Job ID = 6367729 SRX = SRX4082343 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:35:35 prefetch.2.10.7: 1) Downloading 'SRR7164161'... 2020-06-15T23:35:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:38:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:38:47 prefetch.2.10.7: 'SRR7164161' is valid 2020-06-15T23:38:47 prefetch.2.10.7: 1) 'SRR7164161' was downloaded successfully 2020-06-15T23:38:47 prefetch.2.10.7: 'SRR7164161' has 0 unresolved dependencies Read 19830957 spots for SRR7164161/SRR7164161.sra Written 19830957 spots for SRR7164161/SRR7164161.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: 00:03:49 19830957 reads; of these: 19830957 (100.00%) were unpaired; of these: 3093055 (15.60%) aligned 0 times 15367590 (77.49%) aligned exactly 1 time 1370312 (6.91%) aligned >1 times 84.40% overall alignment rate Time searching: 00:03:49 Overall time: 00:03:49 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] 6907629 / 16737902 = 0.4127 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 08:47:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.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 08:47:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:47:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:47:17: 1000000 INFO @ Tue, 16 Jun 2020 08:47:23: 2000000 INFO @ Tue, 16 Jun 2020 08:47:29: 3000000 INFO @ Tue, 16 Jun 2020 08:47:36: 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 08:47:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.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 08:47:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:47:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:47:42: 5000000 INFO @ Tue, 16 Jun 2020 08:47:47: 1000000 INFO @ Tue, 16 Jun 2020 08:47:49: 6000000 INFO @ Tue, 16 Jun 2020 08:47:54: 2000000 INFO @ Tue, 16 Jun 2020 08:47:56: 7000000 INFO @ Tue, 16 Jun 2020 08:48:01: 3000000 INFO @ Tue, 16 Jun 2020 08:48:02: 8000000 INFO @ Tue, 16 Jun 2020 08:48:07: 4000000 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 08:48:09: 9000000 INFO @ Tue, 16 Jun 2020 08:48:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.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 08:48:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:14: 5000000 INFO @ Tue, 16 Jun 2020 08:48:15: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:48:15: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:48:15: #1 total tags in treatment: 9830273 INFO @ Tue, 16 Jun 2020 08:48:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:15: #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 08:48:15: #1 tags after filtering in treatment: 9830273 INFO @ Tue, 16 Jun 2020 08:48:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:16: #2 number of paired peaks: 5749 INFO @ Tue, 16 Jun 2020 08:48:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:16: #2 predicted fragment length is 178 bps INFO @ Tue, 16 Jun 2020 08:48:16: #2 alternative fragment length(s) may be 178 bps INFO @ Tue, 16 Jun 2020 08:48:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.05_model.r INFO @ Tue, 16 Jun 2020 08:48:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:48:17: 1000000 INFO @ Tue, 16 Jun 2020 08:48:21: 6000000 INFO @ Tue, 16 Jun 2020 08:48:23: 2000000 INFO @ Tue, 16 Jun 2020 08:48:27: 7000000 INFO @ Tue, 16 Jun 2020 08:48:29: 3000000 INFO @ Tue, 16 Jun 2020 08:48:34: 8000000 INFO @ Tue, 16 Jun 2020 08:48:35: 4000000 INFO @ Tue, 16 Jun 2020 08:48:41: 9000000 INFO @ Tue, 16 Jun 2020 08:48:41: 5000000 INFO @ Tue, 16 Jun 2020 08:48:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:48:46: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:48:46: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:48:46: #1 total tags in treatment: 9830273 INFO @ Tue, 16 Jun 2020 08:48:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:46: #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 08:48:47: #1 tags after filtering in treatment: 9830273 INFO @ Tue, 16 Jun 2020 08:48:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:48: 6000000 INFO @ Tue, 16 Jun 2020 08:48:48: #2 number of paired peaks: 5749 INFO @ Tue, 16 Jun 2020 08:48:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:48: #2 predicted fragment length is 178 bps INFO @ Tue, 16 Jun 2020 08:48:48: #2 alternative fragment length(s) may be 178 bps INFO @ Tue, 16 Jun 2020 08:48:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.10_model.r INFO @ Tue, 16 Jun 2020 08:48:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:48: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:48:53: 7000000 INFO @ Tue, 16 Jun 2020 08:48:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:48:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:48:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.05_summits.bed INFO @ Tue, 16 Jun 2020 08:48:55: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6650 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:48:59: 8000000 INFO @ Tue, 16 Jun 2020 08:49:04: 9000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:49:09: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:49:09: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:49:09: #1 total tags in treatment: 9830273 INFO @ Tue, 16 Jun 2020 08:49:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:49:09: #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 08:49:09: #1 tags after filtering in treatment: 9830273 INFO @ Tue, 16 Jun 2020 08:49:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:49:10: #2 number of paired peaks: 5749 INFO @ Tue, 16 Jun 2020 08:49:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:49:10: start X-correlation... INFO @ Tue, 16 Jun 2020 08:49:10: end of X-cor INFO @ Tue, 16 Jun 2020 08:49:10: #2 finished! INFO @ Tue, 16 Jun 2020 08:49:10: #2 predicted fragment length is 178 bps INFO @ Tue, 16 Jun 2020 08:49:10: #2 alternative fragment length(s) may be 178 bps INFO @ Tue, 16 Jun 2020 08:49:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.20_model.r INFO @ Tue, 16 Jun 2020 08:49:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:49:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:49:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:49:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.10_summits.bed INFO @ Tue, 16 Jun 2020 08:49:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5216 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:49:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:49:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082343/SRX4082343.20_summits.bed INFO @ Tue, 16 Jun 2020 08:49:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3972 records, 4 fields): 5 millis CompletedMACS2peakCalling