Job ID = 6367725 SRX = SRX4082339 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:54:18 prefetch.2.10.7: 1) Downloading 'SRR7164157'... 2020-06-15T23:54:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:56:26 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:56:27 prefetch.2.10.7: 'SRR7164157' is valid 2020-06-15T23:56:27 prefetch.2.10.7: 1) 'SRR7164157' was downloaded successfully 2020-06-15T23:56:27 prefetch.2.10.7: 'SRR7164157' has 0 unresolved dependencies Read 18773563 spots for SRR7164157/SRR7164157.sra Written 18773563 spots for SRR7164157/SRR7164157.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: 00:04:18 18773563 reads; of these: 18773563 (100.00%) were unpaired; of these: 258824 (1.38%) aligned 0 times 16275248 (86.69%) aligned exactly 1 time 2239491 (11.93%) aligned >1 times 98.62% overall alignment rate Time searching: 00:04:18 Overall time: 00:04:18 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] 4217856 / 18514739 = 0.2278 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 09:08:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.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 09:08:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:08: 1000000 INFO @ Tue, 16 Jun 2020 09:08:14: 2000000 INFO @ Tue, 16 Jun 2020 09:08:20: 3000000 INFO @ Tue, 16 Jun 2020 09:08:26: 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 09:08:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.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 09:08:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:32: 5000000 INFO @ Tue, 16 Jun 2020 09:08:39: 6000000 INFO @ Tue, 16 Jun 2020 09:08:39: 1000000 INFO @ Tue, 16 Jun 2020 09:08:45: 7000000 INFO @ Tue, 16 Jun 2020 09:08:46: 2000000 INFO @ Tue, 16 Jun 2020 09:08:53: 8000000 INFO @ Tue, 16 Jun 2020 09:08:54: 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 09:09:00: 9000000 INFO @ Tue, 16 Jun 2020 09:09:01: 4000000 INFO @ Tue, 16 Jun 2020 09:09:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.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 09:09:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:08: 10000000 INFO @ Tue, 16 Jun 2020 09:09:09: 5000000 INFO @ Tue, 16 Jun 2020 09:09:09: 1000000 INFO @ Tue, 16 Jun 2020 09:09:16: 11000000 INFO @ Tue, 16 Jun 2020 09:09:16: 2000000 INFO @ Tue, 16 Jun 2020 09:09:17: 6000000 INFO @ Tue, 16 Jun 2020 09:09:23: 3000000 INFO @ Tue, 16 Jun 2020 09:09:24: 12000000 INFO @ Tue, 16 Jun 2020 09:09:25: 7000000 INFO @ Tue, 16 Jun 2020 09:09:31: 4000000 INFO @ Tue, 16 Jun 2020 09:09:33: 13000000 INFO @ Tue, 16 Jun 2020 09:09:34: 8000000 INFO @ Tue, 16 Jun 2020 09:09:38: 5000000 INFO @ Tue, 16 Jun 2020 09:09:41: 14000000 INFO @ Tue, 16 Jun 2020 09:09:42: 9000000 INFO @ Tue, 16 Jun 2020 09:09:43: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:09:43: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:09:43: #1 total tags in treatment: 14296883 INFO @ Tue, 16 Jun 2020 09:09:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:43: #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 09:09:44: #1 tags after filtering in treatment: 14296883 INFO @ Tue, 16 Jun 2020 09:09:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:09:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:45: 6000000 INFO @ Tue, 16 Jun 2020 09:09:45: #2 number of paired peaks: 3806 INFO @ Tue, 16 Jun 2020 09:09:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:45: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:45: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:45: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:45: #2 predicted fragment length is 152 bps INFO @ Tue, 16 Jun 2020 09:09:45: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 16 Jun 2020 09:09:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.05_model.r INFO @ Tue, 16 Jun 2020 09:09:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:09:51: 10000000 INFO @ Tue, 16 Jun 2020 09:09:52: 7000000 INFO @ Tue, 16 Jun 2020 09:09:59: 8000000 INFO @ Tue, 16 Jun 2020 09:09:59: 11000000 INFO @ Tue, 16 Jun 2020 09:10:06: 9000000 INFO @ Tue, 16 Jun 2020 09:10:08: 12000000 INFO @ Tue, 16 Jun 2020 09:10:14: 10000000 INFO @ Tue, 16 Jun 2020 09:10:16: 13000000 INFO @ Tue, 16 Jun 2020 09:10:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:21: 11000000 INFO @ Tue, 16 Jun 2020 09:10:25: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:10:28: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:10:28: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:10:28: #1 total tags in treatment: 14296883 INFO @ Tue, 16 Jun 2020 09:10:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:28: #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 09:10:28: 12000000 INFO @ Tue, 16 Jun 2020 09:10:28: #1 tags after filtering in treatment: 14296883 INFO @ Tue, 16 Jun 2020 09:10:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:28: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:30: #2 number of paired peaks: 3806 INFO @ Tue, 16 Jun 2020 09:10:30: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:30: #2 predicted fragment length is 152 bps INFO @ Tue, 16 Jun 2020 09:10:30: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 16 Jun 2020 09:10:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.10_model.r INFO @ Tue, 16 Jun 2020 09:10:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:35: 13000000 INFO @ Tue, 16 Jun 2020 09:10:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.05_summits.bed INFO @ Tue, 16 Jun 2020 09:10:37: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6726 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:10:42: 14000000 INFO @ Tue, 16 Jun 2020 09:10:44: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:10:44: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:10:44: #1 total tags in treatment: 14296883 INFO @ Tue, 16 Jun 2020 09:10:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:44: #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 09:10:45: #1 tags after filtering in treatment: 14296883 INFO @ Tue, 16 Jun 2020 09:10:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:46: #2 number of paired peaks: 3806 INFO @ Tue, 16 Jun 2020 09:10:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:46: #2 predicted fragment length is 152 bps INFO @ Tue, 16 Jun 2020 09:10:46: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 16 Jun 2020 09:10:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.20_model.r INFO @ Tue, 16 Jun 2020 09:10:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:11:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.10_summits.bed INFO @ Tue, 16 Jun 2020 09:11:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5253 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082339/SRX4082339.20_summits.bed INFO @ Tue, 16 Jun 2020 09:11:36: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4130 records, 4 fields): 6 millis CompletedMACS2peakCalling