Job ID = 6452810 SRX = SRX040613 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:39:36 prefetch.2.10.7: 1) Downloading 'SRR097982'... 2020-06-21T07:39:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:43:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:43:10 prefetch.2.10.7: 1) 'SRR097982' was downloaded successfully Read 32201005 spots for SRR097982/SRR097982.sra Written 32201005 spots for SRR097982/SRR097982.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: 00:04:39 32201005 reads; of these: 32201005 (100.00%) were unpaired; of these: 850629 (2.64%) aligned 0 times 30013367 (93.21%) aligned exactly 1 time 1337009 (4.15%) aligned >1 times 97.36% overall alignment rate Time searching: 00:04:39 Overall time: 00:04:39 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] 22829551 / 31350376 = 0.7282 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 16:55:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.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 16:55:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:55:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:56:02: 1000000 INFO @ Sun, 21 Jun 2020 16:56:08: 2000000 INFO @ Sun, 21 Jun 2020 16:56:14: 3000000 INFO @ Sun, 21 Jun 2020 16:56:20: 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 16:56:25: 5000000 INFO @ Sun, 21 Jun 2020 16:56:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.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 16:56:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:56:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:56:31: 6000000 INFO @ Sun, 21 Jun 2020 16:56:32: 1000000 INFO @ Sun, 21 Jun 2020 16:56:37: 7000000 INFO @ Sun, 21 Jun 2020 16:56:38: 2000000 INFO @ Sun, 21 Jun 2020 16:56:43: 8000000 INFO @ Sun, 21 Jun 2020 16:56:44: 3000000 INFO @ Sun, 21 Jun 2020 16:56:47: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 16:56:47: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 16:56:47: #1 total tags in treatment: 8520825 INFO @ Sun, 21 Jun 2020 16:56:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:56:47: #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 16:56:47: #1 tags after filtering in treatment: 8520391 INFO @ Sun, 21 Jun 2020 16:56:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:56:47: #1 finished! INFO @ Sun, 21 Jun 2020 16:56:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:56:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:56:49: #2 number of paired peaks: 11730 INFO @ Sun, 21 Jun 2020 16:56:49: start model_add_line... INFO @ Sun, 21 Jun 2020 16:56:49: start X-correlation... INFO @ Sun, 21 Jun 2020 16:56:49: end of X-cor INFO @ Sun, 21 Jun 2020 16:56:49: #2 finished! INFO @ Sun, 21 Jun 2020 16:56:49: #2 predicted fragment length is 215 bps INFO @ Sun, 21 Jun 2020 16:56:49: #2 alternative fragment length(s) may be 215 bps INFO @ Sun, 21 Jun 2020 16:56:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.05_model.r INFO @ Sun, 21 Jun 2020 16:56:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:56:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:56:50: 4000000 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 16:56:55: 5000000 INFO @ Sun, 21 Jun 2020 16:56:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.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 16:56:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:56:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:57:01: 6000000 INFO @ Sun, 21 Jun 2020 16:57:02: 1000000 INFO @ Sun, 21 Jun 2020 16:57:07: 7000000 INFO @ Sun, 21 Jun 2020 16:57:08: 2000000 INFO @ Sun, 21 Jun 2020 16:57:13: 8000000 INFO @ Sun, 21 Jun 2020 16:57:14: 3000000 INFO @ Sun, 21 Jun 2020 16:57:16: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 16:57:16: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 16:57:16: #1 total tags in treatment: 8520825 INFO @ Sun, 21 Jun 2020 16:57:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:57:16: #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 16:57:16: #1 tags after filtering in treatment: 8520391 INFO @ Sun, 21 Jun 2020 16:57:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:57:16: #1 finished! INFO @ Sun, 21 Jun 2020 16:57:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:57:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:57:18: #2 number of paired peaks: 11730 INFO @ Sun, 21 Jun 2020 16:57:18: start model_add_line... INFO @ Sun, 21 Jun 2020 16:57:18: start X-correlation... INFO @ Sun, 21 Jun 2020 16:57:18: end of X-cor INFO @ Sun, 21 Jun 2020 16:57:18: #2 finished! INFO @ Sun, 21 Jun 2020 16:57:18: #2 predicted fragment length is 215 bps INFO @ Sun, 21 Jun 2020 16:57:18: #2 alternative fragment length(s) may be 215 bps INFO @ Sun, 21 Jun 2020 16:57:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.10_model.r INFO @ Sun, 21 Jun 2020 16:57:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:57:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:57:20: 4000000 INFO @ Sun, 21 Jun 2020 16:57:26: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:57:31: 6000000 INFO @ Sun, 21 Jun 2020 16:57:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:57:37: 7000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:57:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:57:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:57:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.05_summits.bed INFO @ Sun, 21 Jun 2020 16:57:40: Done! pass1 - making usageList (59 chroms): 2 millis pass2 - checking and writing primary data (8479 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:57:43: 8000000 INFO @ Sun, 21 Jun 2020 16:57:46: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 16:57:46: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 16:57:46: #1 total tags in treatment: 8520825 INFO @ Sun, 21 Jun 2020 16:57:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:57:46: #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 16:57:46: #1 tags after filtering in treatment: 8520391 INFO @ Sun, 21 Jun 2020 16:57:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:57:46: #1 finished! INFO @ Sun, 21 Jun 2020 16:57:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:57:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:57:48: #2 number of paired peaks: 11730 INFO @ Sun, 21 Jun 2020 16:57:48: start model_add_line... INFO @ Sun, 21 Jun 2020 16:57:48: start X-correlation... INFO @ Sun, 21 Jun 2020 16:57:48: end of X-cor INFO @ Sun, 21 Jun 2020 16:57:48: #2 finished! INFO @ Sun, 21 Jun 2020 16:57:48: #2 predicted fragment length is 215 bps INFO @ Sun, 21 Jun 2020 16:57:48: #2 alternative fragment length(s) may be 215 bps INFO @ Sun, 21 Jun 2020 16:57:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.20_model.r INFO @ Sun, 21 Jun 2020 16:57:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:57:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:58:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:58:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:58:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:58:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.10_summits.bed INFO @ Sun, 21 Jun 2020 16:58:10: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (7718 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:58:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:58:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:58:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:58:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX040613/SRX040613.20_summits.bed INFO @ Sun, 21 Jun 2020 16:58:40: Done! pass1 - making usageList (44 chroms): 2 millis pass2 - checking and writing primary data (6905 records, 4 fields): 13 millis CompletedMACS2peakCalling