Job ID = 6452831 SRX = SRX041388 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:58:43 prefetch.2.10.7: 1) Downloading 'SRR099118'... 2020-06-21T07:58:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:01:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:01:42 prefetch.2.10.7: 1) 'SRR099118' was downloaded successfully Read 24780472 spots for SRR099118/SRR099118.sra Written 24780472 spots for SRR099118/SRR099118.sra 2020-06-21T08:03:01 prefetch.2.10.7: 1) Downloading 'SRR099119'... 2020-06-21T08:03:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:05:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:05:58 prefetch.2.10.7: 'SRR099119' is valid 2020-06-21T08:05:58 prefetch.2.10.7: 1) 'SRR099119' was downloaded successfully Read 21115027 spots for SRR099119/SRR099119.sra Written 21115027 spots for SRR099119/SRR099119.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: 00:09:19 45895499 reads; of these: 45895499 (100.00%) were unpaired; of these: 6282705 (13.69%) aligned 0 times 31315767 (68.23%) aligned exactly 1 time 8297027 (18.08%) aligned >1 times 86.31% overall alignment rate Time searching: 00:09:19 Overall time: 00:09:19 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 12 files... [bam_rmdupse_core] 34305215 / 39612794 = 0.8660 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 17:22:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.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 17:22:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:22:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:22:21: 1000000 INFO @ Sun, 21 Jun 2020 17:22:26: 2000000 INFO @ Sun, 21 Jun 2020 17:22:31: 3000000 INFO @ Sun, 21 Jun 2020 17:22:36: 4000000 INFO @ Sun, 21 Jun 2020 17:22:41: 5000000 INFO @ Sun, 21 Jun 2020 17:22:42: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:22:42: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:22:42: #1 total tags in treatment: 5307579 INFO @ Sun, 21 Jun 2020 17:22:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:22:42: #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 17:22:43: #1 tags after filtering in treatment: 5307476 INFO @ Sun, 21 Jun 2020 17:22:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:22:43: #1 finished! INFO @ Sun, 21 Jun 2020 17:22:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:22:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:22:43: #2 number of paired peaks: 4292 INFO @ Sun, 21 Jun 2020 17:22:43: start model_add_line... INFO @ Sun, 21 Jun 2020 17:22:43: start X-correlation... INFO @ Sun, 21 Jun 2020 17:22:43: end of X-cor INFO @ Sun, 21 Jun 2020 17:22:43: #2 finished! INFO @ Sun, 21 Jun 2020 17:22:43: #2 predicted fragment length is 232 bps INFO @ Sun, 21 Jun 2020 17:22:43: #2 alternative fragment length(s) may be 232 bps INFO @ Sun, 21 Jun 2020 17:22:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.05_model.r INFO @ Sun, 21 Jun 2020 17:22:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:22:43: #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 17:22:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.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 17:22:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:22:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:22:50: 1000000 INFO @ Sun, 21 Jun 2020 17:22:55: 2000000 INFO @ Sun, 21 Jun 2020 17:22:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:23:00: 3000000 INFO @ Sun, 21 Jun 2020 17:23:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:23:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:23:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.05_summits.bed INFO @ Sun, 21 Jun 2020 17:23:05: Done! pass1 - making usageList (1073 chroms): 2 millis pass2 - checking and writing primary data (5837 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:23:06: 4000000 INFO @ Sun, 21 Jun 2020 17:23:11: 5000000 INFO @ Sun, 21 Jun 2020 17:23:12: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:23:12: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:23:12: #1 total tags in treatment: 5307579 INFO @ Sun, 21 Jun 2020 17:23:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:23:12: #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 17:23:13: #1 tags after filtering in treatment: 5307476 INFO @ Sun, 21 Jun 2020 17:23:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:23:13: #1 finished! INFO @ Sun, 21 Jun 2020 17:23:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:23:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:23:13: #2 number of paired peaks: 4292 INFO @ Sun, 21 Jun 2020 17:23:13: start model_add_line... INFO @ Sun, 21 Jun 2020 17:23:13: start X-correlation... INFO @ Sun, 21 Jun 2020 17:23:13: end of X-cor INFO @ Sun, 21 Jun 2020 17:23:13: #2 finished! INFO @ Sun, 21 Jun 2020 17:23:13: #2 predicted fragment length is 232 bps INFO @ Sun, 21 Jun 2020 17:23:13: #2 alternative fragment length(s) may be 232 bps INFO @ Sun, 21 Jun 2020 17:23:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.10_model.r INFO @ Sun, 21 Jun 2020 17:23:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:23:13: #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 17:23:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.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 17:23:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:23:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:23:21: 1000000 INFO @ Sun, 21 Jun 2020 17:23:25: 2000000 INFO @ Sun, 21 Jun 2020 17:23:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:23:30: 3000000 INFO @ Sun, 21 Jun 2020 17:23:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:23:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:23:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.10_summits.bed INFO @ Sun, 21 Jun 2020 17:23:35: Done! pass1 - making usageList (978 chroms): 1 millis pass2 - checking and writing primary data (4017 records, 4 fields): 28 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:23:36: 4000000 INFO @ Sun, 21 Jun 2020 17:23:41: 5000000 INFO @ Sun, 21 Jun 2020 17:23:42: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:23:42: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:23:42: #1 total tags in treatment: 5307579 INFO @ Sun, 21 Jun 2020 17:23:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:23:42: #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 17:23:43: #1 tags after filtering in treatment: 5307476 INFO @ Sun, 21 Jun 2020 17:23:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:23:43: #1 finished! INFO @ Sun, 21 Jun 2020 17:23:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:23:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:23:43: #2 number of paired peaks: 4292 INFO @ Sun, 21 Jun 2020 17:23:43: start model_add_line... INFO @ Sun, 21 Jun 2020 17:23:43: start X-correlation... INFO @ Sun, 21 Jun 2020 17:23:43: end of X-cor INFO @ Sun, 21 Jun 2020 17:23:43: #2 finished! INFO @ Sun, 21 Jun 2020 17:23:43: #2 predicted fragment length is 232 bps INFO @ Sun, 21 Jun 2020 17:23:43: #2 alternative fragment length(s) may be 232 bps INFO @ Sun, 21 Jun 2020 17:23:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.20_model.r INFO @ Sun, 21 Jun 2020 17:23:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:23:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:23:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:24:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:24:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:24:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041388/SRX041388.20_summits.bed INFO @ Sun, 21 Jun 2020 17:24:05: Done! pass1 - making usageList (813 chroms): 2 millis pass2 - checking and writing primary data (2646 records, 4 fields): 47 millis CompletedMACS2peakCalling