Job ID = 6457908 SRX = SRX485213 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:01:32 prefetch.2.10.7: 1) Downloading 'SRR1187971'... 2020-06-21T12:01:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:04:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:04:04 prefetch.2.10.7: 1) 'SRR1187971' was downloaded successfully 2020-06-21T12:04:04 prefetch.2.10.7: 'SRR1187971' has 0 unresolved dependencies Read 20210628 spots for SRR1187971/SRR1187971.sra Written 20210628 spots for SRR1187971/SRR1187971.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: 00:05:16 20210628 reads; of these: 20210628 (100.00%) were unpaired; of these: 3432638 (16.98%) aligned 0 times 9644717 (47.72%) aligned exactly 1 time 7133273 (35.29%) aligned >1 times 83.02% overall alignment rate Time searching: 00:05:16 Overall time: 00:05:16 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] 6191485 / 16777990 = 0.3690 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 21:14:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.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 21:14:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:14:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:14:28: 1000000 INFO @ Sun, 21 Jun 2020 21:14:33: 2000000 INFO @ Sun, 21 Jun 2020 21:14:38: 3000000 INFO @ Sun, 21 Jun 2020 21:14:43: 4000000 INFO @ Sun, 21 Jun 2020 21:14:48: 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 21:14:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.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 21:14:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:14:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:14:53: 6000000 INFO @ Sun, 21 Jun 2020 21:14:59: 7000000 INFO @ Sun, 21 Jun 2020 21:14:59: 1000000 INFO @ Sun, 21 Jun 2020 21:15:04: 8000000 INFO @ Sun, 21 Jun 2020 21:15:05: 2000000 INFO @ Sun, 21 Jun 2020 21:15:10: 9000000 INFO @ Sun, 21 Jun 2020 21:15:11: 3000000 INFO @ Sun, 21 Jun 2020 21:15:15: 10000000 INFO @ Sun, 21 Jun 2020 21:15:16: 4000000 INFO @ Sun, 21 Jun 2020 21:15:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:15:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:15:19: #1 total tags in treatment: 10586505 INFO @ Sun, 21 Jun 2020 21:15:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:15:19: #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 21:15:19: #1 tags after filtering in treatment: 10586478 INFO @ Sun, 21 Jun 2020 21:15:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:15:19: #1 finished! INFO @ Sun, 21 Jun 2020 21:15:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:15:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:15:20: #2 number of paired peaks: 4366 INFO @ Sun, 21 Jun 2020 21:15:20: start model_add_line... INFO @ Sun, 21 Jun 2020 21:15:20: start X-correlation... INFO @ Sun, 21 Jun 2020 21:15:20: end of X-cor INFO @ Sun, 21 Jun 2020 21:15:20: #2 finished! INFO @ Sun, 21 Jun 2020 21:15:20: #2 predicted fragment length is 234 bps INFO @ Sun, 21 Jun 2020 21:15:20: #2 alternative fragment length(s) may be 234 bps INFO @ Sun, 21 Jun 2020 21:15:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.05_model.r INFO @ Sun, 21 Jun 2020 21:15:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:15:20: #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 21:15:22: 5000000 INFO @ Sun, 21 Jun 2020 21:15:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.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 21:15:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:15:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:15:28: 6000000 INFO @ Sun, 21 Jun 2020 21:15:28: 1000000 INFO @ Sun, 21 Jun 2020 21:15:34: 2000000 INFO @ Sun, 21 Jun 2020 21:15:34: 7000000 INFO @ Sun, 21 Jun 2020 21:15:39: 3000000 INFO @ Sun, 21 Jun 2020 21:15:41: 8000000 INFO @ Sun, 21 Jun 2020 21:15:44: 4000000 INFO @ Sun, 21 Jun 2020 21:15:47: 9000000 INFO @ Sun, 21 Jun 2020 21:15:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:15:49: 5000000 INFO @ Sun, 21 Jun 2020 21:15:53: 10000000 INFO @ Sun, 21 Jun 2020 21:15:55: 6000000 INFO @ Sun, 21 Jun 2020 21:15:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:15:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:15:56: #1 total tags in treatment: 10586505 INFO @ Sun, 21 Jun 2020 21:15:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:15:56: #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 21:15:57: #1 tags after filtering in treatment: 10586478 INFO @ Sun, 21 Jun 2020 21:15:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:15:57: #1 finished! INFO @ Sun, 21 Jun 2020 21:15:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:15:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:15:58: #2 number of paired peaks: 4366 INFO @ Sun, 21 Jun 2020 21:15:58: start model_add_line... INFO @ Sun, 21 Jun 2020 21:15:58: start X-correlation... INFO @ Sun, 21 Jun 2020 21:15:58: end of X-cor INFO @ Sun, 21 Jun 2020 21:15:58: #2 finished! INFO @ Sun, 21 Jun 2020 21:15:58: #2 predicted fragment length is 234 bps INFO @ Sun, 21 Jun 2020 21:15:58: #2 alternative fragment length(s) may be 234 bps INFO @ Sun, 21 Jun 2020 21:15:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.10_model.r INFO @ Sun, 21 Jun 2020 21:15:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:15:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:16:00: 7000000 INFO @ Sun, 21 Jun 2020 21:16:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:16:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:16:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.05_summits.bed INFO @ Sun, 21 Jun 2020 21:16:03: Done! pass1 - making usageList (885 chroms): 2 millis pass2 - checking and writing primary data (7844 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:16:05: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:16:10: 9000000 INFO @ Sun, 21 Jun 2020 21:16:16: 10000000 INFO @ Sun, 21 Jun 2020 21:16:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:16:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:16:19: #1 total tags in treatment: 10586505 INFO @ Sun, 21 Jun 2020 21:16:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:16:19: #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 21:16:19: #1 tags after filtering in treatment: 10586478 INFO @ Sun, 21 Jun 2020 21:16:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:16:19: #1 finished! INFO @ Sun, 21 Jun 2020 21:16:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:16:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:16:20: #2 number of paired peaks: 4366 INFO @ Sun, 21 Jun 2020 21:16:20: start model_add_line... INFO @ Sun, 21 Jun 2020 21:16:20: start X-correlation... INFO @ Sun, 21 Jun 2020 21:16:20: end of X-cor INFO @ Sun, 21 Jun 2020 21:16:20: #2 finished! INFO @ Sun, 21 Jun 2020 21:16:20: #2 predicted fragment length is 234 bps INFO @ Sun, 21 Jun 2020 21:16:20: #2 alternative fragment length(s) may be 234 bps INFO @ Sun, 21 Jun 2020 21:16:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.20_model.r INFO @ Sun, 21 Jun 2020 21:16:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:16:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:16:27: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:16:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:16:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:16:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.10_summits.bed INFO @ Sun, 21 Jun 2020 21:16:41: Done! pass1 - making usageList (788 chroms): 1 millis pass2 - checking and writing primary data (4674 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:16:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:17:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:17:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:17:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX485213/SRX485213.20_summits.bed INFO @ Sun, 21 Jun 2020 21:17:01: Done! pass1 - making usageList (645 chroms): 2 millis pass2 - checking and writing primary data (2395 records, 4 fields): 18 millis CompletedMACS2peakCalling