Job ID = 6367336 SRX = SRX331098 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:17:16 prefetch.2.10.7: 1) Downloading 'SRR947328'... 2020-06-15T23:17:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:17:50 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:17:51 prefetch.2.10.7: 'SRR947328' is valid 2020-06-15T23:17:51 prefetch.2.10.7: 1) 'SRR947328' was downloaded successfully Read 9300667 spots for SRR947328/SRR947328.sra Written 9300667 spots for SRR947328/SRR947328.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: 00:01:24 9300667 reads; of these: 9300667 (100.00%) were unpaired; of these: 1479395 (15.91%) aligned 0 times 6714922 (72.20%) aligned exactly 1 time 1106350 (11.90%) aligned >1 times 84.09% overall alignment rate Time searching: 00:01:24 Overall time: 00:01:24 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] 1012906 / 7821272 = 0.1295 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 08:22:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.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 08:22:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:22:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:22:06: 1000000 INFO @ Tue, 16 Jun 2020 08:22:10: 2000000 INFO @ Tue, 16 Jun 2020 08:22:14: 3000000 INFO @ Tue, 16 Jun 2020 08:22:19: 4000000 INFO @ Tue, 16 Jun 2020 08:22:23: 5000000 INFO @ Tue, 16 Jun 2020 08:22:27: 6000000 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 08:22:30: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:22:30: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:22:30: #1 total tags in treatment: 6808366 INFO @ Tue, 16 Jun 2020 08:22:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:30: #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 08:22:30: #1 tags after filtering in treatment: 6808366 INFO @ Tue, 16 Jun 2020 08:22:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:31: #2 number of paired peaks: 1198 INFO @ Tue, 16 Jun 2020 08:22:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:31: #2 predicted fragment length is 162 bps INFO @ Tue, 16 Jun 2020 08:22:31: #2 alternative fragment length(s) may be 162 bps INFO @ Tue, 16 Jun 2020 08:22:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.05_model.r INFO @ Tue, 16 Jun 2020 08:22:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:22:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.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 08:22:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:22:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:22:36: 1000000 INFO @ Tue, 16 Jun 2020 08:22:40: 2000000 INFO @ Tue, 16 Jun 2020 08:22:44: 3000000 INFO @ Tue, 16 Jun 2020 08:22:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:48: 4000000 INFO @ Tue, 16 Jun 2020 08:22:53: 5000000 INFO @ Tue, 16 Jun 2020 08:22:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.05_summits.bed INFO @ Tue, 16 Jun 2020 08:22:54: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6324 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:22:57: 6000000 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 08:23:00: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:23:00: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:23:00: #1 total tags in treatment: 6808366 INFO @ Tue, 16 Jun 2020 08:23:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:00: #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 08:23:00: #1 tags after filtering in treatment: 6808366 INFO @ Tue, 16 Jun 2020 08:23:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:23:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:01: #2 number of paired peaks: 1198 INFO @ Tue, 16 Jun 2020 08:23:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:01: #2 predicted fragment length is 162 bps INFO @ Tue, 16 Jun 2020 08:23:01: #2 alternative fragment length(s) may be 162 bps INFO @ Tue, 16 Jun 2020 08:23:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.10_model.r INFO @ Tue, 16 Jun 2020 08:23:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:23:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.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 08:23:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:23:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:23:06: 1000000 INFO @ Tue, 16 Jun 2020 08:23:10: 2000000 INFO @ Tue, 16 Jun 2020 08:23:14: 3000000 INFO @ Tue, 16 Jun 2020 08:23:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:23:18: 4000000 INFO @ Tue, 16 Jun 2020 08:23:23: 5000000 INFO @ Tue, 16 Jun 2020 08:23:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.10_summits.bed INFO @ Tue, 16 Jun 2020 08:23:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4037 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:23:27: 6000000 INFO @ Tue, 16 Jun 2020 08:23:30: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:23:30: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:23:30: #1 total tags in treatment: 6808366 INFO @ Tue, 16 Jun 2020 08:23:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:30: #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 08:23:30: #1 tags after filtering in treatment: 6808366 INFO @ Tue, 16 Jun 2020 08:23:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:23:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:31: #2 number of paired peaks: 1198 INFO @ Tue, 16 Jun 2020 08:23:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:31: #2 predicted fragment length is 162 bps INFO @ Tue, 16 Jun 2020 08:23:31: #2 alternative fragment length(s) may be 162 bps INFO @ Tue, 16 Jun 2020 08:23:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.20_model.r INFO @ Tue, 16 Jun 2020 08:23:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:31: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:23:46: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:23:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331098/SRX331098.20_summits.bed INFO @ Tue, 16 Jun 2020 08:23:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2091 records, 4 fields): 4 millis CompletedMACS2peakCalling