Job ID = 6367413 SRX = SRX331172 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:26:51 prefetch.2.10.7: 1) Downloading 'SRR947404'... 2020-06-15T23:26:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:27:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:27:46 prefetch.2.10.7: 'SRR947404' is valid 2020-06-15T23:27:46 prefetch.2.10.7: 1) 'SRR947404' was downloaded successfully Read 8980981 spots for SRR947404/SRR947404.sra Written 8980981 spots for SRR947404/SRR947404.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: 00:01:19 8980981 reads; of these: 8980981 (100.00%) were unpaired; of these: 379752 (4.23%) aligned 0 times 7530998 (83.85%) aligned exactly 1 time 1070231 (11.92%) aligned >1 times 95.77% overall alignment rate Time searching: 00:01:19 Overall time: 00:01:19 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] 1768873 / 8601229 = 0.2057 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 08:31:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.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 08:31:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:39: 1000000 INFO @ Tue, 16 Jun 2020 08:31:45: 2000000 INFO @ Tue, 16 Jun 2020 08:31:50: 3000000 INFO @ Tue, 16 Jun 2020 08:31:56: 4000000 INFO @ Tue, 16 Jun 2020 08:32:01: 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 08:32:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.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 08:32:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:07: 6000000 INFO @ Tue, 16 Jun 2020 08:32:10: 1000000 INFO @ Tue, 16 Jun 2020 08:32:12: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:32:12: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:32:12: #1 total tags in treatment: 6832356 INFO @ Tue, 16 Jun 2020 08:32:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:12: #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 08:32:12: #1 tags after filtering in treatment: 6832356 INFO @ Tue, 16 Jun 2020 08:32:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:12: #2 number of paired peaks: 2171 INFO @ Tue, 16 Jun 2020 08:32:12: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:12: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:12: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:12: #2 predicted fragment length is 172 bps INFO @ Tue, 16 Jun 2020 08:32:12: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 16 Jun 2020 08:32:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.05_model.r INFO @ Tue, 16 Jun 2020 08:32:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:16: 2000000 INFO @ Tue, 16 Jun 2020 08:32:22: 3000000 INFO @ Tue, 16 Jun 2020 08:32:28: 4000000 INFO @ Tue, 16 Jun 2020 08:32:31: #3 Call peaks for each chromosome... 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 08:32:33: 5000000 INFO @ Tue, 16 Jun 2020 08:32:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.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 08:32:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:39: 6000000 INFO @ Tue, 16 Jun 2020 08:32:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.05_summits.bed INFO @ Tue, 16 Jun 2020 08:32:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7439 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:32:40: 1000000 INFO @ Tue, 16 Jun 2020 08:32:45: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:32:45: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:32:45: #1 total tags in treatment: 6832356 INFO @ Tue, 16 Jun 2020 08:32:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:45: #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 08:32:45: #1 tags after filtering in treatment: 6832356 INFO @ Tue, 16 Jun 2020 08:32:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:45: #2 number of paired peaks: 2171 INFO @ Tue, 16 Jun 2020 08:32:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:45: #2 predicted fragment length is 172 bps INFO @ Tue, 16 Jun 2020 08:32:45: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 16 Jun 2020 08:32:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.10_model.r INFO @ Tue, 16 Jun 2020 08:32:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:47: 2000000 INFO @ Tue, 16 Jun 2020 08:32:54: 3000000 INFO @ Tue, 16 Jun 2020 08:33:00: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:33:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:06: 5000000 INFO @ Tue, 16 Jun 2020 08:33:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.10_summits.bed INFO @ Tue, 16 Jun 2020 08:33:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5384 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:33:13: 6000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:33:18: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:33:18: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:33:18: #1 total tags in treatment: 6832356 INFO @ Tue, 16 Jun 2020 08:33:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:18: #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 08:33:18: #1 tags after filtering in treatment: 6832356 INFO @ Tue, 16 Jun 2020 08:33:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:19: #2 number of paired peaks: 2171 INFO @ Tue, 16 Jun 2020 08:33:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:19: #2 predicted fragment length is 172 bps INFO @ Tue, 16 Jun 2020 08:33:19: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 16 Jun 2020 08:33:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.20_model.r INFO @ Tue, 16 Jun 2020 08:33:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:33:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331172/SRX331172.20_summits.bed INFO @ Tue, 16 Jun 2020 08:33:45: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (3583 records, 4 fields): 5 millis CompletedMACS2peakCalling