Job ID = 6367728 SRX = SRX4082342 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 'SRR7164160'... 2020-06-15T23:30:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:32:37 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:32:38 prefetch.2.10.7: 'SRR7164160' is valid 2020-06-15T23:32:38 prefetch.2.10.7: 1) 'SRR7164160' was downloaded successfully 2020-06-15T23:32:38 prefetch.2.10.7: 'SRR7164160' has 0 unresolved dependencies Read 20737442 spots for SRR7164160/SRR7164160.sra Written 20737442 spots for SRR7164160/SRR7164160.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: 00:03:54 20737442 reads; of these: 20737442 (100.00%) were unpaired; of these: 501633 (2.42%) aligned 0 times 18576726 (89.58%) aligned exactly 1 time 1659083 (8.00%) aligned >1 times 97.58% overall alignment rate Time searching: 00:03:54 Overall time: 00:03:54 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] 6187748 / 20235809 = 0.3058 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 08:43:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.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 08:43:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:43:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:43:38: 1000000 INFO @ Tue, 16 Jun 2020 08:43:45: 2000000 INFO @ Tue, 16 Jun 2020 08:43:52: 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 08:43:59: 4000000 INFO @ Tue, 16 Jun 2020 08:44:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.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 08:44:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:07: 5000000 INFO @ Tue, 16 Jun 2020 08:44:08: 1000000 INFO @ Tue, 16 Jun 2020 08:44:14: 6000000 INFO @ Tue, 16 Jun 2020 08:44:16: 2000000 INFO @ Tue, 16 Jun 2020 08:44:22: 7000000 INFO @ Tue, 16 Jun 2020 08:44:24: 3000000 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 08:44:29: 8000000 INFO @ Tue, 16 Jun 2020 08:44:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.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 08:44:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:31: 4000000 INFO @ Tue, 16 Jun 2020 08:44:37: 9000000 INFO @ Tue, 16 Jun 2020 08:44:39: 1000000 INFO @ Tue, 16 Jun 2020 08:44:39: 5000000 INFO @ Tue, 16 Jun 2020 08:44:44: 10000000 INFO @ Tue, 16 Jun 2020 08:44:46: 2000000 INFO @ Tue, 16 Jun 2020 08:44:47: 6000000 INFO @ Tue, 16 Jun 2020 08:44:52: 11000000 INFO @ Tue, 16 Jun 2020 08:44:54: 3000000 INFO @ Tue, 16 Jun 2020 08:44:54: 7000000 INFO @ Tue, 16 Jun 2020 08:44:59: 12000000 INFO @ Tue, 16 Jun 2020 08:45:01: 4000000 INFO @ Tue, 16 Jun 2020 08:45:02: 8000000 INFO @ Tue, 16 Jun 2020 08:45:07: 13000000 INFO @ Tue, 16 Jun 2020 08:45:09: 5000000 INFO @ Tue, 16 Jun 2020 08:45:09: 9000000 INFO @ Tue, 16 Jun 2020 08:45:14: 14000000 INFO @ Tue, 16 Jun 2020 08:45:14: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:45:14: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:45:14: #1 total tags in treatment: 14048061 INFO @ Tue, 16 Jun 2020 08:45:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:14: #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 08:45:15: #1 tags after filtering in treatment: 14048061 INFO @ Tue, 16 Jun 2020 08:45:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:16: #2 number of paired peaks: 5152 INFO @ Tue, 16 Jun 2020 08:45:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:16: #2 predicted fragment length is 135 bps INFO @ Tue, 16 Jun 2020 08:45:16: #2 alternative fragment length(s) may be 135 bps INFO @ Tue, 16 Jun 2020 08:45:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.05_model.r INFO @ Tue, 16 Jun 2020 08:45:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:45:16: 6000000 INFO @ Tue, 16 Jun 2020 08:45:17: 10000000 INFO @ Tue, 16 Jun 2020 08:45:23: 7000000 INFO @ Tue, 16 Jun 2020 08:45:23: 11000000 INFO @ Tue, 16 Jun 2020 08:45:29: 8000000 INFO @ Tue, 16 Jun 2020 08:45:30: 12000000 INFO @ Tue, 16 Jun 2020 08:45:36: 9000000 INFO @ Tue, 16 Jun 2020 08:45:36: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:45:42: 10000000 INFO @ Tue, 16 Jun 2020 08:45:42: 14000000 INFO @ Tue, 16 Jun 2020 08:45:42: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:45:42: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:45:42: #1 total tags in treatment: 14048061 INFO @ Tue, 16 Jun 2020 08:45:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:42: #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 08:45:43: #1 tags after filtering in treatment: 14048061 INFO @ Tue, 16 Jun 2020 08:45:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:44: #2 number of paired peaks: 5152 INFO @ Tue, 16 Jun 2020 08:45:44: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:44: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:44: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:44: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:44: #2 predicted fragment length is 135 bps INFO @ Tue, 16 Jun 2020 08:45:44: #2 alternative fragment length(s) may be 135 bps INFO @ Tue, 16 Jun 2020 08:45:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.10_model.r INFO @ Tue, 16 Jun 2020 08:45:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:45:47: 11000000 INFO @ Tue, 16 Jun 2020 08:45:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:53: 12000000 INFO @ Tue, 16 Jun 2020 08:45:59: 13000000 INFO @ Tue, 16 Jun 2020 08:46:05: 14000000 INFO @ Tue, 16 Jun 2020 08:46:05: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:46:05: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:46:05: #1 total tags in treatment: 14048061 INFO @ Tue, 16 Jun 2020 08:46:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:46:05: #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 08:46:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.05_summits.bed INFO @ Tue, 16 Jun 2020 08:46:05: Done! INFO @ Tue, 16 Jun 2020 08:46:05: #1 tags after filtering in treatment: 14048061 INFO @ Tue, 16 Jun 2020 08:46:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:46:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:46:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:46:05: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (7647 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:46:07: #2 number of paired peaks: 5152 INFO @ Tue, 16 Jun 2020 08:46:07: start model_add_line... INFO @ Tue, 16 Jun 2020 08:46:07: start X-correlation... INFO @ Tue, 16 Jun 2020 08:46:07: end of X-cor INFO @ Tue, 16 Jun 2020 08:46:07: #2 finished! INFO @ Tue, 16 Jun 2020 08:46:07: #2 predicted fragment length is 135 bps INFO @ Tue, 16 Jun 2020 08:46:07: #2 alternative fragment length(s) may be 135 bps INFO @ Tue, 16 Jun 2020 08:46:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.20_model.r INFO @ Tue, 16 Jun 2020 08:46:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:46:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:46:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:46:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.10_summits.bed INFO @ Tue, 16 Jun 2020 08:46:32: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (5867 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:46:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:46:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082342/SRX4082342.20_summits.bed INFO @ Tue, 16 Jun 2020 08:46:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4370 records, 4 fields): 7 millis CompletedMACS2peakCalling