Job ID = 6458301 SRX = SRX5011057 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:45:10 prefetch.2.10.7: 1) Downloading 'SRR8191506'... 2020-06-21T12:45:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:46:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:46:44 prefetch.2.10.7: 'SRR8191506' is valid 2020-06-21T12:46:44 prefetch.2.10.7: 1) 'SRR8191506' was downloaded successfully 2020-06-21T12:46:44 prefetch.2.10.7: 'SRR8191506' has 0 unresolved dependencies Read 20422023 spots for SRR8191506/SRR8191506.sra Written 20422023 spots for SRR8191506/SRR8191506.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: 00:04:27 20422023 reads; of these: 20422023 (100.00%) were unpaired; of these: 3727350 (18.25%) aligned 0 times 13510127 (66.15%) aligned exactly 1 time 3184546 (15.59%) aligned >1 times 81.75% overall alignment rate Time searching: 00:04:27 Overall time: 00:04:27 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] 7992646 / 16694673 = 0.4788 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 21:55:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.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 21:55:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:55:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:55:13: 1000000 INFO @ Sun, 21 Jun 2020 21:55:19: 2000000 INFO @ Sun, 21 Jun 2020 21:55:25: 3000000 INFO @ Sun, 21 Jun 2020 21:55:31: 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 21:55:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.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 21:55:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:55:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:55:38: 5000000 INFO @ Sun, 21 Jun 2020 21:55:43: 1000000 INFO @ Sun, 21 Jun 2020 21:55:44: 6000000 INFO @ Sun, 21 Jun 2020 21:55:49: 2000000 INFO @ Sun, 21 Jun 2020 21:55:51: 7000000 INFO @ Sun, 21 Jun 2020 21:55:54: 3000000 INFO @ Sun, 21 Jun 2020 21:55:57: 8000000 INFO @ Sun, 21 Jun 2020 21:56:00: 4000000 INFO @ Sun, 21 Jun 2020 21:56:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:56:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:56:02: #1 total tags in treatment: 8702027 INFO @ Sun, 21 Jun 2020 21:56:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:56:02: #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 21:56:02: #1 tags after filtering in treatment: 8701887 INFO @ Sun, 21 Jun 2020 21:56:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:56:02: #1 finished! INFO @ Sun, 21 Jun 2020 21:56:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:56:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:56:03: #2 number of paired peaks: 3704 INFO @ Sun, 21 Jun 2020 21:56:03: start model_add_line... INFO @ Sun, 21 Jun 2020 21:56:03: start X-correlation... INFO @ Sun, 21 Jun 2020 21:56:03: end of X-cor INFO @ Sun, 21 Jun 2020 21:56:03: #2 finished! INFO @ Sun, 21 Jun 2020 21:56:03: #2 predicted fragment length is 238 bps INFO @ Sun, 21 Jun 2020 21:56:03: #2 alternative fragment length(s) may be 238 bps INFO @ Sun, 21 Jun 2020 21:56:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.05_model.r INFO @ Sun, 21 Jun 2020 21:56:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:56:03: #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 21:56:06: 5000000 INFO @ Sun, 21 Jun 2020 21:56:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.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 21:56:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:56:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:56:11: 6000000 INFO @ Sun, 21 Jun 2020 21:56:12: 1000000 INFO @ Sun, 21 Jun 2020 21:56:17: 7000000 INFO @ Sun, 21 Jun 2020 21:56:18: 2000000 INFO @ Sun, 21 Jun 2020 21:56:23: 8000000 INFO @ Sun, 21 Jun 2020 21:56:24: 3000000 INFO @ Sun, 21 Jun 2020 21:56:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:56:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:56:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:56:27: #1 total tags in treatment: 8702027 INFO @ Sun, 21 Jun 2020 21:56:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:56:27: #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 21:56:28: #1 tags after filtering in treatment: 8701887 INFO @ Sun, 21 Jun 2020 21:56:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:56:28: #1 finished! INFO @ Sun, 21 Jun 2020 21:56:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:56:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:56:28: #2 number of paired peaks: 3704 INFO @ Sun, 21 Jun 2020 21:56:28: start model_add_line... INFO @ Sun, 21 Jun 2020 21:56:28: start X-correlation... INFO @ Sun, 21 Jun 2020 21:56:28: end of X-cor INFO @ Sun, 21 Jun 2020 21:56:28: #2 finished! INFO @ Sun, 21 Jun 2020 21:56:28: #2 predicted fragment length is 238 bps INFO @ Sun, 21 Jun 2020 21:56:28: #2 alternative fragment length(s) may be 238 bps INFO @ Sun, 21 Jun 2020 21:56:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.10_model.r INFO @ Sun, 21 Jun 2020 21:56:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:56:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:56:29: 4000000 INFO @ Sun, 21 Jun 2020 21:56:35: 5000000 INFO @ Sun, 21 Jun 2020 21:56:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:56:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:56:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.05_summits.bed INFO @ Sun, 21 Jun 2020 21:56:36: Done! pass1 - making usageList (381 chroms): 2 millis pass2 - checking and writing primary data (9077 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:56:40: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:56:46: 7000000 INFO @ Sun, 21 Jun 2020 21:56:51: 8000000 INFO @ Sun, 21 Jun 2020 21:56:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:56:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:56:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:56:55: #1 total tags in treatment: 8702027 INFO @ Sun, 21 Jun 2020 21:56:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:56:55: #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 21:56:56: #1 tags after filtering in treatment: 8701887 INFO @ Sun, 21 Jun 2020 21:56:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:56:56: #1 finished! INFO @ Sun, 21 Jun 2020 21:56:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:56:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:56:57: #2 number of paired peaks: 3704 INFO @ Sun, 21 Jun 2020 21:56:57: start model_add_line... INFO @ Sun, 21 Jun 2020 21:56:57: start X-correlation... INFO @ Sun, 21 Jun 2020 21:56:57: end of X-cor INFO @ Sun, 21 Jun 2020 21:56:57: #2 finished! INFO @ Sun, 21 Jun 2020 21:56:57: #2 predicted fragment length is 238 bps INFO @ Sun, 21 Jun 2020 21:56:57: #2 alternative fragment length(s) may be 238 bps INFO @ Sun, 21 Jun 2020 21:56:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.20_model.r INFO @ Sun, 21 Jun 2020 21:56:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:56:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:57:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:57:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:57:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.10_summits.bed INFO @ Sun, 21 Jun 2020 21:57:03: Done! pass1 - making usageList (318 chroms): 1 millis pass2 - checking and writing primary data (6406 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:57:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:57:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:57:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:57:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011057/SRX5011057.20_summits.bed INFO @ Sun, 21 Jun 2020 21:57:30: Done! pass1 - making usageList (210 chroms): 1 millis pass2 - checking and writing primary data (3815 records, 4 fields): 10 millis CompletedMACS2peakCalling