Job ID = 6455538 SRX = SRX287868 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:16:36 prefetch.2.10.7: 1) Downloading 'SRR870057'... 2020-06-21T10:16:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:19:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:19:52 prefetch.2.10.7: 1) 'SRR870057' was downloaded successfully Read 17726465 spots for SRR870057/SRR870057.sra Written 17726465 spots for SRR870057/SRR870057.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: 00:03:51 17726465 reads; of these: 17726465 (100.00%) were unpaired; of these: 1089728 (6.15%) aligned 0 times 14767433 (83.31%) aligned exactly 1 time 1869304 (10.55%) aligned >1 times 93.85% overall alignment rate Time searching: 00:03:51 Overall time: 00:03:51 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] 2773294 / 16636737 = 0.1667 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 19:30:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.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 19:30:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:30:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:30:29: 1000000 INFO @ Sun, 21 Jun 2020 19:30:36: 2000000 INFO @ Sun, 21 Jun 2020 19:30:43: 3000000 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 19:30:50: 4000000 INFO @ Sun, 21 Jun 2020 19:30:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.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 19:30:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:30:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:30:58: 5000000 INFO @ Sun, 21 Jun 2020 19:31:00: 1000000 INFO @ Sun, 21 Jun 2020 19:31:05: 6000000 INFO @ Sun, 21 Jun 2020 19:31:06: 2000000 INFO @ Sun, 21 Jun 2020 19:31:12: 7000000 INFO @ Sun, 21 Jun 2020 19:31:13: 3000000 INFO @ Sun, 21 Jun 2020 19:31:19: 4000000 INFO @ Sun, 21 Jun 2020 19:31:19: 8000000 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 19:31:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.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 19:31:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:31:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:31:26: 5000000 INFO @ Sun, 21 Jun 2020 19:31:27: 9000000 INFO @ Sun, 21 Jun 2020 19:31:30: 1000000 INFO @ Sun, 21 Jun 2020 19:31:32: 6000000 INFO @ Sun, 21 Jun 2020 19:31:34: 10000000 INFO @ Sun, 21 Jun 2020 19:31:37: 2000000 INFO @ Sun, 21 Jun 2020 19:31:38: 7000000 INFO @ Sun, 21 Jun 2020 19:31:41: 11000000 INFO @ Sun, 21 Jun 2020 19:31:44: 3000000 INFO @ Sun, 21 Jun 2020 19:31:44: 8000000 INFO @ Sun, 21 Jun 2020 19:31:49: 12000000 INFO @ Sun, 21 Jun 2020 19:31:51: 9000000 INFO @ Sun, 21 Jun 2020 19:31:51: 4000000 INFO @ Sun, 21 Jun 2020 19:31:56: 13000000 INFO @ Sun, 21 Jun 2020 19:31:56: 10000000 INFO @ Sun, 21 Jun 2020 19:31:58: 5000000 INFO @ Sun, 21 Jun 2020 19:32:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:32:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:32:02: #1 total tags in treatment: 13863443 INFO @ Sun, 21 Jun 2020 19:32:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:32:02: #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 19:32:03: #1 tags after filtering in treatment: 13863393 INFO @ Sun, 21 Jun 2020 19:32:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:32:03: #1 finished! INFO @ Sun, 21 Jun 2020 19:32:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:32:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:32:03: 11000000 INFO @ Sun, 21 Jun 2020 19:32:04: #2 number of paired peaks: 2038 INFO @ Sun, 21 Jun 2020 19:32:04: start model_add_line... INFO @ Sun, 21 Jun 2020 19:32:04: start X-correlation... INFO @ Sun, 21 Jun 2020 19:32:04: end of X-cor INFO @ Sun, 21 Jun 2020 19:32:04: #2 finished! INFO @ Sun, 21 Jun 2020 19:32:04: #2 predicted fragment length is 217 bps INFO @ Sun, 21 Jun 2020 19:32:04: #2 alternative fragment length(s) may be 4,217 bps INFO @ Sun, 21 Jun 2020 19:32:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.05_model.r INFO @ Sun, 21 Jun 2020 19:32:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:32:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:32:05: 6000000 INFO @ Sun, 21 Jun 2020 19:32:09: 12000000 INFO @ Sun, 21 Jun 2020 19:32:12: 7000000 INFO @ Sun, 21 Jun 2020 19:32:14: 13000000 INFO @ Sun, 21 Jun 2020 19:32:19: 8000000 INFO @ Sun, 21 Jun 2020 19:32:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:32:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:32:20: #1 total tags in treatment: 13863443 INFO @ Sun, 21 Jun 2020 19:32:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:32:20: #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 19:32:21: #1 tags after filtering in treatment: 13863393 INFO @ Sun, 21 Jun 2020 19:32:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:32:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:32:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:32:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:32:22: #2 number of paired peaks: 2038 INFO @ Sun, 21 Jun 2020 19:32:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:32:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:32:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:32:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:32:22: #2 predicted fragment length is 217 bps INFO @ Sun, 21 Jun 2020 19:32:22: #2 alternative fragment length(s) may be 4,217 bps INFO @ Sun, 21 Jun 2020 19:32:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.10_model.r INFO @ Sun, 21 Jun 2020 19:32:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:32:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:32:25: 9000000 INFO @ Sun, 21 Jun 2020 19:32:30: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:32:36: 11000000 INFO @ Sun, 21 Jun 2020 19:32:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:32:42: 12000000 INFO @ Sun, 21 Jun 2020 19:32:47: 13000000 INFO @ Sun, 21 Jun 2020 19:32:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:32:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:32:52: #1 total tags in treatment: 13863443 INFO @ Sun, 21 Jun 2020 19:32:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:32:52: #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 19:32:53: #1 tags after filtering in treatment: 13863393 INFO @ Sun, 21 Jun 2020 19:32:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:32:53: #1 finished! INFO @ Sun, 21 Jun 2020 19:32:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:32:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:32:54: #2 number of paired peaks: 2038 INFO @ Sun, 21 Jun 2020 19:32:54: start model_add_line... INFO @ Sun, 21 Jun 2020 19:32:54: start X-correlation... INFO @ Sun, 21 Jun 2020 19:32:54: end of X-cor INFO @ Sun, 21 Jun 2020 19:32:54: #2 finished! INFO @ Sun, 21 Jun 2020 19:32:54: #2 predicted fragment length is 217 bps INFO @ Sun, 21 Jun 2020 19:32:54: #2 alternative fragment length(s) may be 4,217 bps INFO @ Sun, 21 Jun 2020 19:32:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.20_model.r INFO @ Sun, 21 Jun 2020 19:32:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:32:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:32:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:32:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:32:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.05_summits.bed INFO @ Sun, 21 Jun 2020 19:32:56: Done! pass1 - making usageList (167 chroms): 2 millis pass2 - checking and writing primary data (6218 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:32:56: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:33:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:33:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:33:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.10_summits.bed INFO @ Sun, 21 Jun 2020 19:33:11: Done! pass1 - making usageList (129 chroms): 2 millis pass2 - checking and writing primary data (2739 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:33:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:33:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:33:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:33:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287868/SRX287868.20_summits.bed INFO @ Sun, 21 Jun 2020 19:33:43: Done! pass1 - making usageList (95 chroms): 1 millis pass2 - checking and writing primary data (901 records, 4 fields): 8 millis CompletedMACS2peakCalling