Job ID = 6366542 SRX = SRX1769997 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:02:12 prefetch.2.10.7: 1) Downloading 'SRR3535777'... 2020-06-15T23:02:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:05:42 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:05:42 prefetch.2.10.7: 1) 'SRR3535777' was downloaded successfully Read 53147964 spots for SRR3535777/SRR3535777.sra Written 53147964 spots for SRR3535777/SRR3535777.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: 00:07:17 53147964 reads; of these: 53147964 (100.00%) were unpaired; of these: 32408398 (60.98%) aligned 0 times 17106838 (32.19%) aligned exactly 1 time 3632728 (6.84%) aligned >1 times 39.02% overall alignment rate Time searching: 00:07:17 Overall time: 00:07:17 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] 10701880 / 20739566 = 0.5160 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 08:20:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.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 08:20:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:37: 1000000 INFO @ Tue, 16 Jun 2020 08:20:45: 2000000 INFO @ Tue, 16 Jun 2020 08:20:52: 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 @ Tue, 16 Jun 2020 08:20:59: 4000000 INFO @ Tue, 16 Jun 2020 08:21:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.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 08:21:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:07: 5000000 INFO @ Tue, 16 Jun 2020 08:21:08: 1000000 INFO @ Tue, 16 Jun 2020 08:21:15: 2000000 INFO @ Tue, 16 Jun 2020 08:21:15: 6000000 INFO @ Tue, 16 Jun 2020 08:21:22: 3000000 INFO @ Tue, 16 Jun 2020 08:21:23: 7000000 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 08:21:30: 4000000 INFO @ Tue, 16 Jun 2020 08:21:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.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 08:21:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:31: 8000000 INFO @ Tue, 16 Jun 2020 08:21:37: 5000000 INFO @ Tue, 16 Jun 2020 08:21:38: 1000000 INFO @ Tue, 16 Jun 2020 08:21:39: 9000000 INFO @ Tue, 16 Jun 2020 08:21:45: 6000000 INFO @ Tue, 16 Jun 2020 08:21:46: 2000000 INFO @ Tue, 16 Jun 2020 08:21:46: 10000000 INFO @ Tue, 16 Jun 2020 08:21:47: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:21:47: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:21:47: #1 total tags in treatment: 10037686 INFO @ Tue, 16 Jun 2020 08:21:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:47: #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 08:21:47: #1 tags after filtering in treatment: 10037686 INFO @ Tue, 16 Jun 2020 08:21:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:48: #2 number of paired peaks: 3222 INFO @ Tue, 16 Jun 2020 08:21:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:48: #2 predicted fragment length is 406 bps INFO @ Tue, 16 Jun 2020 08:21:48: #2 alternative fragment length(s) may be 406 bps INFO @ Tue, 16 Jun 2020 08:21:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.05_model.r INFO @ Tue, 16 Jun 2020 08:21:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:52: 7000000 INFO @ Tue, 16 Jun 2020 08:21:55: 3000000 INFO @ Tue, 16 Jun 2020 08:22:00: 8000000 INFO @ Tue, 16 Jun 2020 08:22:03: 4000000 INFO @ Tue, 16 Jun 2020 08:22:07: 9000000 INFO @ Tue, 16 Jun 2020 08:22:11: 5000000 INFO @ Tue, 16 Jun 2020 08:22:15: 10000000 INFO @ Tue, 16 Jun 2020 08:22:15: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:22:15: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:22:15: #1 total tags in treatment: 10037686 INFO @ Tue, 16 Jun 2020 08:22:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:15: #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 08:22:15: #1 tags after filtering in treatment: 10037686 INFO @ Tue, 16 Jun 2020 08:22:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:15: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:22:16: #2 number of paired peaks: 3222 INFO @ Tue, 16 Jun 2020 08:22:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:16: #2 predicted fragment length is 406 bps INFO @ Tue, 16 Jun 2020 08:22:16: #2 alternative fragment length(s) may be 406 bps INFO @ Tue, 16 Jun 2020 08:22:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.10_model.r INFO @ Tue, 16 Jun 2020 08:22:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:22:19: 6000000 INFO @ Tue, 16 Jun 2020 08:22:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:26: 7000000 INFO @ Tue, 16 Jun 2020 08:22:34: 8000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:22:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.05_summits.bed INFO @ Tue, 16 Jun 2020 08:22:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6311 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:22:41: 9000000 INFO @ Tue, 16 Jun 2020 08:22:48: 10000000 INFO @ Tue, 16 Jun 2020 08:22:48: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:22:48: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:22:48: #1 total tags in treatment: 10037686 INFO @ Tue, 16 Jun 2020 08:22:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:48: #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 08:22:48: #1 tags after filtering in treatment: 10037686 INFO @ Tue, 16 Jun 2020 08:22:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:49: #2 number of paired peaks: 3222 INFO @ Tue, 16 Jun 2020 08:22:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:49: #2 predicted fragment length is 406 bps INFO @ Tue, 16 Jun 2020 08:22:49: #2 alternative fragment length(s) may be 406 bps INFO @ Tue, 16 Jun 2020 08:22:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.20_model.r INFO @ Tue, 16 Jun 2020 08:22:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:22:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:23:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.10_summits.bed INFO @ Tue, 16 Jun 2020 08:23:07: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5115 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:23:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:23:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769997/SRX1769997.20_summits.bed INFO @ Tue, 16 Jun 2020 08:23:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3849 records, 4 fields): 6 millis CompletedMACS2peakCalling