu, 12 Dec 2019 00:45:25: 3000000 INFO @ Thu, 12 Dec 2019 00:45:28: 10000000 INFO @ Thu, 12 Dec 2019 00:45:30: 4000000 INFO @ Thu, 12 Dec 2019 00:45:30: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:45:30: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:45:30: #1 total tags in treatment: 10522762 INFO @ Thu, 12 Dec 2019 00:45:30: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:45:30: #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 00:45:30: #1 tags after filtering in treatment: 10522762 INFO @ Thu, 12 Dec 2019 00:45:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:45:30: #1 finished! INFO @ Thu, 12 Dec 2019 00:45:30: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:45:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:45:31: #2 number of paired peaks: 1112 INFO @ Thu, 12 Dec 2019 00:45:31: start model_add_line... INFO @ Thu, 12 Dec 2019 00:45:31: start X-correlation... INFO @ Thu, 12 Dec 2019 00:45:31: end of X-cor INFO @ Thu, 12 Dec 2019 00:45:31: #2 finished! INFO @ Thu, 12 Dec 2019 00:45:31: #2 predicted fragment length is 144 bps INFO @ Thu, 12 Dec 2019 00:45:31: #2 alternative fragment length(s) may be 144 bps INFO @ Thu, 12 Dec 2019 00:45:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.05_model.r INFO @ Thu, 12 Dec 2019 00:45:31: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:45:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:45:34: 5000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:45:39: 6000000 INFO @ Thu, 12 Dec 2019 00:45:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.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 00:45:40: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:45:40: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:45:44: 7000000 INFO @ Thu, 12 Dec 2019 00:45:46: 1000000 INFO @ Thu, 12 Dec 2019 00:45:48: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:45:50: 8000000 INFO @ Thu, 12 Dec 2019 00:45:51: 2000000 INFO @ Thu, 12 Dec 2019 00:45:55: 9000000 INFO @ Thu, 12 Dec 2019 00:45:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:45:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:45:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.05_summits.bed INFO @ Thu, 12 Dec 2019 00:45:56: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6003 records, 4 fields): 15 millis INFO @ Thu, 12 Dec 2019 00:45:57: 3000000 CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:46:00: 10000000 INFO @ Thu, 12 Dec 2019 00:46:01: 4000000 INFO @ Thu, 12 Dec 2019 00:46:02: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:46:02: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:46:02: #1 total tags in treatment: 10522762 INFO @ Thu, 12 Dec 2019 00:46:02: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:46:02: #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 00:46:03: #1 tags after filtering in treatment: 10522762 INFO @ Thu, 12 Dec 2019 00:46:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:46:03: #1 finished! INFO @ Thu, 12 Dec 2019 00:46:03: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:46:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:46:03: #2 number of paired peaks: 1112 INFO @ Thu, 12 Dec 2019 00:46:03: start model_add_line... INFO @ Thu, 12 Dec 2019 00:46:03: start X-correlation... INFO @ Thu, 12 Dec 2019 00:46:03: end of X-cor INFO @ Thu, 12 Dec 2019 00:46:03: #2 finished! INFO @ Thu, 12 Dec 2019 00:46:03: #2 predicted fragment length is 144 bps INFO @ Thu, 12 Dec 2019 00:46:03: #2 alternative fragment length(s) may be 144 bps INFO @ Thu, 12 Dec 2019 00:46:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.10_model.r INFO @ Thu, 12 Dec 2019 00:46:03: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:46:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:46:06: 5000000 INFO @ Thu, 12 Dec 2019 00:46:11: 6000000 INFO @ Thu, 12 Dec 2019 00:46:16: 7000000 INFO @ Thu, 12 Dec 2019 00:46:21: 8000000 INFO @ Thu, 12 Dec 2019 00:46:21: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:46:25: 9000000 INFO @ Thu, 12 Dec 2019 00:46:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:46:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:46:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.10_summits.bed INFO @ Thu, 12 Dec 2019 00:46:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4023 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:46:30: 10000000 INFO @ Thu, 12 Dec 2019 00:46:33: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:46:33: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:46:33: #1 total tags in treatment: 10522762 INFO @ Thu, 12 Dec 2019 00:46:33: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:46:33: #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 00:46:33: #1 tags after filtering in treatment: 10522762 INFO @ Thu, 12 Dec 2019 00:46:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:46:33: #1 finished! INFO @ Thu, 12 Dec 2019 00:46:33: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:46:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:46:33: #2 number of paired peaks: 1112 INFO @ Thu, 12 Dec 2019 00:46:33: start model_add_line... INFO @ Thu, 12 Dec 2019 00:46:33: start X-correlation... INFO @ Thu, 12 Dec 2019 00:46:33: end of X-cor INFO @ Thu, 12 Dec 2019 00:46:33: #2 finished! INFO @ Thu, 12 Dec 2019 00:46:33: #2 predicted fragment length is 144 bps INFO @ Thu, 12 Dec 2019 00:46:33: #2 alternative fragment length(s) may be 144 bps INFO @ Thu, 12 Dec 2019 00:46:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.20_model.r INFO @ Thu, 12 Dec 2019 00:46:33: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:46:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:46:51: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:46:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:46:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:46:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494905/SRX494905.20_summits.bed INFO @ Thu, 12 Dec 2019 00:46:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2322 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。