Job ID = 6367620 SRX = SRX341788 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:30:35 prefetch.2.10.7: 1) Downloading 'SRR959929'... 2020-06-15T23:30:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:34:25 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:34:25 prefetch.2.10.7: 1) 'SRR959929' was downloaded successfully Read 20555672 spots for SRR959929/SRR959929.sra Written 20555672 spots for SRR959929/SRR959929.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:48 20555672 reads; of these: 20555672 (100.00%) were unpaired; of these: 1964534 (9.56%) aligned 0 times 17241779 (83.88%) aligned exactly 1 time 1349359 (6.56%) aligned >1 times 90.44% overall alignment rate Time searching: 00:04:49 Overall time: 00:04:49 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] 10230696 / 18591138 = 0.5503 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 08:44:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.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 08:44:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:52: 1000000 INFO @ Tue, 16 Jun 2020 08:44:57: 2000000 INFO @ Tue, 16 Jun 2020 08:45:02: 3000000 INFO @ Tue, 16 Jun 2020 08:45:08: 4000000 INFO @ Tue, 16 Jun 2020 08:45:13: 5000000 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 08:45:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.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 08:45:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:45:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:45:19: 6000000 INFO @ Tue, 16 Jun 2020 08:45:22: 1000000 INFO @ Tue, 16 Jun 2020 08:45:24: 7000000 INFO @ Tue, 16 Jun 2020 08:45:27: 2000000 INFO @ Tue, 16 Jun 2020 08:45:30: 8000000 INFO @ Tue, 16 Jun 2020 08:45:32: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:45:32: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:45:32: #1 total tags in treatment: 8360442 INFO @ Tue, 16 Jun 2020 08:45:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:32: #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 08:45:32: #1 tags after filtering in treatment: 8360442 INFO @ Tue, 16 Jun 2020 08:45:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:33: 3000000 INFO @ Tue, 16 Jun 2020 08:45:33: #2 number of paired peaks: 2466 INFO @ Tue, 16 Jun 2020 08:45:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:33: #2 predicted fragment length is 270 bps INFO @ Tue, 16 Jun 2020 08:45:33: #2 alternative fragment length(s) may be 270 bps INFO @ Tue, 16 Jun 2020 08:45:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.05_model.r INFO @ Tue, 16 Jun 2020 08:45:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:45:38: 4000000 INFO @ Tue, 16 Jun 2020 08:45:44: 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 08:45:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.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 08:45:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:45:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:45:49: 6000000 INFO @ Tue, 16 Jun 2020 08:45:52: 1000000 INFO @ Tue, 16 Jun 2020 08:45:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:55: 7000000 INFO @ Tue, 16 Jun 2020 08:45:57: 2000000 INFO @ Tue, 16 Jun 2020 08:46:01: 8000000 INFO @ Tue, 16 Jun 2020 08:46:03: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:46:03: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:46:03: #1 total tags in treatment: 8360442 INFO @ Tue, 16 Jun 2020 08:46:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:46:03: #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 08:46:03: 3000000 INFO @ Tue, 16 Jun 2020 08:46:03: #1 tags after filtering in treatment: 8360442 INFO @ Tue, 16 Jun 2020 08:46:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:46:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:46:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:46:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:46:04: #2 number of paired peaks: 2466 INFO @ Tue, 16 Jun 2020 08:46:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:46:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:46:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:46:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:46:04: #2 predicted fragment length is 270 bps INFO @ Tue, 16 Jun 2020 08:46:04: #2 alternative fragment length(s) may be 270 bps INFO @ Tue, 16 Jun 2020 08:46:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.10_model.r INFO @ Tue, 16 Jun 2020 08:46:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:46:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:46:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.05_summits.bed INFO @ Tue, 16 Jun 2020 08:46:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5483 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:46:09: 4000000 INFO @ Tue, 16 Jun 2020 08:46:14: 5000000 INFO @ Tue, 16 Jun 2020 08:46:20: 6000000 INFO @ Tue, 16 Jun 2020 08:46:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:46:26: 7000000 INFO @ Tue, 16 Jun 2020 08:46:32: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:46:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.10_summits.bed INFO @ Tue, 16 Jun 2020 08:46:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4167 records, 4 fields): 6 millis INFO @ Tue, 16 Jun 2020 08:46:34: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:46:34: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:46:34: #1 total tags in treatment: 8360442 INFO @ Tue, 16 Jun 2020 08:46:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:46:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:46:35: #1 tags after filtering in treatment: 8360442 INFO @ Tue, 16 Jun 2020 08:46:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:46:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:46:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:46:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:46:35: #2 number of paired peaks: 2466 INFO @ Tue, 16 Jun 2020 08:46:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:46:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:46:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:46:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:46:35: #2 predicted fragment length is 270 bps INFO @ Tue, 16 Jun 2020 08:46:35: #2 alternative fragment length(s) may be 270 bps INFO @ Tue, 16 Jun 2020 08:46:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.20_model.r INFO @ Tue, 16 Jun 2020 08:46:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:46:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:46:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:47:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:47:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:47:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX341788/SRX341788.20_summits.bed INFO @ Tue, 16 Jun 2020 08:47:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2848 records, 4 fields): 5 millis CompletedMACS2peakCalling