Job ID = 2589649 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,859,700 reads read : 6,859,700 reads written : 6,859,700 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:05 6859700 reads; of these: 6859700 (100.00%) were unpaired; of these: 742379 (10.82%) aligned 0 times 5252663 (76.57%) aligned exactly 1 time 864658 (12.60%) aligned >1 times 89.18% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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] 999802 / 6117321 = 0.1634 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 18:13:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.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 18:13:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:13:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:13:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.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 18:13:32: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:13:32: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:13:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.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 18:13:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:13:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:13:40: 1000000 INFO @ Mon, 12 Aug 2019 18:13:40: 1000000 INFO @ Mon, 12 Aug 2019 18:13:41: 1000000 INFO @ Mon, 12 Aug 2019 18:13:47: 2000000 INFO @ Mon, 12 Aug 2019 18:13:49: 2000000 INFO @ Mon, 12 Aug 2019 18:13:50: 2000000 INFO @ Mon, 12 Aug 2019 18:13:55: 3000000 INFO @ Mon, 12 Aug 2019 18:13:57: 3000000 INFO @ Mon, 12 Aug 2019 18:13:58: 3000000 INFO @ Mon, 12 Aug 2019 18:14:02: 4000000 INFO @ Mon, 12 Aug 2019 18:14:06: 4000000 INFO @ Mon, 12 Aug 2019 18:14:07: 4000000 INFO @ Mon, 12 Aug 2019 18:14:09: 5000000 INFO @ Mon, 12 Aug 2019 18:14:10: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:14:10: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:14:10: #1 total tags in treatment: 5117519 INFO @ Mon, 12 Aug 2019 18:14:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:14:10: #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 18:14:10: #1 tags after filtering in treatment: 5117519 INFO @ Mon, 12 Aug 2019 18:14:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:14:10: #1 finished! INFO @ Mon, 12 Aug 2019 18:14:10: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:14:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:14:11: #2 number of paired peaks: 863 WARNING @ Mon, 12 Aug 2019 18:14:11: Fewer paired peaks (863) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 863 pairs to build model! INFO @ Mon, 12 Aug 2019 18:14:11: start model_add_line... INFO @ Mon, 12 Aug 2019 18:14:11: start X-correlation... INFO @ Mon, 12 Aug 2019 18:14:11: end of X-cor INFO @ Mon, 12 Aug 2019 18:14:11: #2 finished! INFO @ Mon, 12 Aug 2019 18:14:11: #2 predicted fragment length is 132 bps INFO @ Mon, 12 Aug 2019 18:14:11: #2 alternative fragment length(s) may be 132 bps INFO @ Mon, 12 Aug 2019 18:14:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.10_model.r INFO @ Mon, 12 Aug 2019 18:14:11: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:14:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:14:14: 5000000 INFO @ Mon, 12 Aug 2019 18:14:15: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:14:15: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:14:15: #1 total tags in treatment: 5117519 INFO @ Mon, 12 Aug 2019 18:14:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:14:15: #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 18:14:15: #1 tags after filtering in treatment: 5117519 INFO @ Mon, 12 Aug 2019 18:14:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:14:15: #1 finished! INFO @ Mon, 12 Aug 2019 18:14:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:14:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:14:15: 5000000 INFO @ Mon, 12 Aug 2019 18:14:15: #2 number of paired peaks: 863 WARNING @ Mon, 12 Aug 2019 18:14:15: Fewer paired peaks (863) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 863 pairs to build model! INFO @ Mon, 12 Aug 2019 18:14:15: start model_add_line... INFO @ Mon, 12 Aug 2019 18:14:15: start X-correlation... INFO @ Mon, 12 Aug 2019 18:14:15: end of X-cor INFO @ Mon, 12 Aug 2019 18:14:15: #2 finished! INFO @ Mon, 12 Aug 2019 18:14:15: #2 predicted fragment length is 132 bps INFO @ Mon, 12 Aug 2019 18:14:15: #2 alternative fragment length(s) may be 132 bps INFO @ Mon, 12 Aug 2019 18:14:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.05_model.r INFO @ Mon, 12 Aug 2019 18:14:15: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:14:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:14:16: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:14:16: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:14:16: #1 total tags in treatment: 5117519 INFO @ Mon, 12 Aug 2019 18:14:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:14:16: #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 18:14:16: #1 tags after filtering in treatment: 5117519 INFO @ Mon, 12 Aug 2019 18:14:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:14:16: #1 finished! INFO @ Mon, 12 Aug 2019 18:14:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:14:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:14:16: #2 number of paired peaks: 863 WARNING @ Mon, 12 Aug 2019 18:14:16: Fewer paired peaks (863) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 863 pairs to build model! INFO @ Mon, 12 Aug 2019 18:14:16: start model_add_line... INFO @ Mon, 12 Aug 2019 18:14:16: start X-correlation... INFO @ Mon, 12 Aug 2019 18:14:16: end of X-cor INFO @ Mon, 12 Aug 2019 18:14:16: #2 finished! INFO @ Mon, 12 Aug 2019 18:14:16: #2 predicted fragment length is 132 bps INFO @ Mon, 12 Aug 2019 18:14:16: #2 alternative fragment length(s) may be 132 bps INFO @ Mon, 12 Aug 2019 18:14:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.20_model.r INFO @ Mon, 12 Aug 2019 18:14:16: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:14:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:14:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:14:31: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:14:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:14:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:14:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:14:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.10_summits.bed INFO @ Mon, 12 Aug 2019 18:14:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2017 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:14:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:14:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:14:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.05_summits.bed INFO @ Mon, 12 Aug 2019 18:14:39: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3465 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:14:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:14:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:14:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277093/SRX277093.20_summits.bed INFO @ Mon, 12 Aug 2019 18:14:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (853 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。