Job ID = 6458681 SRX = SRX5379464 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:59:04 prefetch.2.10.7: 1) Downloading 'SRR8578658'... 2020-06-21T12:59:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:01:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:01:44 prefetch.2.10.7: 1) 'SRR8578658' was downloaded successfully 2020-06-21T13:01:44 prefetch.2.10.7: 'SRR8578658' has 0 unresolved dependencies Read 29168706 spots for SRR8578658/SRR8578658.sra Written 29168706 spots for SRR8578658/SRR8578658.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: 00:04:57 29168706 reads; of these: 29168706 (100.00%) were unpaired; of these: 13491720 (46.25%) aligned 0 times 13417000 (46.00%) aligned exactly 1 time 2259986 (7.75%) aligned >1 times 53.75% overall alignment rate Time searching: 00:04:57 Overall time: 00:04:57 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] 10436500 / 15676986 = 0.6657 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 22:10:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.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 22:10:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:10:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:10:57: 1000000 INFO @ Sun, 21 Jun 2020 22:11:02: 2000000 INFO @ Sun, 21 Jun 2020 22:11:07: 3000000 INFO @ Sun, 21 Jun 2020 22:11:12: 4000000 INFO @ Sun, 21 Jun 2020 22:11:17: 5000000 INFO @ Sun, 21 Jun 2020 22:11:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:11:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:11:18: #1 total tags in treatment: 5240486 INFO @ Sun, 21 Jun 2020 22:11:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:11:18: #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 22:11:18: #1 tags after filtering in treatment: 5240343 INFO @ Sun, 21 Jun 2020 22:11:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:11:18: #1 finished! INFO @ Sun, 21 Jun 2020 22:11:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:11:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:11:19: #2 number of paired peaks: 1388 INFO @ Sun, 21 Jun 2020 22:11:19: start model_add_line... INFO @ Sun, 21 Jun 2020 22:11:19: start X-correlation... INFO @ Sun, 21 Jun 2020 22:11:19: end of X-cor INFO @ Sun, 21 Jun 2020 22:11:19: #2 finished! INFO @ Sun, 21 Jun 2020 22:11:19: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 22:11:19: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 22:11:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.05_model.r INFO @ Sun, 21 Jun 2020 22:11:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:11:19: #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 22:11:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.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 22:11:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:11:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:11:27: 1000000 INFO @ Sun, 21 Jun 2020 22:11:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:11:32: 2000000 INFO @ Sun, 21 Jun 2020 22:11:36: 3000000 INFO @ Sun, 21 Jun 2020 22:11:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:11:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:11:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.05_summits.bed INFO @ Sun, 21 Jun 2020 22:11:36: Done! pass1 - making usageList (409 chroms): 1 millis pass2 - checking and writing primary data (2898 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:11:41: 4000000 INFO @ Sun, 21 Jun 2020 22:11:46: 5000000 INFO @ Sun, 21 Jun 2020 22:11:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:11:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:11:47: #1 total tags in treatment: 5240486 INFO @ Sun, 21 Jun 2020 22:11:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:11:47: #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 22:11:48: #1 tags after filtering in treatment: 5240343 INFO @ Sun, 21 Jun 2020 22:11:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:11:48: #1 finished! INFO @ Sun, 21 Jun 2020 22:11:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:11:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:11:48: #2 number of paired peaks: 1388 INFO @ Sun, 21 Jun 2020 22:11:48: start model_add_line... INFO @ Sun, 21 Jun 2020 22:11:48: start X-correlation... INFO @ Sun, 21 Jun 2020 22:11:48: end of X-cor INFO @ Sun, 21 Jun 2020 22:11:48: #2 finished! INFO @ Sun, 21 Jun 2020 22:11:48: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 22:11:48: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 22:11:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.10_model.r INFO @ Sun, 21 Jun 2020 22:11:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:11:48: #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 22:11:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.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 22:11:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:11:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:11:57: 1000000 INFO @ Sun, 21 Jun 2020 22:12:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:12:01: 2000000 INFO @ Sun, 21 Jun 2020 22:12:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:12:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:12:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.10_summits.bed INFO @ Sun, 21 Jun 2020 22:12:06: Done! INFO @ Sun, 21 Jun 2020 22:12:06: 3000000 pass1 - making usageList (307 chroms): 1 millis pass2 - checking and writing primary data (1534 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:12:11: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:12:16: 5000000 INFO @ Sun, 21 Jun 2020 22:12:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:12:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:12:17: #1 total tags in treatment: 5240486 INFO @ Sun, 21 Jun 2020 22:12:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:12:17: #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 22:12:18: #1 tags after filtering in treatment: 5240343 INFO @ Sun, 21 Jun 2020 22:12:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:12:18: #1 finished! INFO @ Sun, 21 Jun 2020 22:12:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:12:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:12:18: #2 number of paired peaks: 1388 INFO @ Sun, 21 Jun 2020 22:12:18: start model_add_line... INFO @ Sun, 21 Jun 2020 22:12:18: start X-correlation... INFO @ Sun, 21 Jun 2020 22:12:18: end of X-cor INFO @ Sun, 21 Jun 2020 22:12:18: #2 finished! INFO @ Sun, 21 Jun 2020 22:12:18: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 22:12:18: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 22:12:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.20_model.r INFO @ Sun, 21 Jun 2020 22:12:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:12:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:12:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:12:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:12:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:12:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5379464/SRX5379464.20_summits.bed INFO @ Sun, 21 Jun 2020 22:12:36: Done! pass1 - making usageList (111 chroms): 1 millis pass2 - checking and writing primary data (639 records, 4 fields): 6 millis CompletedMACS2peakCalling