Job ID = 6366896 SRX = SRX257641 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:10:16 prefetch.2.10.7: 1) Downloading 'SRR800651'... 2020-06-15T23:10:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:11:32 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:11:32 prefetch.2.10.7: 'SRR800651' is valid 2020-06-15T23:11:32 prefetch.2.10.7: 1) 'SRR800651' was downloaded successfully Read 10886815 spots for SRR800651/SRR800651.sra Written 10886815 spots for SRR800651/SRR800651.sra 2020-06-15T23:12:15 prefetch.2.10.7: 1) Downloading 'SRR800652'... 2020-06-15T23:12:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:13:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:13:35 prefetch.2.10.7: 'SRR800652' is valid 2020-06-15T23:13:35 prefetch.2.10.7: 1) 'SRR800652' was downloaded successfully Read 13300010 spots for SRR800652/SRR800652.sra Written 13300010 spots for SRR800652/SRR800652.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: 00:04:52 24186825 reads; of these: 24186825 (100.00%) were unpaired; of these: 4197787 (17.36%) aligned 0 times 17098597 (70.69%) aligned exactly 1 time 2890441 (11.95%) aligned >1 times 82.64% overall alignment rate Time searching: 00:04:52 Overall time: 00:04:52 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] 5253986 / 19989038 = 0.2628 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 08:24:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.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 08:24:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:19: 1000000 INFO @ Tue, 16 Jun 2020 08:24:24: 2000000 INFO @ Tue, 16 Jun 2020 08:24:29: 3000000 INFO @ Tue, 16 Jun 2020 08:24:34: 4000000 INFO @ Tue, 16 Jun 2020 08:24:39: 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 08:24:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.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 08:24:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:45: 6000000 INFO @ Tue, 16 Jun 2020 08:24:49: 1000000 INFO @ Tue, 16 Jun 2020 08:24:50: 7000000 INFO @ Tue, 16 Jun 2020 08:24:55: 2000000 INFO @ Tue, 16 Jun 2020 08:24:56: 8000000 INFO @ Tue, 16 Jun 2020 08:25:01: 3000000 INFO @ Tue, 16 Jun 2020 08:25:02: 9000000 INFO @ Tue, 16 Jun 2020 08:25:07: 4000000 INFO @ Tue, 16 Jun 2020 08:25:08: 10000000 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 08:25:13: 5000000 INFO @ Tue, 16 Jun 2020 08:25:13: 11000000 INFO @ Tue, 16 Jun 2020 08:25:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.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 08:25:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:19: 6000000 INFO @ Tue, 16 Jun 2020 08:25:19: 12000000 INFO @ Tue, 16 Jun 2020 08:25:19: 1000000 INFO @ Tue, 16 Jun 2020 08:25:24: 7000000 INFO @ Tue, 16 Jun 2020 08:25:25: 13000000 INFO @ Tue, 16 Jun 2020 08:25:25: 2000000 INFO @ Tue, 16 Jun 2020 08:25:30: 8000000 INFO @ Tue, 16 Jun 2020 08:25:31: 14000000 INFO @ Tue, 16 Jun 2020 08:25:31: 3000000 INFO @ Tue, 16 Jun 2020 08:25:35: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:25:35: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:25:35: #1 total tags in treatment: 14735052 INFO @ Tue, 16 Jun 2020 08:25:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:35: #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 08:25:35: #1 tags after filtering in treatment: 14735052 INFO @ Tue, 16 Jun 2020 08:25:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:36: 9000000 INFO @ Tue, 16 Jun 2020 08:25:36: #2 number of paired peaks: 619 WARNING @ Tue, 16 Jun 2020 08:25:36: Fewer paired peaks (619) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 619 pairs to build model! INFO @ Tue, 16 Jun 2020 08:25:36: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:36: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:36: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:36: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:36: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:25:36: #2 alternative fragment length(s) may be 4,132,147 bps INFO @ Tue, 16 Jun 2020 08:25:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.05_model.r INFO @ Tue, 16 Jun 2020 08:25:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:25:36: 4000000 INFO @ Tue, 16 Jun 2020 08:25:42: 10000000 INFO @ Tue, 16 Jun 2020 08:25:42: 5000000 INFO @ Tue, 16 Jun 2020 08:25:47: 11000000 INFO @ Tue, 16 Jun 2020 08:25:48: 6000000 INFO @ Tue, 16 Jun 2020 08:25:53: 12000000 INFO @ Tue, 16 Jun 2020 08:25:54: 7000000 INFO @ Tue, 16 Jun 2020 08:25:59: 13000000 INFO @ Tue, 16 Jun 2020 08:26:00: 8000000 INFO @ Tue, 16 Jun 2020 08:26:05: 14000000 INFO @ Tue, 16 Jun 2020 08:26:06: 9000000 INFO @ Tue, 16 Jun 2020 08:26:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:09: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:26:09: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:26:09: #1 total tags in treatment: 14735052 INFO @ Tue, 16 Jun 2020 08:26:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:09: #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 08:26:10: #1 tags after filtering in treatment: 14735052 INFO @ Tue, 16 Jun 2020 08:26:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:10: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:11: #2 number of paired peaks: 619 WARNING @ Tue, 16 Jun 2020 08:26:11: Fewer paired peaks (619) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 619 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:11: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:11: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:11: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:11: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:11: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:26:11: #2 alternative fragment length(s) may be 4,132,147 bps INFO @ Tue, 16 Jun 2020 08:26:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.10_model.r INFO @ Tue, 16 Jun 2020 08:26:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:11: 10000000 INFO @ Tue, 16 Jun 2020 08:26:17: 11000000 INFO @ Tue, 16 Jun 2020 08:26:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.05_summits.bed INFO @ Tue, 16 Jun 2020 08:26:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3459 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:26:22: 12000000 INFO @ Tue, 16 Jun 2020 08:26:28: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:26:33: 14000000 INFO @ Tue, 16 Jun 2020 08:26:37: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:26:37: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:26:37: #1 total tags in treatment: 14735052 INFO @ Tue, 16 Jun 2020 08:26:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:37: #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 08:26:38: #1 tags after filtering in treatment: 14735052 INFO @ Tue, 16 Jun 2020 08:26:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:39: #2 number of paired peaks: 619 WARNING @ Tue, 16 Jun 2020 08:26:39: Fewer paired peaks (619) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 619 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:39: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:26:39: #2 alternative fragment length(s) may be 4,132,147 bps INFO @ Tue, 16 Jun 2020 08:26:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.20_model.r INFO @ Tue, 16 Jun 2020 08:26:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.10_summits.bed INFO @ Tue, 16 Jun 2020 08:26:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1691 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:27:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257641/SRX257641.20_summits.bed INFO @ Tue, 16 Jun 2020 08:27:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (617 records, 4 fields): 2 millis CompletedMACS2peakCalling