Job ID = 6368698 SRX = SRX5402723 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:32:16 prefetch.2.10.7: 1) Downloading 'SRR8602957'... 2020-06-16T00:32:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:32:57 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:32:58 prefetch.2.10.7: 'SRR8602957' is valid 2020-06-16T00:32:58 prefetch.2.10.7: 1) 'SRR8602957' was downloaded successfully 2020-06-16T00:32:58 prefetch.2.10.7: 'SRR8602957' has 0 unresolved dependencies Read 5092384 spots for SRR8602957/SRR8602957.sra Written 5092384 spots for SRR8602957/SRR8602957.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: 00:01:02 5092384 reads; of these: 5092384 (100.00%) were unpaired; of these: 51546 (1.01%) aligned 0 times 4503451 (88.44%) aligned exactly 1 time 537387 (10.55%) aligned >1 times 98.99% overall alignment rate Time searching: 00:01:02 Overall time: 00:01:02 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_rmdupse_core] 1269662 / 5040838 = 0.2519 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 09:35:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.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 09:35:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:46: 1000000 INFO @ Tue, 16 Jun 2020 09:35:51: 2000000 INFO @ Tue, 16 Jun 2020 09:35:56: 3000000 INFO @ Tue, 16 Jun 2020 09:36:00: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:36:00: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:36:00: #1 total tags in treatment: 3771176 INFO @ Tue, 16 Jun 2020 09:36:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:00: #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 09:36:00: #1 tags after filtering in treatment: 3771176 INFO @ Tue, 16 Jun 2020 09:36:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:00: #2 number of paired peaks: 4313 INFO @ Tue, 16 Jun 2020 09:36:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:00: #2 predicted fragment length is 167 bps INFO @ Tue, 16 Jun 2020 09:36:00: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 16 Jun 2020 09:36:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.05_model.r INFO @ Tue, 16 Jun 2020 09:36:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:00: #3 Pre-compute pvalue-qvalue table... 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 09:36:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.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 09:36:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:16: 1000000 INFO @ Tue, 16 Jun 2020 09:36:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.05_summits.bed INFO @ Tue, 16 Jun 2020 09:36:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4829 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:21: 2000000 INFO @ Tue, 16 Jun 2020 09:36:25: 3000000 INFO @ Tue, 16 Jun 2020 09:36:29: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:36:29: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:36:29: #1 total tags in treatment: 3771176 INFO @ Tue, 16 Jun 2020 09:36:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:29: #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 09:36:29: #1 tags after filtering in treatment: 3771176 INFO @ Tue, 16 Jun 2020 09:36:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:30: #2 number of paired peaks: 4313 INFO @ Tue, 16 Jun 2020 09:36:30: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:30: #2 predicted fragment length is 167 bps INFO @ Tue, 16 Jun 2020 09:36:30: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 16 Jun 2020 09:36:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.10_model.r INFO @ Tue, 16 Jun 2020 09:36:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:30: #3 Pre-compute pvalue-qvalue table... 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 09:36:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.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 09:36:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.10_summits.bed INFO @ Tue, 16 Jun 2020 09:36:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4014 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:46: 1000000 INFO @ Tue, 16 Jun 2020 09:36:50: 2000000 INFO @ Tue, 16 Jun 2020 09:36:55: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:36:59: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:36:59: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:36:59: #1 total tags in treatment: 3771176 INFO @ Tue, 16 Jun 2020 09:36:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:59: #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 09:36:59: #1 tags after filtering in treatment: 3771176 INFO @ Tue, 16 Jun 2020 09:36:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:59: #2 number of paired peaks: 4313 INFO @ Tue, 16 Jun 2020 09:36:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:00: #2 predicted fragment length is 167 bps INFO @ Tue, 16 Jun 2020 09:37:00: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 16 Jun 2020 09:37:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.20_model.r INFO @ Tue, 16 Jun 2020 09:37:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:37:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402723/SRX5402723.20_summits.bed INFO @ Tue, 16 Jun 2020 09:37:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3216 records, 4 fields): 4 millis CompletedMACS2peakCalling