Job ID = 6458291 SRX = SRX5011048 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:28:22 prefetch.2.10.7: 1) Downloading 'SRR8191497'... 2020-06-21T12:28:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:30:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:30:29 prefetch.2.10.7: 'SRR8191497' is valid 2020-06-21T12:30:29 prefetch.2.10.7: 1) 'SRR8191497' was downloaded successfully 2020-06-21T12:30:29 prefetch.2.10.7: 'SRR8191497' has 0 unresolved dependencies Read 19535480 spots for SRR8191497/SRR8191497.sra Written 19535480 spots for SRR8191497/SRR8191497.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: 00:04:47 19535480 reads; of these: 19535480 (100.00%) were unpaired; of these: 3893567 (19.93%) aligned 0 times 11744763 (60.12%) aligned exactly 1 time 3897150 (19.95%) aligned >1 times 80.07% overall alignment rate Time searching: 00:04:47 Overall time: 00:04:47 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] 7272719 / 15641913 = 0.4650 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 21:39:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.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 21:39:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:39:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:39:31: 1000000 INFO @ Sun, 21 Jun 2020 21:39:37: 2000000 INFO @ Sun, 21 Jun 2020 21:39:42: 3000000 INFO @ Sun, 21 Jun 2020 21:39:47: 4000000 INFO @ Sun, 21 Jun 2020 21:39:52: 5000000 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 21:39:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.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 21:39:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:39:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:39:58: 6000000 INFO @ Sun, 21 Jun 2020 21:40:01: 1000000 INFO @ Sun, 21 Jun 2020 21:40:03: 7000000 INFO @ Sun, 21 Jun 2020 21:40:06: 2000000 INFO @ Sun, 21 Jun 2020 21:40:09: 8000000 INFO @ Sun, 21 Jun 2020 21:40:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:40:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:40:11: #1 total tags in treatment: 8369194 INFO @ Sun, 21 Jun 2020 21:40:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:40:11: #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 21:40:12: 3000000 INFO @ Sun, 21 Jun 2020 21:40:12: #1 tags after filtering in treatment: 8369089 INFO @ Sun, 21 Jun 2020 21:40:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:40:12: #1 finished! INFO @ Sun, 21 Jun 2020 21:40:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:40:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:40:12: #2 number of paired peaks: 2537 INFO @ Sun, 21 Jun 2020 21:40:12: start model_add_line... INFO @ Sun, 21 Jun 2020 21:40:13: start X-correlation... INFO @ Sun, 21 Jun 2020 21:40:13: end of X-cor INFO @ Sun, 21 Jun 2020 21:40:13: #2 finished! INFO @ Sun, 21 Jun 2020 21:40:13: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 21:40:13: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 21:40:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.05_model.r INFO @ Sun, 21 Jun 2020 21:40:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:40:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:40:17: 4000000 INFO @ Sun, 21 Jun 2020 21:40:22: 5000000 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 21:40:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.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 21:40:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:40:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:40:28: 6000000 INFO @ Sun, 21 Jun 2020 21:40:31: 1000000 INFO @ Sun, 21 Jun 2020 21:40:34: 7000000 INFO @ Sun, 21 Jun 2020 21:40:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:40:36: 2000000 INFO @ Sun, 21 Jun 2020 21:40:39: 8000000 INFO @ Sun, 21 Jun 2020 21:40:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:40:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:40:41: #1 total tags in treatment: 8369194 INFO @ Sun, 21 Jun 2020 21:40:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:40:41: #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 21:40:42: 3000000 INFO @ Sun, 21 Jun 2020 21:40:42: #1 tags after filtering in treatment: 8369089 INFO @ Sun, 21 Jun 2020 21:40:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:40:42: #1 finished! INFO @ Sun, 21 Jun 2020 21:40:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:40:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:40:43: #2 number of paired peaks: 2537 INFO @ Sun, 21 Jun 2020 21:40:43: start model_add_line... INFO @ Sun, 21 Jun 2020 21:40:43: start X-correlation... INFO @ Sun, 21 Jun 2020 21:40:43: end of X-cor INFO @ Sun, 21 Jun 2020 21:40:43: #2 finished! INFO @ Sun, 21 Jun 2020 21:40:43: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 21:40:43: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 21:40:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.10_model.r INFO @ Sun, 21 Jun 2020 21:40:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:40:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:40:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:40:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:40:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.05_summits.bed INFO @ Sun, 21 Jun 2020 21:40:45: Done! pass1 - making usageList (707 chroms): 2 millis pass2 - checking and writing primary data (5392 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:40:47: 4000000 INFO @ Sun, 21 Jun 2020 21:40:52: 5000000 INFO @ Sun, 21 Jun 2020 21:40:57: 6000000 INFO @ Sun, 21 Jun 2020 21:41:03: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:41:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:08: 8000000 INFO @ Sun, 21 Jun 2020 21:41:10: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:41:10: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:41:10: #1 total tags in treatment: 8369194 INFO @ Sun, 21 Jun 2020 21:41:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:41:10: #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 21:41:11: #1 tags after filtering in treatment: 8369089 INFO @ Sun, 21 Jun 2020 21:41:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:41:11: #1 finished! INFO @ Sun, 21 Jun 2020 21:41:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:41:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:41:12: #2 number of paired peaks: 2537 INFO @ Sun, 21 Jun 2020 21:41:12: start model_add_line... INFO @ Sun, 21 Jun 2020 21:41:12: start X-correlation... INFO @ Sun, 21 Jun 2020 21:41:12: end of X-cor INFO @ Sun, 21 Jun 2020 21:41:12: #2 finished! INFO @ Sun, 21 Jun 2020 21:41:12: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 21:41:12: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 21:41:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.20_model.r INFO @ Sun, 21 Jun 2020 21:41:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:41:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:41:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:41:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:41:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.10_summits.bed INFO @ Sun, 21 Jun 2020 21:41:16: Done! pass1 - making usageList (605 chroms): 2 millis pass2 - checking and writing primary data (3551 records, 4 fields): 22 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:41:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:41:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:41:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011048/SRX5011048.20_summits.bed INFO @ Sun, 21 Jun 2020 21:41:46: Done! pass1 - making usageList (363 chroms): 1 millis pass2 - checking and writing primary data (1899 records, 4 fields): 14 millis CompletedMACS2peakCalling