Job ID = 1290623 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,238,748 reads read : 11,238,748 reads written : 11,238,748 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:03:05 11238748 reads; of these: 11238748 (100.00%) were unpaired; of these: 1750259 (15.57%) aligned 0 times 7997911 (71.16%) aligned exactly 1 time 1490578 (13.26%) aligned >1 times 84.43% overall alignment rate Time searching: 00:03:05 Overall time: 00:03:05 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] 2645335 / 9488489 = 0.2788 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 @ Sat, 01 Jun 2019 21:51:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.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 @ Sat, 01 Jun 2019 21:51:30: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:30: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.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 @ Sat, 01 Jun 2019 21:51:30: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:30: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.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 @ Sat, 01 Jun 2019 21:51:30: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:30: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:37: 1000000 INFO @ Sat, 01 Jun 2019 21:51:41: 1000000 INFO @ Sat, 01 Jun 2019 21:51:41: 1000000 INFO @ Sat, 01 Jun 2019 21:51:45: 2000000 INFO @ Sat, 01 Jun 2019 21:51:51: 2000000 INFO @ Sat, 01 Jun 2019 21:51:51: 2000000 INFO @ Sat, 01 Jun 2019 21:51:52: 3000000 INFO @ Sat, 01 Jun 2019 21:51:59: 4000000 INFO @ Sat, 01 Jun 2019 21:52:01: 3000000 INFO @ Sat, 01 Jun 2019 21:52:01: 3000000 INFO @ Sat, 01 Jun 2019 21:52:05: 5000000 INFO @ Sat, 01 Jun 2019 21:52:11: 4000000 INFO @ Sat, 01 Jun 2019 21:52:11: 4000000 INFO @ Sat, 01 Jun 2019 21:52:12: 6000000 INFO @ Sat, 01 Jun 2019 21:52:18: #1 tag size is determined as 49 bps INFO @ Sat, 01 Jun 2019 21:52:18: #1 tag size = 49 INFO @ Sat, 01 Jun 2019 21:52:18: #1 total tags in treatment: 6843154 INFO @ Sat, 01 Jun 2019 21:52:18: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:52:18: #1 tags after filtering in treatment: 6843154 INFO @ Sat, 01 Jun 2019 21:52:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:18: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:18: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:19: #2 number of paired peaks: 513 WARNING @ Sat, 01 Jun 2019 21:52:19: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Sat, 01 Jun 2019 21:52:19: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:19: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:19: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:19: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:19: #2 predicted fragment length is 164 bps INFO @ Sat, 01 Jun 2019 21:52:19: #2 alternative fragment length(s) may be 164 bps INFO @ Sat, 01 Jun 2019 21:52:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.10_model.r INFO @ Sat, 01 Jun 2019 21:52:19: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:21: 5000000 INFO @ Sat, 01 Jun 2019 21:52:21: 5000000 INFO @ Sat, 01 Jun 2019 21:52:31: 6000000 INFO @ Sat, 01 Jun 2019 21:52:31: 6000000 INFO @ Sat, 01 Jun 2019 21:52:39: #1 tag size is determined as 49 bps INFO @ Sat, 01 Jun 2019 21:52:39: #1 tag size = 49 INFO @ Sat, 01 Jun 2019 21:52:39: #1 total tags in treatment: 6843154 INFO @ Sat, 01 Jun 2019 21:52:39: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:52:39: #1 tag size is determined as 49 bps INFO @ Sat, 01 Jun 2019 21:52:39: #1 tag size = 49 INFO @ Sat, 01 Jun 2019 21:52:39: #1 total tags in treatment: 6843154 INFO @ Sat, 01 Jun 2019 21:52:39: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:52:39: #1 tags after filtering in treatment: 6843154 INFO @ Sat, 01 Jun 2019 21:52:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:39: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:39: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:39: #1 tags after filtering in treatment: 6843154 INFO @ Sat, 01 Jun 2019 21:52:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:39: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:39: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:40: #2 number of paired peaks: 513 WARNING @ Sat, 01 Jun 2019 21:52:40: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Sat, 01 Jun 2019 21:52:40: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:40: #2 number of paired peaks: 513 WARNING @ Sat, 01 Jun 2019 21:52:40: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Sat, 01 Jun 2019 21:52:40: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:40: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:40: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:40: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:40: #2 predicted fragment length is 164 bps INFO @ Sat, 01 Jun 2019 21:52:40: #2 alternative fragment length(s) may be 164 bps INFO @ Sat, 01 Jun 2019 21:52:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.05_model.r INFO @ Sat, 01 Jun 2019 21:52:40: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:40: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:40: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:40: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:40: #2 predicted fragment length is 164 bps INFO @ Sat, 01 Jun 2019 21:52:40: #2 alternative fragment length(s) may be 164 bps INFO @ Sat, 01 Jun 2019 21:52:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.20_model.r INFO @ Sat, 01 Jun 2019 21:52:40: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:40: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:52:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.10_peaks.xls INFO @ Sat, 01 Jun 2019 21:52:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:52:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.10_summits.bed INFO @ Sat, 01 Jun 2019 21:52:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1020 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:53:01: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:01: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.20_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.20_summits.bed INFO @ Sat, 01 Jun 2019 21:53:11: Done! INFO @ Sat, 01 Jun 2019 21:53:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.05_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1949396/SRX1949396.05_summits.bed pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (469 records, 4 fields): 4 millis INFO @ Sat, 01 Jun 2019 21:53:11: Done! CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1932 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。