Job ID = 2008397 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,626,437 reads read : 6,626,437 reads written : 6,626,437 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR637554.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: 00:02:53 6626437 reads; of these: 6626437 (100.00%) were unpaired; of these: 3066193 (46.27%) aligned 0 times 2533697 (38.24%) aligned exactly 1 time 1026547 (15.49%) aligned >1 times 53.73% overall alignment rate Time searching: 00:02:53 Overall time: 00:02:53 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 1780356 / 3560244 = 0.5001 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 @ Fri, 05 Jul 2019 19:06:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 19:06:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:06:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:06:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 19:06:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:06:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:06:14: 1000000 INFO @ Fri, 05 Jul 2019 19:06:17: 1000000 INFO @ Fri, 05 Jul 2019 19:06:21: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:06:21: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:06:21: #1 total tags in treatment: 1779888 INFO @ Fri, 05 Jul 2019 19:06:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:06:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:06:21: #1 tags after filtering in treatment: 1779888 INFO @ Fri, 05 Jul 2019 19:06:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:06:21: #1 finished! INFO @ Fri, 05 Jul 2019 19:06:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:06:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:06:21: #2 number of paired peaks: 442 WARNING @ Fri, 05 Jul 2019 19:06:21: Fewer paired peaks (442) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 442 pairs to build model! INFO @ Fri, 05 Jul 2019 19:06:21: start model_add_line... INFO @ Fri, 05 Jul 2019 19:06:21: start X-correlation... INFO @ Fri, 05 Jul 2019 19:06:21: end of X-cor INFO @ Fri, 05 Jul 2019 19:06:21: #2 finished! INFO @ Fri, 05 Jul 2019 19:06:21: #2 predicted fragment length is 164 bps INFO @ Fri, 05 Jul 2019 19:06:21: #2 alternative fragment length(s) may be 164 bps INFO @ Fri, 05 Jul 2019 19:06:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.10_model.r INFO @ Fri, 05 Jul 2019 19:06:25: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:06:25: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:06:25: #1 total tags in treatment: 1779888 INFO @ Fri, 05 Jul 2019 19:06:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:06:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:06:25: #1 tags after filtering in treatment: 1779888 INFO @ Fri, 05 Jul 2019 19:06:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:06:25: #1 finished! INFO @ Fri, 05 Jul 2019 19:06:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:06:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:06:25: #2 number of paired peaks: 442 WARNING @ Fri, 05 Jul 2019 19:06:25: Fewer paired peaks (442) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 442 pairs to build model! INFO @ Fri, 05 Jul 2019 19:06:25: start model_add_line... INFO @ Fri, 05 Jul 2019 19:06:25: start X-correlation... INFO @ Fri, 05 Jul 2019 19:06:25: end of X-cor INFO @ Fri, 05 Jul 2019 19:06:25: #2 finished! INFO @ Fri, 05 Jul 2019 19:06:25: #2 predicted fragment length is 164 bps INFO @ Fri, 05 Jul 2019 19:06:25: #2 alternative fragment length(s) may be 164 bps INFO @ Fri, 05 Jul 2019 19:06:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.05_model.r INFO @ Fri, 05 Jul 2019 19:06:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:06:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:06:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:06:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:06:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 19:06:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:06:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:06:42: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:06:42: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:06:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:06:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:06:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.10_summits.bed INFO @ Fri, 05 Jul 2019 19:06:44: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (2323 records, 4 fields): 9 millis INFO @ Fri, 05 Jul 2019 19:06:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:06:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:06:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.05_summits.bed INFO @ Fri, 05 Jul 2019 19:06:44: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (2950 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:06:46: 1000000 CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:06:52: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:06:52: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:06:52: #1 total tags in treatment: 1779888 INFO @ Fri, 05 Jul 2019 19:06:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:06:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:06:52: #1 tags after filtering in treatment: 1779888 INFO @ Fri, 05 Jul 2019 19:06:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:06:52: #1 finished! INFO @ Fri, 05 Jul 2019 19:06:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:06:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:06:53: #2 number of paired peaks: 442 WARNING @ Fri, 05 Jul 2019 19:06:53: Fewer paired peaks (442) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 442 pairs to build model! INFO @ Fri, 05 Jul 2019 19:06:53: start model_add_line... INFO @ Fri, 05 Jul 2019 19:06:53: start X-correlation... INFO @ Fri, 05 Jul 2019 19:06:53: end of X-cor INFO @ Fri, 05 Jul 2019 19:06:53: #2 finished! INFO @ Fri, 05 Jul 2019 19:06:53: #2 predicted fragment length is 164 bps INFO @ Fri, 05 Jul 2019 19:06:53: #2 alternative fragment length(s) may be 164 bps INFO @ Fri, 05 Jul 2019 19:06:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.20_model.r BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 19:07:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:07:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 19:07:39: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:07:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:07:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:07:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594007/ERX594007.20_summits.bed INFO @ Fri, 05 Jul 2019 19:07:45: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (1637 records, 4 fields): 8 millis CompletedMACS2peakCalling