Job ID = 6366224 SRX = SRX080078 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:22:14 prefetch.2.10.7: 1) Downloading 'SRR298898'... 2020-06-15T22:22:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:22:51 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:22:51 prefetch.2.10.7: 'SRR298898' is valid 2020-06-15T22:22:51 prefetch.2.10.7: 1) 'SRR298898' was downloaded successfully Read 5303031 spots for SRR298898/SRR298898.sra Written 5303031 spots for SRR298898/SRR298898.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: 00:00:32 5303031 reads; of these: 5303031 (100.00%) were unpaired; of these: 2257188 (42.56%) aligned 0 times 2664810 (50.25%) aligned exactly 1 time 381033 (7.19%) aligned >1 times 57.44% overall alignment rate Time searching: 00:00:32 Overall time: 00:00:32 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] 1065197 / 3045843 = 0.3497 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 07:24:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.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 07:24:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:24:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:25:00: 1000000 INFO @ Tue, 16 Jun 2020 07:25:05: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:25:05: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:25:05: #1 total tags in treatment: 1980646 INFO @ Tue, 16 Jun 2020 07:25:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:25:05: #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 07:25:05: #1 tags after filtering in treatment: 1980646 INFO @ Tue, 16 Jun 2020 07:25:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:25:05: #1 finished! INFO @ Tue, 16 Jun 2020 07:25:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:25:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:25:06: #2 number of paired peaks: 4062 INFO @ Tue, 16 Jun 2020 07:25:06: start model_add_line... INFO @ Tue, 16 Jun 2020 07:25:06: start X-correlation... INFO @ Tue, 16 Jun 2020 07:25:06: end of X-cor INFO @ Tue, 16 Jun 2020 07:25:06: #2 finished! INFO @ Tue, 16 Jun 2020 07:25:06: #2 predicted fragment length is 135 bps INFO @ Tue, 16 Jun 2020 07:25:06: #2 alternative fragment length(s) may be 135 bps INFO @ Tue, 16 Jun 2020 07:25:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.05_model.r INFO @ Tue, 16 Jun 2020 07:25:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:25:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:25:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:25:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:25:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:25:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.05_summits.bed INFO @ Tue, 16 Jun 2020 07:25:14: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5769 records, 4 fields): 8 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 07:25:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.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 07:25:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:25:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:25:30: 1000000 INFO @ Tue, 16 Jun 2020 07:25:36: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:25:36: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:25:36: #1 total tags in treatment: 1980646 INFO @ Tue, 16 Jun 2020 07:25:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:25:36: #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 07:25:36: #1 tags after filtering in treatment: 1980646 INFO @ Tue, 16 Jun 2020 07:25:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:25:36: #1 finished! INFO @ Tue, 16 Jun 2020 07:25:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:25:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:25:36: #2 number of paired peaks: 4062 INFO @ Tue, 16 Jun 2020 07:25:36: start model_add_line... INFO @ Tue, 16 Jun 2020 07:25:37: start X-correlation... INFO @ Tue, 16 Jun 2020 07:25:37: end of X-cor INFO @ Tue, 16 Jun 2020 07:25:37: #2 finished! INFO @ Tue, 16 Jun 2020 07:25:37: #2 predicted fragment length is 135 bps INFO @ Tue, 16 Jun 2020 07:25:37: #2 alternative fragment length(s) may be 135 bps INFO @ Tue, 16 Jun 2020 07:25:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.10_model.r INFO @ Tue, 16 Jun 2020 07:25:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:25:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:25:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:25:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:25:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:25:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.10_summits.bed INFO @ Tue, 16 Jun 2020 07:25:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4135 records, 4 fields): 6 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 07:25:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.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 07:25:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:25:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:25:59: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:26:04: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:26:04: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:26:04: #1 total tags in treatment: 1980646 INFO @ Tue, 16 Jun 2020 07:26:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:26:04: #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 07:26:04: #1 tags after filtering in treatment: 1980646 INFO @ Tue, 16 Jun 2020 07:26:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:26:04: #1 finished! INFO @ Tue, 16 Jun 2020 07:26:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:26:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:26:04: #2 number of paired peaks: 4062 INFO @ Tue, 16 Jun 2020 07:26:04: start model_add_line... INFO @ Tue, 16 Jun 2020 07:26:04: start X-correlation... INFO @ Tue, 16 Jun 2020 07:26:04: end of X-cor INFO @ Tue, 16 Jun 2020 07:26:04: #2 finished! INFO @ Tue, 16 Jun 2020 07:26:04: #2 predicted fragment length is 135 bps INFO @ Tue, 16 Jun 2020 07:26:04: #2 alternative fragment length(s) may be 135 bps INFO @ Tue, 16 Jun 2020 07:26:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.20_model.r INFO @ Tue, 16 Jun 2020 07:26:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:26:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:26:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:26:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:26:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:26:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080078/SRX080078.20_summits.bed INFO @ Tue, 16 Jun 2020 07:26:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2919 records, 4 fields): 5 millis CompletedMACS2peakCalling