Job ID = 6368730 SRX = SRX5402754 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:29:04 prefetch.2.10.7: 1) Downloading 'SRR8602988'... 2020-06-16T00:29:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:32:00 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:32:00 prefetch.2.10.7: 1) 'SRR8602988' was downloaded successfully Read 25740955 spots for SRR8602988/SRR8602988.sra Written 25740955 spots for SRR8602988/SRR8602988.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: 00:06:01 25740955 reads; of these: 25740955 (100.00%) were unpaired; of these: 4545930 (17.66%) aligned 0 times 13379835 (51.98%) aligned exactly 1 time 7815190 (30.36%) aligned >1 times 82.34% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 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] 6302593 / 21195025 = 0.2974 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 09:44:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.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 09:44:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:23: 1000000 INFO @ Tue, 16 Jun 2020 09:44:30: 2000000 INFO @ Tue, 16 Jun 2020 09:44:36: 3000000 INFO @ Tue, 16 Jun 2020 09:44:42: 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 09:44:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.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 09:44:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:48: 5000000 INFO @ Tue, 16 Jun 2020 09:44:54: 1000000 INFO @ Tue, 16 Jun 2020 09:44:55: 6000000 INFO @ Tue, 16 Jun 2020 09:45:01: 2000000 INFO @ Tue, 16 Jun 2020 09:45:02: 7000000 INFO @ Tue, 16 Jun 2020 09:45:07: 3000000 INFO @ Tue, 16 Jun 2020 09:45:08: 8000000 INFO @ Tue, 16 Jun 2020 09:45:14: 4000000 INFO @ Tue, 16 Jun 2020 09:45:15: 9000000 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 09:45:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.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 09:45:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:45:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:21: 5000000 INFO @ Tue, 16 Jun 2020 09:45:21: 10000000 INFO @ Tue, 16 Jun 2020 09:45:23: 1000000 INFO @ Tue, 16 Jun 2020 09:45:27: 6000000 INFO @ Tue, 16 Jun 2020 09:45:28: 11000000 INFO @ Tue, 16 Jun 2020 09:45:30: 2000000 INFO @ Tue, 16 Jun 2020 09:45:34: 7000000 INFO @ Tue, 16 Jun 2020 09:45:35: 12000000 INFO @ Tue, 16 Jun 2020 09:45:36: 3000000 INFO @ Tue, 16 Jun 2020 09:45:41: 8000000 INFO @ Tue, 16 Jun 2020 09:45:42: 4000000 INFO @ Tue, 16 Jun 2020 09:45:42: 13000000 INFO @ Tue, 16 Jun 2020 09:45:48: 5000000 INFO @ Tue, 16 Jun 2020 09:45:48: 9000000 INFO @ Tue, 16 Jun 2020 09:45:49: 14000000 INFO @ Tue, 16 Jun 2020 09:45:54: 6000000 INFO @ Tue, 16 Jun 2020 09:45:55: 10000000 INFO @ Tue, 16 Jun 2020 09:45:55: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:45:55: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:45:55: #1 total tags in treatment: 14892432 INFO @ Tue, 16 Jun 2020 09:45:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:55: #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 09:45:55: #1 tags after filtering in treatment: 14892432 INFO @ Tue, 16 Jun 2020 09:45:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:45:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:56: #2 number of paired peaks: 2094 INFO @ Tue, 16 Jun 2020 09:45:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:56: #2 predicted fragment length is 98 bps INFO @ Tue, 16 Jun 2020 09:45:56: #2 alternative fragment length(s) may be 4,98 bps INFO @ Tue, 16 Jun 2020 09:45:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.05_model.r WARNING @ Tue, 16 Jun 2020 09:45:56: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:45:56: #2 You may need to consider one of the other alternative d(s): 4,98 WARNING @ Tue, 16 Jun 2020 09:45:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:45:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:46:00: 7000000 INFO @ Tue, 16 Jun 2020 09:46:02: 11000000 INFO @ Tue, 16 Jun 2020 09:46:06: 8000000 INFO @ Tue, 16 Jun 2020 09:46:08: 12000000 INFO @ Tue, 16 Jun 2020 09:46:12: 9000000 INFO @ Tue, 16 Jun 2020 09:46:15: 13000000 INFO @ Tue, 16 Jun 2020 09:46:18: 10000000 INFO @ Tue, 16 Jun 2020 09:46:22: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:46:25: 11000000 INFO @ Tue, 16 Jun 2020 09:46:28: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:46:28: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:46:28: #1 total tags in treatment: 14892432 INFO @ Tue, 16 Jun 2020 09:46:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:46:28: #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 09:46:28: #1 tags after filtering in treatment: 14892432 INFO @ Tue, 16 Jun 2020 09:46:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:46:28: #1 finished! INFO @ Tue, 16 Jun 2020 09:46:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:46:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:46:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:46:29: #2 number of paired peaks: 2094 INFO @ Tue, 16 Jun 2020 09:46:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:46:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:46:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:46:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:46:30: #2 predicted fragment length is 98 bps INFO @ Tue, 16 Jun 2020 09:46:30: #2 alternative fragment length(s) may be 4,98 bps INFO @ Tue, 16 Jun 2020 09:46:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.10_model.r WARNING @ Tue, 16 Jun 2020 09:46:30: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:46:30: #2 You may need to consider one of the other alternative d(s): 4,98 WARNING @ Tue, 16 Jun 2020 09:46:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:46:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:46:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:46:31: 12000000 INFO @ Tue, 16 Jun 2020 09:46:36: 13000000 INFO @ Tue, 16 Jun 2020 09:46:42: 14000000 INFO @ Tue, 16 Jun 2020 09:46:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:46:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:46:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.05_summits.bed INFO @ Tue, 16 Jun 2020 09:46:45: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (10211 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:46:47: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:46:47: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:46:47: #1 total tags in treatment: 14892432 INFO @ Tue, 16 Jun 2020 09:46:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:46:47: #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 09:46:48: #1 tags after filtering in treatment: 14892432 INFO @ Tue, 16 Jun 2020 09:46:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:46:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:46:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:46:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:46:49: #2 number of paired peaks: 2094 INFO @ Tue, 16 Jun 2020 09:46:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:46:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:46:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:46:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:46:49: #2 predicted fragment length is 98 bps INFO @ Tue, 16 Jun 2020 09:46:49: #2 alternative fragment length(s) may be 4,98 bps INFO @ Tue, 16 Jun 2020 09:46:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.20_model.r WARNING @ Tue, 16 Jun 2020 09:46:49: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:46:49: #2 You may need to consider one of the other alternative d(s): 4,98 WARNING @ Tue, 16 Jun 2020 09:46:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:46:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:46:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:47:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:47:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:47:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:47:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.10_summits.bed INFO @ Tue, 16 Jun 2020 09:47:18: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6705 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:47:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:47:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:47:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:47:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402754/SRX5402754.20_summits.bed INFO @ Tue, 16 Jun 2020 09:47:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3377 records, 4 fields): 5 millis CompletedMACS2peakCalling