Job ID = 6368485 SRX = SRX5020715 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:16:51 prefetch.2.10.7: 1) Downloading 'SRR8201338'... 2020-06-16T00:16:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:18:07 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:18:08 prefetch.2.10.7: 'SRR8201338' is valid 2020-06-16T00:18:08 prefetch.2.10.7: 1) 'SRR8201338' was downloaded successfully Read 10825090 spots for SRR8201338/SRR8201338.sra Written 10825090 spots for SRR8201338/SRR8201338.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: 00:02:28 10825090 reads; of these: 10825090 (100.00%) were unpaired; of these: 885381 (8.18%) aligned 0 times 8383003 (77.44%) aligned exactly 1 time 1556706 (14.38%) aligned >1 times 91.82% overall alignment rate Time searching: 00:02:28 Overall time: 00:02:28 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 8 files... [bam_rmdupse_core] 775961 / 9939709 = 0.0781 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 09:24:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.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 09:24:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:17: 1000000 INFO @ Tue, 16 Jun 2020 09:24:21: 2000000 INFO @ Tue, 16 Jun 2020 09:24:26: 3000000 INFO @ Tue, 16 Jun 2020 09:24:31: 4000000 INFO @ Tue, 16 Jun 2020 09:24:37: 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 09:24:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.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 09:24:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:42: 6000000 INFO @ Tue, 16 Jun 2020 09:24:47: 7000000 INFO @ Tue, 16 Jun 2020 09:24:48: 1000000 INFO @ Tue, 16 Jun 2020 09:24:52: 8000000 INFO @ Tue, 16 Jun 2020 09:24:54: 2000000 INFO @ Tue, 16 Jun 2020 09:24:58: 9000000 INFO @ Tue, 16 Jun 2020 09:24:59: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:24:59: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:24:59: #1 total tags in treatment: 9163748 INFO @ Tue, 16 Jun 2020 09:24:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:24:59: #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 09:24:59: #1 tags after filtering in treatment: 9163748 INFO @ Tue, 16 Jun 2020 09:24:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:24:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:24:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:24:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:24:59: #2 number of paired peaks: 425 WARNING @ Tue, 16 Jun 2020 09:24:59: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Tue, 16 Jun 2020 09:24:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:24:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:24:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:24:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:24:59: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 09:24:59: #2 alternative fragment length(s) may be 132,585 bps INFO @ Tue, 16 Jun 2020 09:24:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.05_model.r INFO @ Tue, 16 Jun 2020 09:24:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:24:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:25:00: 3000000 INFO @ Tue, 16 Jun 2020 09:25:06: 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 09:25:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.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 09:25:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:25:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:25:12: 5000000 INFO @ Tue, 16 Jun 2020 09:25:17: 1000000 INFO @ Tue, 16 Jun 2020 09:25:18: 6000000 INFO @ Tue, 16 Jun 2020 09:25:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:25:22: 2000000 INFO @ Tue, 16 Jun 2020 09:25:24: 7000000 INFO @ Tue, 16 Jun 2020 09:25:27: 3000000 INFO @ Tue, 16 Jun 2020 09:25:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:25:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:25:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.05_summits.bed INFO @ Tue, 16 Jun 2020 09:25:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2829 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:25:30: 8000000 INFO @ Tue, 16 Jun 2020 09:25:33: 4000000 INFO @ Tue, 16 Jun 2020 09:25:36: 9000000 INFO @ Tue, 16 Jun 2020 09:25:37: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:25:37: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:25:37: #1 total tags in treatment: 9163748 INFO @ Tue, 16 Jun 2020 09:25:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:37: #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 09:25:37: #1 tags after filtering in treatment: 9163748 INFO @ Tue, 16 Jun 2020 09:25:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:38: #2 number of paired peaks: 425 WARNING @ Tue, 16 Jun 2020 09:25:38: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Tue, 16 Jun 2020 09:25:38: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:38: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:38: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:38: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:38: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 09:25:38: #2 alternative fragment length(s) may be 132,585 bps INFO @ Tue, 16 Jun 2020 09:25:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.10_model.r INFO @ Tue, 16 Jun 2020 09:25:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:25:38: 5000000 INFO @ Tue, 16 Jun 2020 09:25:43: 6000000 INFO @ Tue, 16 Jun 2020 09:25:49: 7000000 INFO @ Tue, 16 Jun 2020 09:25:53: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:25:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:25:58: 9000000 INFO @ Tue, 16 Jun 2020 09:25:59: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:25:59: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:25:59: #1 total tags in treatment: 9163748 INFO @ Tue, 16 Jun 2020 09:25:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:59: #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 09:25:59: #1 tags after filtering in treatment: 9163748 INFO @ Tue, 16 Jun 2020 09:25:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:00: #2 number of paired peaks: 425 WARNING @ Tue, 16 Jun 2020 09:26:00: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:00: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 09:26:00: #2 alternative fragment length(s) may be 132,585 bps INFO @ Tue, 16 Jun 2020 09:26:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.20_model.r INFO @ Tue, 16 Jun 2020 09:26:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.10_summits.bed INFO @ Tue, 16 Jun 2020 09:26:08: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1131 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:26:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020715/SRX5020715.20_summits.bed INFO @ Tue, 16 Jun 2020 09:26:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (329 records, 4 fields): 2 millis CompletedMACS2peakCalling