Job ID = 6366796 SRX = SRX233461 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:03:53 prefetch.2.10.7: 1) Downloading 'SRR701517'... 2020-06-15T23:03:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:04:20 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:04:20 prefetch.2.10.7: 'SRR701517' is valid 2020-06-15T23:04:20 prefetch.2.10.7: 1) 'SRR701517' was downloaded successfully Read 7035155 spots for SRR701517/SRR701517.sra Written 7035155 spots for SRR701517/SRR701517.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: 00:01:07 7035155 reads; of these: 7035155 (100.00%) were unpaired; of these: 747766 (10.63%) aligned 0 times 5500375 (78.18%) aligned exactly 1 time 787014 (11.19%) aligned >1 times 89.37% overall alignment rate Time searching: 00:01:07 Overall time: 00:01:07 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] 1147893 / 6287389 = 0.1826 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 08:07:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.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 08:07:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:32: 1000000 INFO @ Tue, 16 Jun 2020 08:07:37: 2000000 INFO @ Tue, 16 Jun 2020 08:07:42: 3000000 INFO @ Tue, 16 Jun 2020 08:07:47: 4000000 INFO @ Tue, 16 Jun 2020 08:07:52: 5000000 INFO @ Tue, 16 Jun 2020 08:07:53: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:07:53: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:07:53: #1 total tags in treatment: 5139496 INFO @ Tue, 16 Jun 2020 08:07:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:53: #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 08:07:53: #1 tags after filtering in treatment: 5139496 INFO @ Tue, 16 Jun 2020 08:07:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:54: #2 number of paired peaks: 3288 INFO @ Tue, 16 Jun 2020 08:07:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:54: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 08:07:54: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 16 Jun 2020 08:07:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.05_model.r INFO @ Tue, 16 Jun 2020 08:07:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:54: #3 Pre-compute pvalue-qvalue table... 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 08:07:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.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 08:07:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:03: 1000000 INFO @ Tue, 16 Jun 2020 08:08:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:08: 2000000 INFO @ Tue, 16 Jun 2020 08:08:13: 3000000 INFO @ Tue, 16 Jun 2020 08:08:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.05_summits.bed INFO @ Tue, 16 Jun 2020 08:08:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (8057 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:08:18: 4000000 INFO @ Tue, 16 Jun 2020 08:08:23: 5000000 INFO @ Tue, 16 Jun 2020 08:08:24: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:08:24: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:08:24: #1 total tags in treatment: 5139496 INFO @ Tue, 16 Jun 2020 08:08:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:24: #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 08:08:24: #1 tags after filtering in treatment: 5139496 INFO @ Tue, 16 Jun 2020 08:08:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:24: #2 number of paired peaks: 3288 INFO @ Tue, 16 Jun 2020 08:08:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:24: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 08:08:24: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 16 Jun 2020 08:08:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.10_model.r INFO @ Tue, 16 Jun 2020 08:08:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:24: #3 Pre-compute pvalue-qvalue table... 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 08:08:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.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 08:08:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:33: 1000000 INFO @ Tue, 16 Jun 2020 08:08:38: 2000000 INFO @ Tue, 16 Jun 2020 08:08:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:43: 3000000 INFO @ Tue, 16 Jun 2020 08:08:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.10_summits.bed INFO @ Tue, 16 Jun 2020 08:08:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5760 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:08:48: 4000000 INFO @ Tue, 16 Jun 2020 08:08:53: 5000000 INFO @ Tue, 16 Jun 2020 08:08:54: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:08:54: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:08:54: #1 total tags in treatment: 5139496 INFO @ Tue, 16 Jun 2020 08:08:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:54: #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 08:08:54: #1 tags after filtering in treatment: 5139496 INFO @ Tue, 16 Jun 2020 08:08:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:55: #2 number of paired peaks: 3288 INFO @ Tue, 16 Jun 2020 08:08:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:55: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 08:08:55: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 16 Jun 2020 08:08:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.20_model.r INFO @ Tue, 16 Jun 2020 08:08:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:09:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX233461/SRX233461.20_summits.bed INFO @ Tue, 16 Jun 2020 08:09:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3734 records, 4 fields): 5 millis CompletedMACS2peakCalling