Job ID = 6452401 SRX = SRX013035 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:49:00 prefetch.2.10.7: 1) Downloading 'SRR030301'... 2020-06-21T07:49:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:49:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:49:50 prefetch.2.10.7: 'SRR030301' is valid 2020-06-21T07:49:50 prefetch.2.10.7: 1) 'SRR030301' was downloaded successfully Read 4731386 spots for SRR030301/SRR030301.sra Written 4731386 spots for SRR030301/SRR030301.sra 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: 00:00:46 4731386 reads; of these: 4731386 (100.00%) were unpaired; of these: 655844 (13.86%) aligned 0 times 3696185 (78.12%) aligned exactly 1 time 379357 (8.02%) aligned >1 times 86.14% overall alignment rate Time searching: 00:00:46 Overall time: 00:00:46 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 140802 / 4075542 = 0.0345 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 16:52:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 16:52:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:52:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:52:29: 1000000 INFO @ Sun, 21 Jun 2020 16:52:35: 2000000 INFO @ Sun, 21 Jun 2020 16:52:40: 3000000 INFO @ Sun, 21 Jun 2020 16:52:45: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:52:45: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:52:45: #1 total tags in treatment: 3934740 INFO @ Sun, 21 Jun 2020 16:52:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:52:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 16:52:46: #1 tags after filtering in treatment: 3934462 INFO @ Sun, 21 Jun 2020 16:52:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:52:46: #1 finished! INFO @ Sun, 21 Jun 2020 16:52:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:52:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:52:46: #2 number of paired peaks: 690 WARNING @ Sun, 21 Jun 2020 16:52:46: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Sun, 21 Jun 2020 16:52:46: start model_add_line... INFO @ Sun, 21 Jun 2020 16:52:46: start X-correlation... INFO @ Sun, 21 Jun 2020 16:52:46: end of X-cor INFO @ Sun, 21 Jun 2020 16:52:46: #2 finished! INFO @ Sun, 21 Jun 2020 16:52:46: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 16:52:46: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 16:52:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.05_model.r INFO @ Sun, 21 Jun 2020 16:52:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:52:46: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 16:52:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 16:52:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:52:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:52:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:53:00: 1000000 INFO @ Sun, 21 Jun 2020 16:53:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:53:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:53:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.05_summits.bed INFO @ Sun, 21 Jun 2020 16:53:01: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (2383 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:53:06: 2000000 INFO @ Sun, 21 Jun 2020 16:53:12: 3000000 INFO @ Sun, 21 Jun 2020 16:53:18: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:53:18: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:53:18: #1 total tags in treatment: 3934740 INFO @ Sun, 21 Jun 2020 16:53:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:53:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 16:53:18: #1 tags after filtering in treatment: 3934462 INFO @ Sun, 21 Jun 2020 16:53:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:53:18: #1 finished! INFO @ Sun, 21 Jun 2020 16:53:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:53:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:53:18: #2 number of paired peaks: 690 WARNING @ Sun, 21 Jun 2020 16:53:18: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Sun, 21 Jun 2020 16:53:18: start model_add_line... INFO @ Sun, 21 Jun 2020 16:53:18: start X-correlation... INFO @ Sun, 21 Jun 2020 16:53:18: end of X-cor INFO @ Sun, 21 Jun 2020 16:53:18: #2 finished! INFO @ Sun, 21 Jun 2020 16:53:18: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 16:53:18: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 16:53:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.10_model.r INFO @ Sun, 21 Jun 2020 16:53:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:53:18: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 16:53:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 16:53:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:53:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:53:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:53:29: 1000000 INFO @ Sun, 21 Jun 2020 16:53:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:53:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:53:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.10_summits.bed INFO @ Sun, 21 Jun 2020 16:53:33: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (623 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:53:34: 2000000 INFO @ Sun, 21 Jun 2020 16:53:39: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:53:45: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:53:45: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:53:45: #1 total tags in treatment: 3934740 INFO @ Sun, 21 Jun 2020 16:53:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:53:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 16:53:45: #1 tags after filtering in treatment: 3934462 INFO @ Sun, 21 Jun 2020 16:53:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:53:45: #1 finished! INFO @ Sun, 21 Jun 2020 16:53:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:53:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:53:46: #2 number of paired peaks: 690 WARNING @ Sun, 21 Jun 2020 16:53:46: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Sun, 21 Jun 2020 16:53:46: start model_add_line... INFO @ Sun, 21 Jun 2020 16:53:46: start X-correlation... INFO @ Sun, 21 Jun 2020 16:53:46: end of X-cor INFO @ Sun, 21 Jun 2020 16:53:46: #2 finished! INFO @ Sun, 21 Jun 2020 16:53:46: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 16:53:46: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 16:53:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.20_model.r INFO @ Sun, 21 Jun 2020 16:53:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:53:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:53:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:54:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:54:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:54:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013035/SRX013035.20_summits.bed INFO @ Sun, 21 Jun 2020 16:54:00: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (93 records, 4 fields): 1 millis CompletedMACS2peakCalling