Job ID = 6367516 SRX = SRX331272 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:29:35 prefetch.2.10.7: 1) Downloading 'SRR947507'... 2020-06-15T23:29:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:30:26 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:30:26 prefetch.2.10.7: 'SRR947507' is valid 2020-06-15T23:30:26 prefetch.2.10.7: 1) 'SRR947507' was downloaded successfully Read 8199658 spots for SRR947507/SRR947507.sra Written 8199658 spots for SRR947507/SRR947507.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: 00:00:56 8199658 reads; of these: 8199658 (100.00%) were unpaired; of these: 2780984 (33.92%) aligned 0 times 4709056 (57.43%) aligned exactly 1 time 709618 (8.65%) aligned >1 times 66.08% overall alignment rate Time searching: 00:00:56 Overall time: 00:00:56 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] 2139403 / 5418674 = 0.3948 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 08:33:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.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 08:33:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:06: 1000000 INFO @ Tue, 16 Jun 2020 08:33:11: 2000000 INFO @ Tue, 16 Jun 2020 08:33:15: 3000000 INFO @ Tue, 16 Jun 2020 08:33:16: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:33:16: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:33:16: #1 total tags in treatment: 3279271 INFO @ Tue, 16 Jun 2020 08:33:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:16: #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 08:33:16: #1 tags after filtering in treatment: 3279271 INFO @ Tue, 16 Jun 2020 08:33:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:16: #2 number of paired peaks: 1735 INFO @ Tue, 16 Jun 2020 08:33:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:16: #2 predicted fragment length is 145 bps INFO @ Tue, 16 Jun 2020 08:33:16: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 16 Jun 2020 08:33:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.05_model.r INFO @ Tue, 16 Jun 2020 08:33:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:33:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.05_summits.bed INFO @ Tue, 16 Jun 2020 08:33:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5024 records, 4 fields): 5 millis CompletedMACS2peakCalling 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 08:33:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.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 08:33:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:37: 1000000 INFO @ Tue, 16 Jun 2020 08:33:42: 2000000 INFO @ Tue, 16 Jun 2020 08:33:47: 3000000 INFO @ Tue, 16 Jun 2020 08:33:48: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:33:48: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:33:48: #1 total tags in treatment: 3279271 INFO @ Tue, 16 Jun 2020 08:33:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:48: #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 08:33:48: #1 tags after filtering in treatment: 3279271 INFO @ Tue, 16 Jun 2020 08:33:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:49: #2 number of paired peaks: 1735 INFO @ Tue, 16 Jun 2020 08:33:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:49: #2 predicted fragment length is 145 bps INFO @ Tue, 16 Jun 2020 08:33:49: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 16 Jun 2020 08:33:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.10_model.r INFO @ Tue, 16 Jun 2020 08:33:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:33:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.10_summits.bed INFO @ Tue, 16 Jun 2020 08:34:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3416 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 08:34:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.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 08:34:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:07: 1000000 INFO @ Tue, 16 Jun 2020 08:34:12: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:34:17: 3000000 INFO @ Tue, 16 Jun 2020 08:34:18: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:34:18: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:34:18: #1 total tags in treatment: 3279271 INFO @ Tue, 16 Jun 2020 08:34:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:18: #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 08:34:18: #1 tags after filtering in treatment: 3279271 INFO @ Tue, 16 Jun 2020 08:34:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:18: #2 number of paired peaks: 1735 INFO @ Tue, 16 Jun 2020 08:34:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:18: #2 predicted fragment length is 145 bps INFO @ Tue, 16 Jun 2020 08:34:18: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 16 Jun 2020 08:34:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.20_model.r INFO @ Tue, 16 Jun 2020 08:34:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:34:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331272/SRX331272.20_summits.bed INFO @ Tue, 16 Jun 2020 08:34:30: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1699 records, 4 fields): 3 millis CompletedMACS2peakCalling