Job ID = 6455710 SRX = SRX288010 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:24:36 prefetch.2.10.7: 1) Downloading 'SRR870199'... 2020-06-21T10:24:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:26:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:26:45 prefetch.2.10.7: 'SRR870199' is valid 2020-06-21T10:26:45 prefetch.2.10.7: 1) 'SRR870199' was downloaded successfully Read 14157899 spots for SRR870199/SRR870199.sra Written 14157899 spots for SRR870199/SRR870199.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: 00:03:22 14157899 reads; of these: 14157899 (100.00%) were unpaired; of these: 1342019 (9.48%) aligned 0 times 10669339 (75.36%) aligned exactly 1 time 2146541 (15.16%) aligned >1 times 90.52% overall alignment rate Time searching: 00:03:22 Overall time: 00:03:22 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2852051 / 12815880 = 0.2225 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 19:34:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.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 19:34:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:34:34: 1000000 INFO @ Sun, 21 Jun 2020 19:34:41: 2000000 INFO @ Sun, 21 Jun 2020 19:34:48: 3000000 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 19:34:56: 4000000 INFO @ Sun, 21 Jun 2020 19:34:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.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 19:34:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:04: 5000000 INFO @ Sun, 21 Jun 2020 19:35:04: 1000000 INFO @ Sun, 21 Jun 2020 19:35:12: 6000000 INFO @ Sun, 21 Jun 2020 19:35:12: 2000000 INFO @ Sun, 21 Jun 2020 19:35:20: 7000000 INFO @ Sun, 21 Jun 2020 19:35:20: 3000000 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 19:35:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.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 19:35:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:28: 8000000 INFO @ Sun, 21 Jun 2020 19:35:29: 4000000 INFO @ Sun, 21 Jun 2020 19:35:34: 1000000 INFO @ Sun, 21 Jun 2020 19:35:37: 5000000 INFO @ Sun, 21 Jun 2020 19:35:37: 9000000 INFO @ Sun, 21 Jun 2020 19:35:41: 2000000 INFO @ Sun, 21 Jun 2020 19:35:45: 6000000 INFO @ Sun, 21 Jun 2020 19:35:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:35:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:35:45: #1 total tags in treatment: 9963829 INFO @ Sun, 21 Jun 2020 19:35:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:35:45: #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 19:35:46: #1 tags after filtering in treatment: 9963827 INFO @ Sun, 21 Jun 2020 19:35:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:35:46: #1 finished! INFO @ Sun, 21 Jun 2020 19:35:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:35:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:35:47: #2 number of paired peaks: 4671 INFO @ Sun, 21 Jun 2020 19:35:47: start model_add_line... INFO @ Sun, 21 Jun 2020 19:35:47: start X-correlation... INFO @ Sun, 21 Jun 2020 19:35:47: end of X-cor INFO @ Sun, 21 Jun 2020 19:35:47: #2 finished! INFO @ Sun, 21 Jun 2020 19:35:47: #2 predicted fragment length is 244 bps INFO @ Sun, 21 Jun 2020 19:35:47: #2 alternative fragment length(s) may be 244 bps INFO @ Sun, 21 Jun 2020 19:35:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.05_model.r INFO @ Sun, 21 Jun 2020 19:35:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:35:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:35:49: 3000000 INFO @ Sun, 21 Jun 2020 19:35:53: 7000000 INFO @ Sun, 21 Jun 2020 19:35:56: 4000000 INFO @ Sun, 21 Jun 2020 19:36:02: 8000000 INFO @ Sun, 21 Jun 2020 19:36:03: 5000000 INFO @ Sun, 21 Jun 2020 19:36:10: 9000000 INFO @ Sun, 21 Jun 2020 19:36:11: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:36:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:18: 7000000 INFO @ Sun, 21 Jun 2020 19:36:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:36:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:36:18: #1 total tags in treatment: 9963829 INFO @ Sun, 21 Jun 2020 19:36:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:18: #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 19:36:19: #1 tags after filtering in treatment: 9963827 INFO @ Sun, 21 Jun 2020 19:36:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:19: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:20: #2 number of paired peaks: 4671 INFO @ Sun, 21 Jun 2020 19:36:20: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:20: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:20: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:20: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:20: #2 predicted fragment length is 244 bps INFO @ Sun, 21 Jun 2020 19:36:20: #2 alternative fragment length(s) may be 244 bps INFO @ Sun, 21 Jun 2020 19:36:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.10_model.r INFO @ Sun, 21 Jun 2020 19:36:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:24: 8000000 INFO @ Sun, 21 Jun 2020 19:36:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.05_summits.bed INFO @ Sun, 21 Jun 2020 19:36:29: Done! pass1 - making usageList (512 chroms): 2 millis pass2 - checking and writing primary data (7790 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:36:30: 9000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:36:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:36:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:36:36: #1 total tags in treatment: 9963829 INFO @ Sun, 21 Jun 2020 19:36:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:36: #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 19:36:37: #1 tags after filtering in treatment: 9963827 INFO @ Sun, 21 Jun 2020 19:36:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:38: #2 number of paired peaks: 4671 INFO @ Sun, 21 Jun 2020 19:36:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:38: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:38: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:38: #2 predicted fragment length is 244 bps INFO @ Sun, 21 Jun 2020 19:36:38: #2 alternative fragment length(s) may be 244 bps INFO @ Sun, 21 Jun 2020 19:36:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.20_model.r INFO @ Sun, 21 Jun 2020 19:36:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.10_summits.bed INFO @ Sun, 21 Jun 2020 19:37:02: Done! pass1 - making usageList (439 chroms): 2 millis pass2 - checking and writing primary data (6355 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:37:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288010/SRX288010.20_summits.bed INFO @ Sun, 21 Jun 2020 19:37:19: Done! pass1 - making usageList (320 chroms): 1 millis pass2 - checking and writing primary data (4797 records, 4 fields): 14 millis CompletedMACS2peakCalling