Job ID = 6366928 SRX = SRX2576630 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:05:39 prefetch.2.10.7: 1) Downloading 'SRR5272587'... 2020-06-15T23:05:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:07:37 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:07:37 prefetch.2.10.7: 1) 'SRR5272587' was downloaded successfully Read 21521044 spots for SRR5272587/SRR5272587.sra Written 21521044 spots for SRR5272587/SRR5272587.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: 00:04:41 21521044 reads; of these: 21521044 (100.00%) were unpaired; of these: 3324887 (15.45%) aligned 0 times 15002843 (69.71%) aligned exactly 1 time 3193314 (14.84%) aligned >1 times 84.55% overall alignment rate Time searching: 00:04:41 Overall time: 00:04:41 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_sort_core] merging from 8 files... [bam_rmdupse_core] 10161573 / 18196157 = 0.5584 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 08:17:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.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 08:17:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:17:38: 1000000 INFO @ Tue, 16 Jun 2020 08:17:44: 2000000 INFO @ Tue, 16 Jun 2020 08:17:49: 3000000 INFO @ Tue, 16 Jun 2020 08:17:55: 4000000 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 08:18:00: 5000000 INFO @ Tue, 16 Jun 2020 08:18:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.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 08:18:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:06: 6000000 INFO @ Tue, 16 Jun 2020 08:18:07: 1000000 INFO @ Tue, 16 Jun 2020 08:18:12: 7000000 INFO @ Tue, 16 Jun 2020 08:18:12: 2000000 INFO @ Tue, 16 Jun 2020 08:18:17: 3000000 INFO @ Tue, 16 Jun 2020 08:18:17: 8000000 INFO @ Tue, 16 Jun 2020 08:18:18: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:18:18: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:18:18: #1 total tags in treatment: 8034584 INFO @ Tue, 16 Jun 2020 08:18:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:18: #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 08:18:18: #1 tags after filtering in treatment: 8034584 INFO @ Tue, 16 Jun 2020 08:18:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:18: #2 number of paired peaks: 1259 INFO @ Tue, 16 Jun 2020 08:18:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:18: #2 predicted fragment length is 170 bps INFO @ Tue, 16 Jun 2020 08:18:18: #2 alternative fragment length(s) may be 170 bps INFO @ Tue, 16 Jun 2020 08:18:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.05_model.r INFO @ Tue, 16 Jun 2020 08:18:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:22: 4000000 INFO @ Tue, 16 Jun 2020 08:18:27: 5000000 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 08:18:32: 6000000 INFO @ Tue, 16 Jun 2020 08:18:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.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 08:18:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:37: 7000000 INFO @ Tue, 16 Jun 2020 08:18:37: 1000000 INFO @ Tue, 16 Jun 2020 08:18:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:18:42: 8000000 INFO @ Tue, 16 Jun 2020 08:18:42: 2000000 INFO @ Tue, 16 Jun 2020 08:18:42: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:18:42: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:18:42: #1 total tags in treatment: 8034584 INFO @ Tue, 16 Jun 2020 08:18:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:42: #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 08:18:42: #1 tags after filtering in treatment: 8034584 INFO @ Tue, 16 Jun 2020 08:18:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:42: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:43: #2 number of paired peaks: 1259 INFO @ Tue, 16 Jun 2020 08:18:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:43: #2 predicted fragment length is 170 bps INFO @ Tue, 16 Jun 2020 08:18:43: #2 alternative fragment length(s) may be 170 bps INFO @ Tue, 16 Jun 2020 08:18:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.10_model.r INFO @ Tue, 16 Jun 2020 08:18:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.05_summits.bed INFO @ Tue, 16 Jun 2020 08:18:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2852 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:18:47: 3000000 INFO @ Tue, 16 Jun 2020 08:18:52: 4000000 INFO @ Tue, 16 Jun 2020 08:18:57: 5000000 INFO @ Tue, 16 Jun 2020 08:19:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:19:02: 6000000 INFO @ Tue, 16 Jun 2020 08:19:07: 7000000 INFO @ Tue, 16 Jun 2020 08:19:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.10_summits.bed INFO @ Tue, 16 Jun 2020 08:19:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2057 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:19:13: 8000000 INFO @ Tue, 16 Jun 2020 08:19:13: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:19:13: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:19:13: #1 total tags in treatment: 8034584 INFO @ Tue, 16 Jun 2020 08:19:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:13: #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 08:19:13: #1 tags after filtering in treatment: 8034584 INFO @ Tue, 16 Jun 2020 08:19:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:14: #2 number of paired peaks: 1259 INFO @ Tue, 16 Jun 2020 08:19:14: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:14: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:14: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:14: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:14: #2 predicted fragment length is 170 bps INFO @ Tue, 16 Jun 2020 08:19:14: #2 alternative fragment length(s) may be 170 bps INFO @ Tue, 16 Jun 2020 08:19:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.20_model.r INFO @ Tue, 16 Jun 2020 08:19:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:14: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:19:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:19:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576630/SRX2576630.20_summits.bed INFO @ Tue, 16 Jun 2020 08:19:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1412 records, 4 fields): 3 millis CompletedMACS2peakCalling