Job ID = 6367031 SRX = SRX2737090 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:16:16 prefetch.2.10.7: 1) Downloading 'SRR5448128'... 2020-06-15T23:16:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:17:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:17:54 prefetch.2.10.7: 'SRR5448128' is valid 2020-06-15T23:17:54 prefetch.2.10.7: 1) 'SRR5448128' was downloaded successfully 2020-06-15T23:17:54 prefetch.2.10.7: 'SRR5448128' has 0 unresolved dependencies Read 28309990 spots for SRR5448128/SRR5448128.sra Written 28309990 spots for SRR5448128/SRR5448128.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: 00:06:02 28309990 reads; of these: 28309990 (100.00%) were unpaired; of these: 3692629 (13.04%) aligned 0 times 21412381 (75.64%) aligned exactly 1 time 3204980 (11.32%) aligned >1 times 86.96% overall alignment rate Time searching: 00:06:03 Overall time: 00:06:03 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 9725414 / 24617361 = 0.3951 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 @ Tue, 16 Jun 2020 08:30:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:30:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:58: 1000000 INFO @ Tue, 16 Jun 2020 08:31:03: 2000000 INFO @ Tue, 16 Jun 2020 08:31:08: 3000000 INFO @ Tue, 16 Jun 2020 08:31:13: 4000000 INFO @ Tue, 16 Jun 2020 08:31:19: 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 @ Tue, 16 Jun 2020 08:31:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:31:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:26: 6000000 INFO @ Tue, 16 Jun 2020 08:31:29: 1000000 INFO @ Tue, 16 Jun 2020 08:31:32: 7000000 INFO @ Tue, 16 Jun 2020 08:31:36: 2000000 INFO @ Tue, 16 Jun 2020 08:31:38: 8000000 INFO @ Tue, 16 Jun 2020 08:31:42: 3000000 INFO @ Tue, 16 Jun 2020 08:31:45: 9000000 INFO @ Tue, 16 Jun 2020 08:31:48: 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 @ Tue, 16 Jun 2020 08:31:51: 10000000 INFO @ Tue, 16 Jun 2020 08:31:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:31:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:54: 5000000 INFO @ Tue, 16 Jun 2020 08:31:57: 11000000 INFO @ Tue, 16 Jun 2020 08:31:59: 1000000 INFO @ Tue, 16 Jun 2020 08:32:01: 6000000 INFO @ Tue, 16 Jun 2020 08:32:03: 12000000 INFO @ Tue, 16 Jun 2020 08:32:05: 2000000 INFO @ Tue, 16 Jun 2020 08:32:07: 7000000 INFO @ Tue, 16 Jun 2020 08:32:09: 13000000 INFO @ Tue, 16 Jun 2020 08:32:10: 3000000 INFO @ Tue, 16 Jun 2020 08:32:13: 8000000 INFO @ Tue, 16 Jun 2020 08:32:15: 14000000 INFO @ Tue, 16 Jun 2020 08:32:17: 4000000 INFO @ Tue, 16 Jun 2020 08:32:19: 9000000 INFO @ Tue, 16 Jun 2020 08:32:20: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:32:20: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:32:20: #1 total tags in treatment: 14891947 INFO @ Tue, 16 Jun 2020 08:32:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:32:21: #1 tags after filtering in treatment: 14891947 INFO @ Tue, 16 Jun 2020 08:32:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:22: #2 number of paired peaks: 2051 INFO @ Tue, 16 Jun 2020 08:32:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:22: #2 predicted fragment length is 154 bps INFO @ Tue, 16 Jun 2020 08:32:22: #2 alternative fragment length(s) may be 4,154 bps INFO @ Tue, 16 Jun 2020 08:32:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.05_model.r INFO @ Tue, 16 Jun 2020 08:32:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:22: 5000000 INFO @ Tue, 16 Jun 2020 08:32:24: 10000000 INFO @ Tue, 16 Jun 2020 08:32:28: 6000000 INFO @ Tue, 16 Jun 2020 08:32:29: 11000000 INFO @ Tue, 16 Jun 2020 08:32:34: 12000000 INFO @ Tue, 16 Jun 2020 08:32:34: 7000000 INFO @ Tue, 16 Jun 2020 08:32:39: 13000000 INFO @ Tue, 16 Jun 2020 08:32:40: 8000000 INFO @ Tue, 16 Jun 2020 08:32:44: 14000000 INFO @ Tue, 16 Jun 2020 08:32:45: 9000000 INFO @ Tue, 16 Jun 2020 08:32:49: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:32:49: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:32:49: #1 total tags in treatment: 14891947 INFO @ Tue, 16 Jun 2020 08:32:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:32:49: #1 tags after filtering in treatment: 14891947 INFO @ Tue, 16 Jun 2020 08:32:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:50: #2 number of paired peaks: 2051 INFO @ Tue, 16 Jun 2020 08:32:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:50: #2 predicted fragment length is 154 bps INFO @ Tue, 16 Jun 2020 08:32:50: #2 alternative fragment length(s) may be 4,154 bps INFO @ Tue, 16 Jun 2020 08:32:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.10_model.r INFO @ Tue, 16 Jun 2020 08:32:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:51: 10000000 INFO @ Tue, 16 Jun 2020 08:32:56: 11000000 INFO @ Tue, 16 Jun 2020 08:32:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:01: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:33:06: 13000000 INFO @ Tue, 16 Jun 2020 08:33:11: 14000000 INFO @ Tue, 16 Jun 2020 08:33:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.05_summits.bed INFO @ Tue, 16 Jun 2020 08:33:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7623 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:33:16: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:33:16: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:33:16: #1 total tags in treatment: 14891947 INFO @ Tue, 16 Jun 2020 08:33:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:33:16: #1 tags after filtering in treatment: 14891947 INFO @ Tue, 16 Jun 2020 08:33:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:18: #2 number of paired peaks: 2051 INFO @ Tue, 16 Jun 2020 08:33:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:18: #2 predicted fragment length is 154 bps INFO @ Tue, 16 Jun 2020 08:33:18: #2 alternative fragment length(s) may be 4,154 bps INFO @ Tue, 16 Jun 2020 08:33:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.20_model.r INFO @ Tue, 16 Jun 2020 08:33:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:33:27: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:33:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.10_summits.bed INFO @ Tue, 16 Jun 2020 08:33:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4786 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:33:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2737090/SRX2737090.20_summits.bed INFO @ Tue, 16 Jun 2020 08:34:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (2323 records, 4 fields): 4 millis CompletedMACS2peakCalling