Job ID = 6457209 SRX = SRX4563531 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:29:10 prefetch.2.10.7: 1) Downloading 'SRR7706258'... 2020-06-21T11:29:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:31:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:31:49 prefetch.2.10.7: 1) 'SRR7706258' was downloaded successfully Read 15898068 spots for SRR7706258/SRR7706258.sra Written 15898068 spots for SRR7706258/SRR7706258.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: 00:03:21 15898068 reads; of these: 15898068 (100.00%) were unpaired; of these: 959030 (6.03%) aligned 0 times 13167780 (82.83%) aligned exactly 1 time 1771258 (11.14%) aligned >1 times 93.97% overall alignment rate Time searching: 00:03:21 Overall time: 00:03:21 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] 9530337 / 14939038 = 0.6379 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 20:39:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.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 20:39:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:39:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:39:19: 1000000 INFO @ Sun, 21 Jun 2020 20:39:25: 2000000 INFO @ Sun, 21 Jun 2020 20:39:31: 3000000 INFO @ Sun, 21 Jun 2020 20:39:36: 4000000 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 20:39:42: 5000000 INFO @ Sun, 21 Jun 2020 20:39:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.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 20:39:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:39:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:39:45: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:39:45: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:39:45: #1 total tags in treatment: 5408701 INFO @ Sun, 21 Jun 2020 20:39:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:39:45: #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 20:39:45: #1 tags after filtering in treatment: 5408517 INFO @ Sun, 21 Jun 2020 20:39:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:39:45: #1 finished! INFO @ Sun, 21 Jun 2020 20:39:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:39:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:39:46: #2 number of paired peaks: 7000 INFO @ Sun, 21 Jun 2020 20:39:46: start model_add_line... INFO @ Sun, 21 Jun 2020 20:39:46: start X-correlation... INFO @ Sun, 21 Jun 2020 20:39:46: end of X-cor INFO @ Sun, 21 Jun 2020 20:39:46: #2 finished! INFO @ Sun, 21 Jun 2020 20:39:46: #2 predicted fragment length is 300 bps INFO @ Sun, 21 Jun 2020 20:39:46: #2 alternative fragment length(s) may be 300 bps INFO @ Sun, 21 Jun 2020 20:39:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.05_model.r INFO @ Sun, 21 Jun 2020 20:39:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:39:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:39:49: 1000000 INFO @ Sun, 21 Jun 2020 20:39:55: 2000000 INFO @ Sun, 21 Jun 2020 20:40:01: 3000000 INFO @ Sun, 21 Jun 2020 20:40:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:40:06: 4000000 INFO @ Sun, 21 Jun 2020 20:40:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:40:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:40:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.05_summits.bed INFO @ Sun, 21 Jun 2020 20:40:10: Done! pass1 - making usageList (360 chroms): 2 millis pass2 - checking and writing primary data (7924 records, 4 fields): 16 millis CompletedMACS2peakCalling 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 20:40:12: 5000000 INFO @ Sun, 21 Jun 2020 20:40:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.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 20:40:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:40:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:40:15: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:40:15: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:40:15: #1 total tags in treatment: 5408701 INFO @ Sun, 21 Jun 2020 20:40:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:40:15: #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 20:40:15: #1 tags after filtering in treatment: 5408517 INFO @ Sun, 21 Jun 2020 20:40:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:40:15: #1 finished! INFO @ Sun, 21 Jun 2020 20:40:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:40:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:40:16: #2 number of paired peaks: 7000 INFO @ Sun, 21 Jun 2020 20:40:16: start model_add_line... INFO @ Sun, 21 Jun 2020 20:40:16: start X-correlation... INFO @ Sun, 21 Jun 2020 20:40:16: end of X-cor INFO @ Sun, 21 Jun 2020 20:40:16: #2 finished! INFO @ Sun, 21 Jun 2020 20:40:16: #2 predicted fragment length is 300 bps INFO @ Sun, 21 Jun 2020 20:40:16: #2 alternative fragment length(s) may be 300 bps INFO @ Sun, 21 Jun 2020 20:40:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.10_model.r INFO @ Sun, 21 Jun 2020 20:40:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:40:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:40:19: 1000000 INFO @ Sun, 21 Jun 2020 20:40:25: 2000000 INFO @ Sun, 21 Jun 2020 20:40:31: 3000000 INFO @ Sun, 21 Jun 2020 20:40:33: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:40:36: 4000000 INFO @ Sun, 21 Jun 2020 20:40:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:40:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:40:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.10_summits.bed INFO @ Sun, 21 Jun 2020 20:40:40: Done! pass1 - making usageList (195 chroms): 1 millis pass2 - checking and writing primary data (6549 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:40:43: 5000000 INFO @ Sun, 21 Jun 2020 20:40:45: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:40:45: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:40:45: #1 total tags in treatment: 5408701 INFO @ Sun, 21 Jun 2020 20:40:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:40:45: #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 20:40:45: #1 tags after filtering in treatment: 5408517 INFO @ Sun, 21 Jun 2020 20:40:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:40:45: #1 finished! INFO @ Sun, 21 Jun 2020 20:40:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:40:45: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:40:46: #2 number of paired peaks: 7000 INFO @ Sun, 21 Jun 2020 20:40:46: start model_add_line... INFO @ Sun, 21 Jun 2020 20:40:46: start X-correlation... INFO @ Sun, 21 Jun 2020 20:40:46: end of X-cor INFO @ Sun, 21 Jun 2020 20:40:46: #2 finished! INFO @ Sun, 21 Jun 2020 20:40:46: #2 predicted fragment length is 300 bps INFO @ Sun, 21 Jun 2020 20:40:46: #2 alternative fragment length(s) may be 300 bps INFO @ Sun, 21 Jun 2020 20:40:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.20_model.r INFO @ Sun, 21 Jun 2020 20:40:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:40:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:41:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:41:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:41:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:41:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4563531/SRX4563531.20_summits.bed INFO @ Sun, 21 Jun 2020 20:41:11: Done! pass1 - making usageList (128 chroms): 1 millis pass2 - checking and writing primary data (5134 records, 4 fields): 9 millis CompletedMACS2peakCalling