Job ID = 6367748 SRX = SRX4082362 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:35:05 prefetch.2.10.7: 1) Downloading 'SRR7164180'... 2020-06-15T23:35:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:36:29 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:36:30 prefetch.2.10.7: 'SRR7164180' is valid 2020-06-15T23:36:30 prefetch.2.10.7: 1) 'SRR7164180' was downloaded successfully 2020-06-15T23:36:30 prefetch.2.10.7: 'SRR7164180' has 0 unresolved dependencies Read 11699193 spots for SRR7164180/SRR7164180.sra Written 11699193 spots for SRR7164180/SRR7164180.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: 00:02:22 11699193 reads; of these: 11699193 (100.00%) were unpaired; of these: 1672612 (14.30%) aligned 0 times 9122508 (77.98%) aligned exactly 1 time 904073 (7.73%) aligned >1 times 85.70% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 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] 1642308 / 10026581 = 0.1638 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 08:42:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.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 08:42:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:42:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:42:14: 1000000 INFO @ Tue, 16 Jun 2020 08:42:20: 2000000 INFO @ Tue, 16 Jun 2020 08:42:26: 3000000 INFO @ Tue, 16 Jun 2020 08:42:32: 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 08:42:37: 5000000 INFO @ Tue, 16 Jun 2020 08:42:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.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 08:42:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:42:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:42:44: 6000000 INFO @ Tue, 16 Jun 2020 08:42:46: 1000000 INFO @ Tue, 16 Jun 2020 08:42:51: 7000000 INFO @ Tue, 16 Jun 2020 08:42:53: 2000000 INFO @ Tue, 16 Jun 2020 08:42:58: 8000000 INFO @ Tue, 16 Jun 2020 08:43:00: 3000000 INFO @ Tue, 16 Jun 2020 08:43:00: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:43:00: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:43:00: #1 total tags in treatment: 8384273 INFO @ Tue, 16 Jun 2020 08:43:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:43:00: #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 08:43:00: #1 tags after filtering in treatment: 8384273 INFO @ Tue, 16 Jun 2020 08:43:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:43:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:43:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:43:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:43:01: #2 number of paired peaks: 5306 INFO @ Tue, 16 Jun 2020 08:43:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:43:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:43:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:43:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:43:01: #2 predicted fragment length is 176 bps INFO @ Tue, 16 Jun 2020 08:43:01: #2 alternative fragment length(s) may be 4,176 bps INFO @ Tue, 16 Jun 2020 08:43:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.05_model.r INFO @ Tue, 16 Jun 2020 08:43:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:43:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:43:06: 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 08:43:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.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 08:43:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:43:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:43:13: 5000000 INFO @ Tue, 16 Jun 2020 08:43:15: 1000000 INFO @ Tue, 16 Jun 2020 08:43:19: 6000000 INFO @ Tue, 16 Jun 2020 08:43:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:43:22: 2000000 INFO @ Tue, 16 Jun 2020 08:43:26: 7000000 INFO @ Tue, 16 Jun 2020 08:43:29: 3000000 INFO @ Tue, 16 Jun 2020 08:43:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:43:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:43:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.05_summits.bed INFO @ Tue, 16 Jun 2020 08:43:31: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (9034 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:43:33: 8000000 INFO @ Tue, 16 Jun 2020 08:43:35: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:43:35: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:43:35: #1 total tags in treatment: 8384273 INFO @ Tue, 16 Jun 2020 08:43:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:43:35: #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 08:43:35: #1 tags after filtering in treatment: 8384273 INFO @ Tue, 16 Jun 2020 08:43:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:43:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:43:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:43:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:43:36: 4000000 INFO @ Tue, 16 Jun 2020 08:43:36: #2 number of paired peaks: 5306 INFO @ Tue, 16 Jun 2020 08:43:36: start model_add_line... INFO @ Tue, 16 Jun 2020 08:43:36: start X-correlation... INFO @ Tue, 16 Jun 2020 08:43:36: end of X-cor INFO @ Tue, 16 Jun 2020 08:43:36: #2 finished! INFO @ Tue, 16 Jun 2020 08:43:36: #2 predicted fragment length is 176 bps INFO @ Tue, 16 Jun 2020 08:43:36: #2 alternative fragment length(s) may be 4,176 bps INFO @ Tue, 16 Jun 2020 08:43:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.10_model.r INFO @ Tue, 16 Jun 2020 08:43:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:43:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:43:42: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:43:48: 6000000 INFO @ Tue, 16 Jun 2020 08:43:54: 7000000 INFO @ Tue, 16 Jun 2020 08:43:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:44:00: 8000000 INFO @ Tue, 16 Jun 2020 08:44:03: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:44:03: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:44:03: #1 total tags in treatment: 8384273 INFO @ Tue, 16 Jun 2020 08:44:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:44:03: #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 08:44:03: #1 tags after filtering in treatment: 8384273 INFO @ Tue, 16 Jun 2020 08:44:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:44:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:44:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:44:03: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:44:04: #2 number of paired peaks: 5306 INFO @ Tue, 16 Jun 2020 08:44:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:44:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:44:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:44:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:44:04: #2 predicted fragment length is 176 bps INFO @ Tue, 16 Jun 2020 08:44:04: #2 alternative fragment length(s) may be 4,176 bps INFO @ Tue, 16 Jun 2020 08:44:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.20_model.r INFO @ Tue, 16 Jun 2020 08:44:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:44:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:44:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:44:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:44:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.10_summits.bed INFO @ Tue, 16 Jun 2020 08:44:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5465 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:44:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:44:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:44:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:44:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082362/SRX4082362.20_summits.bed INFO @ Tue, 16 Jun 2020 08:44:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1817 records, 4 fields): 3 millis CompletedMACS2peakCalling