Job ID = 6367969 SRX = SRX4456928 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:50:37 prefetch.2.10.7: 1) Downloading 'SRR7591869'... 2020-06-15T23:50:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:40 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:41 prefetch.2.10.7: 'SRR7591869' is valid 2020-06-15T23:51:41 prefetch.2.10.7: 1) 'SRR7591869' was downloaded successfully Read 8674234 spots for SRR7591869/SRR7591869.sra Written 8674234 spots for SRR7591869/SRR7591869.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: 00:01:57 8674234 reads; of these: 8674234 (100.00%) were unpaired; of these: 1572213 (18.13%) aligned 0 times 6113554 (70.48%) aligned exactly 1 time 988467 (11.40%) aligned >1 times 81.87% overall alignment rate Time searching: 00:01:57 Overall time: 00:01:57 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] 717278 / 7102021 = 0.1010 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 08:56:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.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 08:56:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:17: 1000000 INFO @ Tue, 16 Jun 2020 08:56:22: 2000000 INFO @ Tue, 16 Jun 2020 08:56:28: 3000000 INFO @ Tue, 16 Jun 2020 08:56:33: 4000000 INFO @ Tue, 16 Jun 2020 08:56:38: 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 08:56:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.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 08:56:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:43: 6000000 INFO @ Tue, 16 Jun 2020 08:56:46: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:56:46: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:56:46: #1 total tags in treatment: 6384743 INFO @ Tue, 16 Jun 2020 08:56:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:56:46: #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 08:56:46: #1 tags after filtering in treatment: 6384743 INFO @ Tue, 16 Jun 2020 08:56:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:56:46: #1 finished! INFO @ Tue, 16 Jun 2020 08:56:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:56:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:56:46: #2 number of paired peaks: 2416 INFO @ Tue, 16 Jun 2020 08:56:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:56:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:56:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:56:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:56:46: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:56:46: #2 alternative fragment length(s) may be 4,132 bps INFO @ Tue, 16 Jun 2020 08:56:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.05_model.r INFO @ Tue, 16 Jun 2020 08:56:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:56:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:56:47: 1000000 INFO @ Tue, 16 Jun 2020 08:56:53: 2000000 INFO @ Tue, 16 Jun 2020 08:56:58: 3000000 INFO @ Tue, 16 Jun 2020 08:57:03: 4000000 INFO @ Tue, 16 Jun 2020 08:57:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:57:08: 5000000 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 08:57:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:57:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:57:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.05_summits.bed INFO @ Tue, 16 Jun 2020 08:57:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3810 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:57:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.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 08:57:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:57:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:57:14: 6000000 INFO @ Tue, 16 Jun 2020 08:57:16: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:57:16: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:57:16: #1 total tags in treatment: 6384743 INFO @ Tue, 16 Jun 2020 08:57:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:16: #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 08:57:16: #1 tags after filtering in treatment: 6384743 INFO @ Tue, 16 Jun 2020 08:57:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:16: #2 number of paired peaks: 2416 INFO @ Tue, 16 Jun 2020 08:57:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:17: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:57:17: #2 alternative fragment length(s) may be 4,132 bps INFO @ Tue, 16 Jun 2020 08:57:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.10_model.r INFO @ Tue, 16 Jun 2020 08:57:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:57:19: 1000000 INFO @ Tue, 16 Jun 2020 08:57:25: 2000000 INFO @ Tue, 16 Jun 2020 08:57:31: 3000000 INFO @ Tue, 16 Jun 2020 08:57:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:57:38: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:57:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:57:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:57:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.10_summits.bed INFO @ Tue, 16 Jun 2020 08:57:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1918 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:57:44: 5000000 INFO @ Tue, 16 Jun 2020 08:57:51: 6000000 INFO @ Tue, 16 Jun 2020 08:57:53: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:57:53: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:57:53: #1 total tags in treatment: 6384743 INFO @ Tue, 16 Jun 2020 08:57:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:53: #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 08:57:53: #1 tags after filtering in treatment: 6384743 INFO @ Tue, 16 Jun 2020 08:57:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:54: #2 number of paired peaks: 2416 INFO @ Tue, 16 Jun 2020 08:57:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:54: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:57:54: #2 alternative fragment length(s) may be 4,132 bps INFO @ Tue, 16 Jun 2020 08:57:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.20_model.r INFO @ Tue, 16 Jun 2020 08:57:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:58:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456928/SRX4456928.20_summits.bed INFO @ Tue, 16 Jun 2020 08:58:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (712 records, 4 fields): 3 millis CompletedMACS2peakCalling