Job ID = 2589982 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,261,247 reads read : 20,261,247 reads written : 20,261,247 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1163634.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: 00:04:56 20261247 reads; of these: 20261247 (100.00%) were unpaired; of these: 3121313 (15.41%) aligned 0 times 13592672 (67.09%) aligned exactly 1 time 3547262 (17.51%) aligned >1 times 84.59% overall alignment rate Time searching: 00:04:56 Overall time: 00:04:56 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 8 files... [bam_rmdupse_core] 10037291 / 17139934 = 0.5856 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 19:05:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.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 19:05:07: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:05:07: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:05:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.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 19:05:07: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:05:07: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:05:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.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 19:05:08: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:05:08: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:05:16: 1000000 INFO @ Mon, 12 Aug 2019 19:05:17: 1000000 INFO @ Mon, 12 Aug 2019 19:05:18: 1000000 INFO @ Mon, 12 Aug 2019 19:05:25: 2000000 INFO @ Mon, 12 Aug 2019 19:05:26: 2000000 INFO @ Mon, 12 Aug 2019 19:05:27: 2000000 INFO @ Mon, 12 Aug 2019 19:05:33: 3000000 INFO @ Mon, 12 Aug 2019 19:05:33: 3000000 INFO @ Mon, 12 Aug 2019 19:05:34: 3000000 INFO @ Mon, 12 Aug 2019 19:05:42: 4000000 INFO @ Mon, 12 Aug 2019 19:05:42: 4000000 INFO @ Mon, 12 Aug 2019 19:05:43: 4000000 INFO @ Mon, 12 Aug 2019 19:05:51: 5000000 INFO @ Mon, 12 Aug 2019 19:05:52: 5000000 INFO @ Mon, 12 Aug 2019 19:05:53: 5000000 INFO @ Mon, 12 Aug 2019 19:06:00: 6000000 INFO @ Mon, 12 Aug 2019 19:06:01: 6000000 INFO @ Mon, 12 Aug 2019 19:06:02: 6000000 INFO @ Mon, 12 Aug 2019 19:06:09: 7000000 INFO @ Mon, 12 Aug 2019 19:06:10: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:06:10: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:06:10: #1 total tags in treatment: 7102643 INFO @ Mon, 12 Aug 2019 19:06:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:06:10: #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 19:06:11: #1 tags after filtering in treatment: 7102643 INFO @ Mon, 12 Aug 2019 19:06:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:06:11: #1 finished! INFO @ Mon, 12 Aug 2019 19:06:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:06:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:06:11: #2 number of paired peaks: 3089 INFO @ Mon, 12 Aug 2019 19:06:11: start model_add_line... INFO @ Mon, 12 Aug 2019 19:06:12: 7000000 INFO @ Mon, 12 Aug 2019 19:06:12: start X-correlation... INFO @ Mon, 12 Aug 2019 19:06:12: end of X-cor INFO @ Mon, 12 Aug 2019 19:06:12: #2 finished! INFO @ Mon, 12 Aug 2019 19:06:12: #2 predicted fragment length is 160 bps INFO @ Mon, 12 Aug 2019 19:06:12: #2 alternative fragment length(s) may be 160 bps INFO @ Mon, 12 Aug 2019 19:06:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.05_model.r INFO @ Mon, 12 Aug 2019 19:06:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:06:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:06:13: 7000000 INFO @ Mon, 12 Aug 2019 19:06:13: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:06:13: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:06:13: #1 total tags in treatment: 7102643 INFO @ Mon, 12 Aug 2019 19:06:13: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:06:13: #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 19:06:13: #1 tags after filtering in treatment: 7102643 INFO @ Mon, 12 Aug 2019 19:06:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:06:13: #1 finished! INFO @ Mon, 12 Aug 2019 19:06:13: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:06:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:06:13: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:06:13: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:06:13: #1 total tags in treatment: 7102643 INFO @ Mon, 12 Aug 2019 19:06:13: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:06:13: #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 19:06:14: #1 tags after filtering in treatment: 7102643 INFO @ Mon, 12 Aug 2019 19:06:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:06:14: #1 finished! INFO @ Mon, 12 Aug 2019 19:06:14: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:06:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:06:14: #2 number of paired peaks: 3089 INFO @ Mon, 12 Aug 2019 19:06:14: start model_add_line... INFO @ Mon, 12 Aug 2019 19:06:14: start X-correlation... INFO @ Mon, 12 Aug 2019 19:06:14: end of X-cor INFO @ Mon, 12 Aug 2019 19:06:14: #2 finished! INFO @ Mon, 12 Aug 2019 19:06:14: #2 predicted fragment length is 160 bps INFO @ Mon, 12 Aug 2019 19:06:14: #2 alternative fragment length(s) may be 160 bps INFO @ Mon, 12 Aug 2019 19:06:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.10_model.r INFO @ Mon, 12 Aug 2019 19:06:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:06:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:06:15: #2 number of paired peaks: 3089 INFO @ Mon, 12 Aug 2019 19:06:15: start model_add_line... INFO @ Mon, 12 Aug 2019 19:06:15: start X-correlation... INFO @ Mon, 12 Aug 2019 19:06:15: end of X-cor INFO @ Mon, 12 Aug 2019 19:06:15: #2 finished! INFO @ Mon, 12 Aug 2019 19:06:15: #2 predicted fragment length is 160 bps INFO @ Mon, 12 Aug 2019 19:06:15: #2 alternative fragment length(s) may be 160 bps INFO @ Mon, 12 Aug 2019 19:06:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.20_model.r INFO @ Mon, 12 Aug 2019 19:06:15: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:06:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:06:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:06:39: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:06:39: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:06:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:06:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:06:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.05_summits.bed INFO @ Mon, 12 Aug 2019 19:06:48: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (6399 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:06:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:06:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:06:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.10_summits.bed INFO @ Mon, 12 Aug 2019 19:06:50: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4504 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:06:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:06:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:06:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466568/SRX466568.20_summits.bed INFO @ Mon, 12 Aug 2019 19:06:51: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2921 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。