Job ID = 6367755 SRX = SRX4082369 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:37:29 prefetch.2.10.7: 1) Downloading 'SRR7164187'... 2020-06-15T23:37:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:40:21 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:40:22 prefetch.2.10.7: 'SRR7164187' is valid 2020-06-15T23:40:22 prefetch.2.10.7: 1) 'SRR7164187' was downloaded successfully 2020-06-15T23:40:22 prefetch.2.10.7: 'SRR7164187' has 0 unresolved dependencies Read 15954721 spots for SRR7164187/SRR7164187.sra Written 15954721 spots for SRR7164187/SRR7164187.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: 00:03:21 15954721 reads; of these: 15954721 (100.00%) were unpaired; of these: 1960593 (12.29%) aligned 0 times 12802806 (80.24%) aligned exactly 1 time 1191322 (7.47%) aligned >1 times 87.71% overall alignment rate Time searching: 00:03:21 Overall time: 00:03:21 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] 6471415 / 13994128 = 0.4624 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 08:47:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.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 08:47:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:47:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:47:47: 1000000 INFO @ Tue, 16 Jun 2020 08:47:52: 2000000 INFO @ Tue, 16 Jun 2020 08:47:57: 3000000 INFO @ Tue, 16 Jun 2020 08:48:02: 4000000 INFO @ Tue, 16 Jun 2020 08:48:07: 5000000 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 08:48:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.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 08:48:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:12: 6000000 INFO @ Tue, 16 Jun 2020 08:48:17: 1000000 INFO @ Tue, 16 Jun 2020 08:48:17: 7000000 INFO @ Tue, 16 Jun 2020 08:48:20: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:48:20: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:48:20: #1 total tags in treatment: 7522713 INFO @ Tue, 16 Jun 2020 08:48:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:20: #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 08:48:20: #1 tags after filtering in treatment: 7522713 INFO @ Tue, 16 Jun 2020 08:48:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:21: #2 number of paired peaks: 6069 INFO @ Tue, 16 Jun 2020 08:48:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:21: #2 predicted fragment length is 212 bps INFO @ Tue, 16 Jun 2020 08:48:21: #2 alternative fragment length(s) may be 4,212 bps INFO @ Tue, 16 Jun 2020 08:48:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.05_model.r INFO @ Tue, 16 Jun 2020 08:48:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:48:22: 2000000 INFO @ Tue, 16 Jun 2020 08:48:27: 3000000 INFO @ Tue, 16 Jun 2020 08:48:32: 4000000 INFO @ Tue, 16 Jun 2020 08:48:37: 5000000 INFO @ Tue, 16 Jun 2020 08:48:40: #3 Call peaks for each chromosome... 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 08:48:42: 6000000 INFO @ Tue, 16 Jun 2020 08:48:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.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 08:48:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:47: 7000000 INFO @ Tue, 16 Jun 2020 08:48:48: 1000000 INFO @ Tue, 16 Jun 2020 08:48:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:48:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:48:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.05_summits.bed INFO @ Tue, 16 Jun 2020 08:48:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7991 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:48:50: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:48:50: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:48:50: #1 total tags in treatment: 7522713 INFO @ Tue, 16 Jun 2020 08:48:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:50: #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 08:48:50: #1 tags after filtering in treatment: 7522713 INFO @ Tue, 16 Jun 2020 08:48:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:51: #2 number of paired peaks: 6069 INFO @ Tue, 16 Jun 2020 08:48:51: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:51: #2 predicted fragment length is 212 bps INFO @ Tue, 16 Jun 2020 08:48:51: #2 alternative fragment length(s) may be 4,212 bps INFO @ Tue, 16 Jun 2020 08:48:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.10_model.r INFO @ Tue, 16 Jun 2020 08:48:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:48:53: 2000000 INFO @ Tue, 16 Jun 2020 08:48:58: 3000000 INFO @ Tue, 16 Jun 2020 08:49:03: 4000000 INFO @ Tue, 16 Jun 2020 08:49:08: 5000000 INFO @ Tue, 16 Jun 2020 08:49:10: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:49:13: 6000000 INFO @ Tue, 16 Jun 2020 08:49:18: 7000000 INFO @ Tue, 16 Jun 2020 08:49:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.10_summits.bed INFO @ Tue, 16 Jun 2020 08:49:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4568 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:49:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:49:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:49:21: #1 total tags in treatment: 7522713 INFO @ Tue, 16 Jun 2020 08:49:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:49:21: #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 08:49:21: #1 tags after filtering in treatment: 7522713 INFO @ Tue, 16 Jun 2020 08:49:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:49:22: #2 number of paired peaks: 6069 INFO @ Tue, 16 Jun 2020 08:49:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:49:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:49:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:49:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:49:22: #2 predicted fragment length is 212 bps INFO @ Tue, 16 Jun 2020 08:49:22: #2 alternative fragment length(s) may be 4,212 bps INFO @ Tue, 16 Jun 2020 08:49:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.20_model.r INFO @ Tue, 16 Jun 2020 08:49:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:49:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:49:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:49:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082369/SRX4082369.20_summits.bed INFO @ Tue, 16 Jun 2020 08:49:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1403 records, 4 fields): 4 millis CompletedMACS2peakCalling