Job ID = 6368130 SRX = SRX467177 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:56:42 prefetch.2.10.7: 1) Downloading 'SRR1164601'... 2020-06-15T23:56:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:57:37 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:57:37 prefetch.2.10.7: 'SRR1164601' is valid 2020-06-15T23:57:37 prefetch.2.10.7: 1) 'SRR1164601' was downloaded successfully Read 8886714 spots for SRR1164601/SRR1164601.sra Written 8886714 spots for SRR1164601/SRR1164601.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: 00:01:11 8886714 reads; of these: 8886714 (100.00%) were unpaired; of these: 2902415 (32.66%) aligned 0 times 5061392 (56.95%) aligned exactly 1 time 922907 (10.39%) aligned >1 times 67.34% overall alignment rate Time searching: 00:01:11 Overall time: 00:01:11 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] 847260 / 5984299 = 0.1416 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 09:00:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.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 09:00:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:00:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:00: 1000000 INFO @ Tue, 16 Jun 2020 09:01:06: 2000000 INFO @ Tue, 16 Jun 2020 09:01:12: 3000000 INFO @ Tue, 16 Jun 2020 09:01:18: 4000000 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 09:01:23: 5000000 INFO @ Tue, 16 Jun 2020 09:01:24: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 09:01:24: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 09:01:24: #1 total tags in treatment: 5137039 INFO @ Tue, 16 Jun 2020 09:01:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:01:24: #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 09:01:24: #1 tags after filtering in treatment: 5137039 INFO @ Tue, 16 Jun 2020 09:01:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:01:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:01:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:01:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:01:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.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 09:01:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:25: #2 number of paired peaks: 1704 INFO @ Tue, 16 Jun 2020 09:01:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:01:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:01:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:01:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:01:25: #2 predicted fragment length is 139 bps INFO @ Tue, 16 Jun 2020 09:01:25: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 16 Jun 2020 09:01:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.05_model.r INFO @ Tue, 16 Jun 2020 09:01:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:01:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:01:30: 1000000 INFO @ Tue, 16 Jun 2020 09:01:36: 2000000 INFO @ Tue, 16 Jun 2020 09:01:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:01:42: 3000000 INFO @ Tue, 16 Jun 2020 09:01:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:01:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:01:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.05_summits.bed INFO @ Tue, 16 Jun 2020 09:01:45: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5203 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:01:48: 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 09:01:54: 5000000 INFO @ Tue, 16 Jun 2020 09:01:54: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 09:01:54: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 09:01:54: #1 total tags in treatment: 5137039 INFO @ Tue, 16 Jun 2020 09:01:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:01:54: #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 09:01:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.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 09:01:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:54: #1 tags after filtering in treatment: 5137039 INFO @ Tue, 16 Jun 2020 09:01:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:01:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:01:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:01:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:01:55: #2 number of paired peaks: 1704 INFO @ Tue, 16 Jun 2020 09:01:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:01:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:01:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:01:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:01:55: #2 predicted fragment length is 139 bps INFO @ Tue, 16 Jun 2020 09:01:55: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 16 Jun 2020 09:01:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.10_model.r INFO @ Tue, 16 Jun 2020 09:01:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:01:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:01:59: 1000000 INFO @ Tue, 16 Jun 2020 09:02:04: 2000000 INFO @ Tue, 16 Jun 2020 09:02:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:02:09: 3000000 INFO @ Tue, 16 Jun 2020 09:02:14: 4000000 INFO @ Tue, 16 Jun 2020 09:02:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:02:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:02:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.10_summits.bed INFO @ Tue, 16 Jun 2020 09:02:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3747 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:02:19: 5000000 INFO @ Tue, 16 Jun 2020 09:02:20: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 09:02:20: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 09:02:20: #1 total tags in treatment: 5137039 INFO @ Tue, 16 Jun 2020 09:02:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:20: #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 09:02:20: #1 tags after filtering in treatment: 5137039 INFO @ Tue, 16 Jun 2020 09:02:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:02:20: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:21: #2 number of paired peaks: 1704 INFO @ Tue, 16 Jun 2020 09:02:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:21: #2 predicted fragment length is 139 bps INFO @ Tue, 16 Jun 2020 09:02:21: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 16 Jun 2020 09:02:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.20_model.r INFO @ Tue, 16 Jun 2020 09:02:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:02:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:02:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:02:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:02:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX467177/SRX467177.20_summits.bed INFO @ Tue, 16 Jun 2020 09:02:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2494 records, 4 fields): 5 millis CompletedMACS2peakCalling