Job ID = 6367721 SRX = SRX4082335 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:47:14 prefetch.2.10.7: 1) Downloading 'SRR7164153'... 2020-06-15T23:47:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:50:05 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:50:06 prefetch.2.10.7: 'SRR7164153' is valid 2020-06-15T23:50:06 prefetch.2.10.7: 1) 'SRR7164153' was downloaded successfully 2020-06-15T23:50:06 prefetch.2.10.7: 'SRR7164153' has 0 unresolved dependencies Read 19108035 spots for SRR7164153/SRR7164153.sra Written 19108035 spots for SRR7164153/SRR7164153.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: 00:04:12 19108035 reads; of these: 19108035 (100.00%) were unpaired; of these: 558142 (2.92%) aligned 0 times 16713025 (87.47%) aligned exactly 1 time 1836868 (9.61%) aligned >1 times 97.08% overall alignment rate Time searching: 00:04:12 Overall time: 00:04:12 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] 9040796 / 18549893 = 0.4874 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 08:59:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.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 08:59:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:59:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:22: 1000000 INFO @ Tue, 16 Jun 2020 08:59:28: 2000000 INFO @ Tue, 16 Jun 2020 08:59:33: 3000000 INFO @ Tue, 16 Jun 2020 08:59:39: 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 08:59:45: 5000000 INFO @ Tue, 16 Jun 2020 08:59:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.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 08:59:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:59:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:51: 6000000 INFO @ Tue, 16 Jun 2020 08:59:53: 1000000 INFO @ Tue, 16 Jun 2020 08:59:58: 7000000 INFO @ Tue, 16 Jun 2020 09:00:00: 2000000 INFO @ Tue, 16 Jun 2020 09:00:05: 8000000 INFO @ Tue, 16 Jun 2020 09:00:07: 3000000 INFO @ Tue, 16 Jun 2020 09:00:12: 9000000 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 09:00:15: 4000000 INFO @ Tue, 16 Jun 2020 09:00:15: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:00:15: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:00:15: #1 total tags in treatment: 9509097 INFO @ Tue, 16 Jun 2020 09:00:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:00:15: #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 09:00:15: #1 tags after filtering in treatment: 9509097 INFO @ Tue, 16 Jun 2020 09:00:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:00:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:00:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:00:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:00:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.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 09:00:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:00:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:00:16: #2 number of paired peaks: 5534 INFO @ Tue, 16 Jun 2020 09:00:16: start model_add_line... INFO @ Tue, 16 Jun 2020 09:00:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:00:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:00:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:00:16: #2 predicted fragment length is 123 bps INFO @ Tue, 16 Jun 2020 09:00:16: #2 alternative fragment length(s) may be 123 bps INFO @ Tue, 16 Jun 2020 09:00:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.05_model.r INFO @ Tue, 16 Jun 2020 09:00:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:00:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:00:22: 5000000 INFO @ Tue, 16 Jun 2020 09:00:23: 1000000 INFO @ Tue, 16 Jun 2020 09:00:30: 6000000 INFO @ Tue, 16 Jun 2020 09:00:31: 2000000 INFO @ Tue, 16 Jun 2020 09:00:37: 7000000 INFO @ Tue, 16 Jun 2020 09:00:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:00:38: 3000000 INFO @ Tue, 16 Jun 2020 09:00:44: 8000000 INFO @ Tue, 16 Jun 2020 09:00:46: 4000000 INFO @ Tue, 16 Jun 2020 09:00:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:00:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:00:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.05_summits.bed INFO @ Tue, 16 Jun 2020 09:00:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7039 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:00:52: 9000000 INFO @ Tue, 16 Jun 2020 09:00:54: 5000000 INFO @ Tue, 16 Jun 2020 09:00:55: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:00:55: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:00:55: #1 total tags in treatment: 9509097 INFO @ Tue, 16 Jun 2020 09:00:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:00:55: #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 09:00:55: #1 tags after filtering in treatment: 9509097 INFO @ Tue, 16 Jun 2020 09:00:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:00:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:00:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:00:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:00:56: #2 number of paired peaks: 5534 INFO @ Tue, 16 Jun 2020 09:00:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:00:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:00:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:00:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:00:57: #2 predicted fragment length is 123 bps INFO @ Tue, 16 Jun 2020 09:00:57: #2 alternative fragment length(s) may be 123 bps INFO @ Tue, 16 Jun 2020 09:00:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.10_model.r INFO @ Tue, 16 Jun 2020 09:00:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:00:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:01:01: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:01:08: 7000000 INFO @ Tue, 16 Jun 2020 09:01:15: 8000000 INFO @ Tue, 16 Jun 2020 09:01:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:01:22: 9000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:01:26: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:01:26: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:01:26: #1 total tags in treatment: 9509097 INFO @ Tue, 16 Jun 2020 09:01:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:01:26: #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 09:01:26: #1 tags after filtering in treatment: 9509097 INFO @ Tue, 16 Jun 2020 09:01:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:01:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:01:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:01:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:01:27: #2 number of paired peaks: 5534 INFO @ Tue, 16 Jun 2020 09:01:27: start model_add_line... INFO @ Tue, 16 Jun 2020 09:01:27: start X-correlation... INFO @ Tue, 16 Jun 2020 09:01:27: end of X-cor INFO @ Tue, 16 Jun 2020 09:01:27: #2 finished! INFO @ Tue, 16 Jun 2020 09:01:27: #2 predicted fragment length is 123 bps INFO @ Tue, 16 Jun 2020 09:01:27: #2 alternative fragment length(s) may be 123 bps INFO @ Tue, 16 Jun 2020 09:01:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.20_model.r INFO @ Tue, 16 Jun 2020 09:01:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:01:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:01:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:01:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:01:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.10_summits.bed INFO @ Tue, 16 Jun 2020 09:01:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5673 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:01:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:02:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:02:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:02:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082335/SRX4082335.20_summits.bed INFO @ Tue, 16 Jun 2020 09:02:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4701 records, 4 fields): 6 millis CompletedMACS2peakCalling