Job ID = 2589187 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,526,980 reads read : 4,526,980 reads written : 4,526,980 spots read : 4,622,207 reads read : 4,622,207 reads written : 4,622,207 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107572.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107573.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: 00:01:39 9149187 reads; of these: 9149187 (100.00%) were unpaired; of these: 760868 (8.32%) aligned 0 times 7523167 (82.23%) aligned exactly 1 time 865152 (9.46%) aligned >1 times 91.68% overall alignment rate Time searching: 00:01:39 Overall time: 00:01:39 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_rmdupse_core] 1647775 / 8388319 = 0.1964 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 @ Mon, 12 Aug 2019 17:10:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.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 @ Mon, 12 Aug 2019 17:10:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:10:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:10:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.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 @ Mon, 12 Aug 2019 17:10:19: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:10:19: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:10:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.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 @ Mon, 12 Aug 2019 17:10:20: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:10:20: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:10:26: 1000000 INFO @ Mon, 12 Aug 2019 17:10:27: 1000000 INFO @ Mon, 12 Aug 2019 17:10:28: 1000000 INFO @ Mon, 12 Aug 2019 17:10:34: 2000000 INFO @ Mon, 12 Aug 2019 17:10:34: 2000000 INFO @ Mon, 12 Aug 2019 17:10:35: 2000000 INFO @ Mon, 12 Aug 2019 17:10:41: 3000000 INFO @ Mon, 12 Aug 2019 17:10:42: 3000000 INFO @ Mon, 12 Aug 2019 17:10:43: 3000000 INFO @ Mon, 12 Aug 2019 17:10:48: 4000000 INFO @ Mon, 12 Aug 2019 17:10:49: 4000000 INFO @ Mon, 12 Aug 2019 17:10:51: 4000000 INFO @ Mon, 12 Aug 2019 17:10:56: 5000000 INFO @ Mon, 12 Aug 2019 17:10:56: 5000000 INFO @ Mon, 12 Aug 2019 17:11:00: 5000000 INFO @ Mon, 12 Aug 2019 17:11:04: 6000000 INFO @ Mon, 12 Aug 2019 17:11:06: 6000000 INFO @ Mon, 12 Aug 2019 17:11:09: 6000000 INFO @ Mon, 12 Aug 2019 17:11:09: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:11:09: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:11:09: #1 total tags in treatment: 6740544 INFO @ Mon, 12 Aug 2019 17:11:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:11:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:11:09: #1 tags after filtering in treatment: 6740544 INFO @ Mon, 12 Aug 2019 17:11:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:11:09: #1 finished! INFO @ Mon, 12 Aug 2019 17:11:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:11:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:11:10: #2 number of paired peaks: 2444 INFO @ Mon, 12 Aug 2019 17:11:10: start model_add_line... INFO @ Mon, 12 Aug 2019 17:11:10: start X-correlation... INFO @ Mon, 12 Aug 2019 17:11:10: end of X-cor INFO @ Mon, 12 Aug 2019 17:11:10: #2 finished! INFO @ Mon, 12 Aug 2019 17:11:10: #2 predicted fragment length is 144 bps INFO @ Mon, 12 Aug 2019 17:11:10: #2 alternative fragment length(s) may be 144 bps INFO @ Mon, 12 Aug 2019 17:11:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.20_model.r INFO @ Mon, 12 Aug 2019 17:11:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:11:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:11:11: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:11:11: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:11:11: #1 total tags in treatment: 6740544 INFO @ Mon, 12 Aug 2019 17:11:11: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:11:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:11:11: #1 tags after filtering in treatment: 6740544 INFO @ Mon, 12 Aug 2019 17:11:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:11:11: #1 finished! INFO @ Mon, 12 Aug 2019 17:11:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:11:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:11:12: #2 number of paired peaks: 2444 INFO @ Mon, 12 Aug 2019 17:11:12: start model_add_line... INFO @ Mon, 12 Aug 2019 17:11:12: start X-correlation... INFO @ Mon, 12 Aug 2019 17:11:12: end of X-cor INFO @ Mon, 12 Aug 2019 17:11:12: #2 finished! INFO @ Mon, 12 Aug 2019 17:11:12: #2 predicted fragment length is 144 bps INFO @ Mon, 12 Aug 2019 17:11:12: #2 alternative fragment length(s) may be 144 bps INFO @ Mon, 12 Aug 2019 17:11:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.10_model.r INFO @ Mon, 12 Aug 2019 17:11:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:11:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:11:15: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:11:15: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:11:15: #1 total tags in treatment: 6740544 INFO @ Mon, 12 Aug 2019 17:11:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:11:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:11:15: #1 tags after filtering in treatment: 6740544 INFO @ Mon, 12 Aug 2019 17:11:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:11:15: #1 finished! INFO @ Mon, 12 Aug 2019 17:11:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:11:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:11:16: #2 number of paired peaks: 2444 INFO @ Mon, 12 Aug 2019 17:11:16: start model_add_line... INFO @ Mon, 12 Aug 2019 17:11:16: start X-correlation... INFO @ Mon, 12 Aug 2019 17:11:16: end of X-cor INFO @ Mon, 12 Aug 2019 17:11:16: #2 finished! INFO @ Mon, 12 Aug 2019 17:11:16: #2 predicted fragment length is 144 bps INFO @ Mon, 12 Aug 2019 17:11:16: #2 alternative fragment length(s) may be 144 bps INFO @ Mon, 12 Aug 2019 17:11:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.05_model.r INFO @ Mon, 12 Aug 2019 17:11:16: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:11:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:11:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:11:34: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:11:38: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:11:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:11:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:11:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.20_summits.bed INFO @ Mon, 12 Aug 2019 17:11:43: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4597 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:11:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:11:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:11:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.10_summits.bed INFO @ Mon, 12 Aug 2019 17:11:44: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (7485 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:11:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:11:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:11:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043994/SRX043994.05_summits.bed INFO @ Mon, 12 Aug 2019 17:11:49: Done! pass1 - making usageList (7 chroms): 5 millis pass2 - checking and writing primary data (9807 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。