Job ID = 6366531 SRX = SRX1769986 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:49:07 prefetch.2.10.7: 1) Downloading 'SRR3535763'... 2020-06-15T22:49:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:49:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:49:47 prefetch.2.10.7: 'SRR3535763' is valid 2020-06-15T22:49:47 prefetch.2.10.7: 1) 'SRR3535763' was downloaded successfully Read 7949569 spots for SRR3535763/SRR3535763.sra Written 7949569 spots for SRR3535763/SRR3535763.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: 00:00:01 Multiseed full-index search: 00:01:31 7949569 reads; of these: 7949569 (100.00%) were unpaired; of these: 2388709 (30.05%) aligned 0 times 4830438 (60.76%) aligned exactly 1 time 730422 (9.19%) aligned >1 times 69.95% overall alignment rate Time searching: 00:01:32 Overall time: 00:01:32 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] 1643650 / 5560860 = 0.2956 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 07:53:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.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 07:53:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:39: 1000000 INFO @ Tue, 16 Jun 2020 07:53:45: 2000000 INFO @ Tue, 16 Jun 2020 07:53:51: 3000000 INFO @ Tue, 16 Jun 2020 07:53:57: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:53:57: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:53:57: #1 total tags in treatment: 3917210 INFO @ Tue, 16 Jun 2020 07:53:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:57: #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 07:53:57: #1 tags after filtering in treatment: 3917210 INFO @ Tue, 16 Jun 2020 07:53:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:57: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:57: #2 number of paired peaks: 1582 INFO @ Tue, 16 Jun 2020 07:53:57: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:57: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:57: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:57: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:57: #2 predicted fragment length is 216 bps INFO @ Tue, 16 Jun 2020 07:53:57: #2 alternative fragment length(s) may be 216 bps INFO @ Tue, 16 Jun 2020 07:53:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.05_model.r INFO @ Tue, 16 Jun 2020 07:53:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:57: #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 07:54:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.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 07:54:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:54:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:54:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:09: 1000000 INFO @ Tue, 16 Jun 2020 07:54:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.05_summits.bed INFO @ Tue, 16 Jun 2020 07:54:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3457 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:54:15: 2000000 INFO @ Tue, 16 Jun 2020 07:54:22: 3000000 INFO @ Tue, 16 Jun 2020 07:54:28: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:54:28: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:54:28: #1 total tags in treatment: 3917210 INFO @ Tue, 16 Jun 2020 07:54:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:54:28: #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 07:54:28: #1 tags after filtering in treatment: 3917210 INFO @ Tue, 16 Jun 2020 07:54:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:54:28: #1 finished! INFO @ Tue, 16 Jun 2020 07:54:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:54:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:54:28: #2 number of paired peaks: 1582 INFO @ Tue, 16 Jun 2020 07:54:28: start model_add_line... INFO @ Tue, 16 Jun 2020 07:54:28: start X-correlation... INFO @ Tue, 16 Jun 2020 07:54:28: end of X-cor INFO @ Tue, 16 Jun 2020 07:54:28: #2 finished! INFO @ Tue, 16 Jun 2020 07:54:28: #2 predicted fragment length is 216 bps INFO @ Tue, 16 Jun 2020 07:54:28: #2 alternative fragment length(s) may be 216 bps INFO @ Tue, 16 Jun 2020 07:54:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.10_model.r INFO @ Tue, 16 Jun 2020 07:54:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:54:28: #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 07:54:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.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 07:54:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:54:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:54:38: 1000000 INFO @ Tue, 16 Jun 2020 07:54:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.10_summits.bed INFO @ Tue, 16 Jun 2020 07:54:44: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1974 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:54:44: 2000000 INFO @ Tue, 16 Jun 2020 07:54:50: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:54:56: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:54:56: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:54:56: #1 total tags in treatment: 3917210 INFO @ Tue, 16 Jun 2020 07:54:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:54:56: #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 07:54:56: #1 tags after filtering in treatment: 3917210 INFO @ Tue, 16 Jun 2020 07:54:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:54:56: #1 finished! INFO @ Tue, 16 Jun 2020 07:54:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:54:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:54:56: #2 number of paired peaks: 1582 INFO @ Tue, 16 Jun 2020 07:54:56: start model_add_line... INFO @ Tue, 16 Jun 2020 07:54:56: start X-correlation... INFO @ Tue, 16 Jun 2020 07:54:56: end of X-cor INFO @ Tue, 16 Jun 2020 07:54:56: #2 finished! INFO @ Tue, 16 Jun 2020 07:54:56: #2 predicted fragment length is 216 bps INFO @ Tue, 16 Jun 2020 07:54:56: #2 alternative fragment length(s) may be 216 bps INFO @ Tue, 16 Jun 2020 07:54:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.20_model.r INFO @ Tue, 16 Jun 2020 07:54:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:54:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:55:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:55:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:55:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:55:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769986/SRX1769986.20_summits.bed INFO @ Tue, 16 Jun 2020 07:55:13: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1012 records, 4 fields): 3 millis CompletedMACS2peakCalling