Job ID = 6498660 SRX = SRX681770 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T00:22:08 prefetch.2.10.7: 1) Downloading 'SRR1552239'... 2020-06-26T00:22:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:22:44 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:22:44 prefetch.2.10.7: 'SRR1552239' is valid 2020-06-26T00:22:44 prefetch.2.10.7: 1) 'SRR1552239' was downloaded successfully Read 4713450 spots for SRR1552239/SRR1552239.sra Written 4713450 spots for SRR1552239/SRR1552239.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: 00:01:20 4713450 reads; of these: 4713450 (100.00%) were unpaired; of these: 223882 (4.75%) aligned 0 times 3420684 (72.57%) aligned exactly 1 time 1068884 (22.68%) aligned >1 times 95.25% overall alignment rate Time searching: 00:01:20 Overall time: 00:01:20 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 412666 / 4489568 = 0.0919 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 @ Fri, 26 Jun 2020 09:25:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.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 @ Fri, 26 Jun 2020 09:25:46: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:25:46: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:25:52: 1000000 INFO @ Fri, 26 Jun 2020 09:25:57: 2000000 INFO @ Fri, 26 Jun 2020 09:26:02: 3000000 INFO @ Fri, 26 Jun 2020 09:26:07: 4000000 INFO @ Fri, 26 Jun 2020 09:26:07: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 09:26:07: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 09:26:07: #1 total tags in treatment: 4076902 INFO @ Fri, 26 Jun 2020 09:26:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:26:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:26:08: #1 tags after filtering in treatment: 4076902 INFO @ Fri, 26 Jun 2020 09:26:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:26:08: #1 finished! INFO @ Fri, 26 Jun 2020 09:26:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:26:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:26:08: #2 number of paired peaks: 321 WARNING @ Fri, 26 Jun 2020 09:26:08: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Fri, 26 Jun 2020 09:26:08: start model_add_line... INFO @ Fri, 26 Jun 2020 09:26:08: start X-correlation... INFO @ Fri, 26 Jun 2020 09:26:08: end of X-cor INFO @ Fri, 26 Jun 2020 09:26:08: #2 finished! INFO @ Fri, 26 Jun 2020 09:26:08: #2 predicted fragment length is 102 bps INFO @ Fri, 26 Jun 2020 09:26:08: #2 alternative fragment length(s) may be 102 bps INFO @ Fri, 26 Jun 2020 09:26:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.05_model.r INFO @ Fri, 26 Jun 2020 09:26:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:26:08: #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 @ Fri, 26 Jun 2020 09:26:16: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:26:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.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 @ Fri, 26 Jun 2020 09:26:16: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:26:16: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:26:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:26:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:26:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.05_summits.bed INFO @ Fri, 26 Jun 2020 09:26:20: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (809 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:26:21: 1000000 INFO @ Fri, 26 Jun 2020 09:26:27: 2000000 INFO @ Fri, 26 Jun 2020 09:26:32: 3000000 INFO @ Fri, 26 Jun 2020 09:26:36: 4000000 INFO @ Fri, 26 Jun 2020 09:26:37: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 09:26:37: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 09:26:37: #1 total tags in treatment: 4076902 INFO @ Fri, 26 Jun 2020 09:26:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:26:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:26:37: #1 tags after filtering in treatment: 4076902 INFO @ Fri, 26 Jun 2020 09:26:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:26:37: #1 finished! INFO @ Fri, 26 Jun 2020 09:26:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:26:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:26:37: #2 number of paired peaks: 321 WARNING @ Fri, 26 Jun 2020 09:26:37: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Fri, 26 Jun 2020 09:26:37: start model_add_line... INFO @ Fri, 26 Jun 2020 09:26:37: start X-correlation... INFO @ Fri, 26 Jun 2020 09:26:37: end of X-cor INFO @ Fri, 26 Jun 2020 09:26:37: #2 finished! INFO @ Fri, 26 Jun 2020 09:26:37: #2 predicted fragment length is 102 bps INFO @ Fri, 26 Jun 2020 09:26:37: #2 alternative fragment length(s) may be 102 bps INFO @ Fri, 26 Jun 2020 09:26:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.10_model.r INFO @ Fri, 26 Jun 2020 09:26:37: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:26:37: #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 @ Fri, 26 Jun 2020 09:26:45: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:26:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.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 @ Fri, 26 Jun 2020 09:26:46: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:26:46: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:26:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:26:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:26:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.10_summits.bed INFO @ Fri, 26 Jun 2020 09:26:50: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (564 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:26:51: 1000000 INFO @ Fri, 26 Jun 2020 09:26:56: 2000000 INFO @ Fri, 26 Jun 2020 09:27:01: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:27:06: 4000000 INFO @ Fri, 26 Jun 2020 09:27:07: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 09:27:07: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 09:27:07: #1 total tags in treatment: 4076902 INFO @ Fri, 26 Jun 2020 09:27:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:27:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:27:07: #1 tags after filtering in treatment: 4076902 INFO @ Fri, 26 Jun 2020 09:27:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:27:07: #1 finished! INFO @ Fri, 26 Jun 2020 09:27:07: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:27:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:27:07: #2 number of paired peaks: 321 WARNING @ Fri, 26 Jun 2020 09:27:07: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Fri, 26 Jun 2020 09:27:07: start model_add_line... INFO @ Fri, 26 Jun 2020 09:27:07: start X-correlation... INFO @ Fri, 26 Jun 2020 09:27:07: end of X-cor INFO @ Fri, 26 Jun 2020 09:27:07: #2 finished! INFO @ Fri, 26 Jun 2020 09:27:07: #2 predicted fragment length is 102 bps INFO @ Fri, 26 Jun 2020 09:27:07: #2 alternative fragment length(s) may be 102 bps INFO @ Fri, 26 Jun 2020 09:27:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.20_model.r INFO @ Fri, 26 Jun 2020 09:27:07: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:27:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:27:15: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:27:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:27:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:27:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681770/SRX681770.20_summits.bed INFO @ Fri, 26 Jun 2020 09:27:19: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (404 records, 4 fields): 2 millis CompletedMACS2peakCalling