Job ID = 6368907 SRX = SRX6720171 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:41:17 prefetch.2.10.7: 1) Downloading 'SRR9972859'... 2020-06-16T00:41:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:48:23 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:48:23 prefetch.2.10.7: 1) 'SRR9972859' was downloaded successfully Read 24401878 spots for SRR9972859/SRR9972859.sra Written 24401878 spots for SRR9972859/SRR9972859.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: 00:05:13 24401878 reads; of these: 24401878 (100.00%) were unpaired; of these: 2369762 (9.71%) aligned 0 times 18719522 (76.71%) aligned exactly 1 time 3312594 (13.58%) aligned >1 times 90.29% overall alignment rate Time searching: 00:05:13 Overall time: 00:05:13 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 12 files... [bam_rmdupse_core] 9163884 / 22032116 = 0.4159 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 09:59:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.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 09:59:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:59:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:59:47: 1000000 INFO @ Tue, 16 Jun 2020 09:59:54: 2000000 INFO @ Tue, 16 Jun 2020 10:00:02: 3000000 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 10:00:09: 4000000 INFO @ Tue, 16 Jun 2020 10:00:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.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 10:00:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:00:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:00:17: 5000000 INFO @ Tue, 16 Jun 2020 10:00:18: 1000000 INFO @ Tue, 16 Jun 2020 10:00:25: 6000000 INFO @ Tue, 16 Jun 2020 10:00:25: 2000000 INFO @ Tue, 16 Jun 2020 10:00:32: 3000000 INFO @ Tue, 16 Jun 2020 10:00:33: 7000000 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 10:00:40: 4000000 INFO @ Tue, 16 Jun 2020 10:00:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.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 10:00:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:00:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:00:41: 8000000 INFO @ Tue, 16 Jun 2020 10:00:47: 5000000 INFO @ Tue, 16 Jun 2020 10:00:48: 1000000 INFO @ Tue, 16 Jun 2020 10:00:49: 9000000 INFO @ Tue, 16 Jun 2020 10:00:55: 6000000 INFO @ Tue, 16 Jun 2020 10:00:55: 2000000 INFO @ Tue, 16 Jun 2020 10:00:57: 10000000 INFO @ Tue, 16 Jun 2020 10:01:02: 7000000 INFO @ Tue, 16 Jun 2020 10:01:02: 3000000 INFO @ Tue, 16 Jun 2020 10:01:05: 11000000 INFO @ Tue, 16 Jun 2020 10:01:10: 8000000 INFO @ Tue, 16 Jun 2020 10:01:10: 4000000 INFO @ Tue, 16 Jun 2020 10:01:13: 12000000 INFO @ Tue, 16 Jun 2020 10:01:17: 9000000 INFO @ Tue, 16 Jun 2020 10:01:17: 5000000 INFO @ Tue, 16 Jun 2020 10:01:20: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:01:20: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:01:20: #1 total tags in treatment: 12868232 INFO @ Tue, 16 Jun 2020 10:01:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:01:20: #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 10:01:20: #1 tags after filtering in treatment: 12868232 INFO @ Tue, 16 Jun 2020 10:01:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:01:20: #1 finished! INFO @ Tue, 16 Jun 2020 10:01:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:01:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:01:21: #2 number of paired peaks: 2486 INFO @ Tue, 16 Jun 2020 10:01:21: start model_add_line... INFO @ Tue, 16 Jun 2020 10:01:21: start X-correlation... INFO @ Tue, 16 Jun 2020 10:01:21: end of X-cor INFO @ Tue, 16 Jun 2020 10:01:21: #2 finished! INFO @ Tue, 16 Jun 2020 10:01:21: #2 predicted fragment length is 168 bps INFO @ Tue, 16 Jun 2020 10:01:21: #2 alternative fragment length(s) may be 168 bps INFO @ Tue, 16 Jun 2020 10:01:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.05_model.r INFO @ Tue, 16 Jun 2020 10:01:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:01:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:01:24: 10000000 INFO @ Tue, 16 Jun 2020 10:01:25: 6000000 INFO @ Tue, 16 Jun 2020 10:01:31: 11000000 INFO @ Tue, 16 Jun 2020 10:01:31: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:01:38: 8000000 INFO @ Tue, 16 Jun 2020 10:01:39: 12000000 INFO @ Tue, 16 Jun 2020 10:01:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:01:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:01:45: #1 total tags in treatment: 12868232 INFO @ Tue, 16 Jun 2020 10:01:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:01:45: #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 10:01:45: #1 tags after filtering in treatment: 12868232 INFO @ Tue, 16 Jun 2020 10:01:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:01:45: #1 finished! INFO @ Tue, 16 Jun 2020 10:01:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:01:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:01:45: 9000000 INFO @ Tue, 16 Jun 2020 10:01:46: #2 number of paired peaks: 2486 INFO @ Tue, 16 Jun 2020 10:01:46: start model_add_line... INFO @ Tue, 16 Jun 2020 10:01:46: start X-correlation... INFO @ Tue, 16 Jun 2020 10:01:46: end of X-cor INFO @ Tue, 16 Jun 2020 10:01:46: #2 finished! INFO @ Tue, 16 Jun 2020 10:01:46: #2 predicted fragment length is 168 bps INFO @ Tue, 16 Jun 2020 10:01:46: #2 alternative fragment length(s) may be 168 bps INFO @ Tue, 16 Jun 2020 10:01:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.10_model.r INFO @ Tue, 16 Jun 2020 10:01:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:01:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:01:52: 10000000 INFO @ Tue, 16 Jun 2020 10:01:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:01:58: 11000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:02:04: 12000000 INFO @ Tue, 16 Jun 2020 10:02:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:02:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:02:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.05_summits.bed INFO @ Tue, 16 Jun 2020 10:02:10: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:02:10: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:02:10: #1 total tags in treatment: 12868232 INFO @ Tue, 16 Jun 2020 10:02:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:02:10: #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 10:02:10: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6404 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:02:10: #1 tags after filtering in treatment: 12868232 INFO @ Tue, 16 Jun 2020 10:02:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:02:10: #1 finished! INFO @ Tue, 16 Jun 2020 10:02:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:02:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:02:11: #2 number of paired peaks: 2486 INFO @ Tue, 16 Jun 2020 10:02:11: start model_add_line... INFO @ Tue, 16 Jun 2020 10:02:11: start X-correlation... INFO @ Tue, 16 Jun 2020 10:02:11: end of X-cor INFO @ Tue, 16 Jun 2020 10:02:11: #2 finished! INFO @ Tue, 16 Jun 2020 10:02:11: #2 predicted fragment length is 168 bps INFO @ Tue, 16 Jun 2020 10:02:11: #2 alternative fragment length(s) may be 168 bps INFO @ Tue, 16 Jun 2020 10:02:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.20_model.r INFO @ Tue, 16 Jun 2020 10:02:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:02:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:02:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:02:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:02:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:02:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.10_summits.bed INFO @ Tue, 16 Jun 2020 10:02:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4376 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:02:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:03:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:03:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:03:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720171/SRX6720171.20_summits.bed INFO @ Tue, 16 Jun 2020 10:03:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2523 records, 4 fields): 3 millis CompletedMACS2peakCalling