Job ID = 6367019 SRX = SRX2710280 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:09:31 prefetch.2.10.7: 1) Downloading 'SRR5418734'... 2020-06-15T23:09:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:14:16 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:14:16 prefetch.2.10.7: 1) 'SRR5418734' was downloaded successfully Read 45384331 spots for SRR5418734/SRR5418734.sra Written 45384331 spots for SRR5418734/SRR5418734.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: 00:11:48 45384331 reads; of these: 45384331 (100.00%) were unpaired; of these: 5980992 (13.18%) aligned 0 times 24195626 (53.31%) aligned exactly 1 time 15207713 (33.51%) aligned >1 times 86.82% overall alignment rate Time searching: 00:11:48 Overall time: 00:11:48 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 20 files... [bam_rmdupse_core] 18150202 / 39403339 = 0.4606 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 08:36:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.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 08:36:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:53: 1000000 INFO @ Tue, 16 Jun 2020 08:36:59: 2000000 INFO @ Tue, 16 Jun 2020 08:37:05: 3000000 INFO @ Tue, 16 Jun 2020 08:37:12: 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 08:37:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.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 08:37:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:37:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:37:18: 5000000 INFO @ Tue, 16 Jun 2020 08:37:25: 1000000 INFO @ Tue, 16 Jun 2020 08:37:26: 6000000 INFO @ Tue, 16 Jun 2020 08:37:33: 2000000 INFO @ Tue, 16 Jun 2020 08:37:34: 7000000 INFO @ Tue, 16 Jun 2020 08:37:41: 3000000 INFO @ Tue, 16 Jun 2020 08:37:42: 8000000 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 08:37:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.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 08:37:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:37:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:37:50: 9000000 INFO @ Tue, 16 Jun 2020 08:37:50: 4000000 INFO @ Tue, 16 Jun 2020 08:37:55: 1000000 INFO @ Tue, 16 Jun 2020 08:37:58: 10000000 INFO @ Tue, 16 Jun 2020 08:37:59: 5000000 INFO @ Tue, 16 Jun 2020 08:38:04: 2000000 INFO @ Tue, 16 Jun 2020 08:38:05: 11000000 INFO @ Tue, 16 Jun 2020 08:38:08: 6000000 INFO @ Tue, 16 Jun 2020 08:38:13: 12000000 INFO @ Tue, 16 Jun 2020 08:38:14: 3000000 INFO @ Tue, 16 Jun 2020 08:38:17: 7000000 INFO @ Tue, 16 Jun 2020 08:38:21: 13000000 INFO @ Tue, 16 Jun 2020 08:38:23: 4000000 INFO @ Tue, 16 Jun 2020 08:38:26: 8000000 INFO @ Tue, 16 Jun 2020 08:38:29: 14000000 INFO @ Tue, 16 Jun 2020 08:38:32: 5000000 INFO @ Tue, 16 Jun 2020 08:38:35: 9000000 INFO @ Tue, 16 Jun 2020 08:38:37: 15000000 INFO @ Tue, 16 Jun 2020 08:38:40: 6000000 INFO @ Tue, 16 Jun 2020 08:38:44: 10000000 INFO @ Tue, 16 Jun 2020 08:38:45: 16000000 INFO @ Tue, 16 Jun 2020 08:38:49: 7000000 INFO @ Tue, 16 Jun 2020 08:38:53: 11000000 INFO @ Tue, 16 Jun 2020 08:38:53: 17000000 INFO @ Tue, 16 Jun 2020 08:38:58: 8000000 INFO @ Tue, 16 Jun 2020 08:39:01: 18000000 INFO @ Tue, 16 Jun 2020 08:39:01: 12000000 INFO @ Tue, 16 Jun 2020 08:39:06: 9000000 INFO @ Tue, 16 Jun 2020 08:39:09: 19000000 INFO @ Tue, 16 Jun 2020 08:39:10: 13000000 INFO @ Tue, 16 Jun 2020 08:39:15: 10000000 INFO @ Tue, 16 Jun 2020 08:39:17: 20000000 INFO @ Tue, 16 Jun 2020 08:39:19: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:39:24: 11000000 INFO @ Tue, 16 Jun 2020 08:39:25: 21000000 INFO @ Tue, 16 Jun 2020 08:39:27: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:39:27: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:39:27: #1 total tags in treatment: 21253137 INFO @ Tue, 16 Jun 2020 08:39:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:39:27: #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 08:39:27: #1 tags after filtering in treatment: 21253137 INFO @ Tue, 16 Jun 2020 08:39:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:39:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:39:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:39:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:39:27: 15000000 INFO @ Tue, 16 Jun 2020 08:39:29: #2 number of paired peaks: 590 WARNING @ Tue, 16 Jun 2020 08:39:29: Fewer paired peaks (590) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 590 pairs to build model! INFO @ Tue, 16 Jun 2020 08:39:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:39:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:39:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:39:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:39:29: #2 predicted fragment length is 77 bps INFO @ Tue, 16 Jun 2020 08:39:29: #2 alternative fragment length(s) may be 2,77 bps INFO @ Tue, 16 Jun 2020 08:39:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.05_model.r WARNING @ Tue, 16 Jun 2020 08:39:29: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:39:29: #2 You may need to consider one of the other alternative d(s): 2,77 WARNING @ Tue, 16 Jun 2020 08:39:29: #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 08:39:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:39:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:39:32: 12000000 INFO @ Tue, 16 Jun 2020 08:39:35: 16000000 INFO @ Tue, 16 Jun 2020 08:39:40: 13000000 INFO @ Tue, 16 Jun 2020 08:39:43: 17000000 INFO @ Tue, 16 Jun 2020 08:39:48: 14000000 INFO @ Tue, 16 Jun 2020 08:39:51: 18000000 INFO @ Tue, 16 Jun 2020 08:39:56: 15000000 INFO @ Tue, 16 Jun 2020 08:39:59: 19000000 INFO @ Tue, 16 Jun 2020 08:40:04: 16000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:40:07: 20000000 INFO @ Tue, 16 Jun 2020 08:40:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:40:12: 17000000 INFO @ Tue, 16 Jun 2020 08:40:15: 21000000 INFO @ Tue, 16 Jun 2020 08:40:17: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:40:17: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:40:17: #1 total tags in treatment: 21253137 INFO @ Tue, 16 Jun 2020 08:40:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:17: #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 08:40:17: #1 tags after filtering in treatment: 21253137 INFO @ Tue, 16 Jun 2020 08:40:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:19: #2 number of paired peaks: 590 WARNING @ Tue, 16 Jun 2020 08:40:19: Fewer paired peaks (590) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 590 pairs to build model! INFO @ Tue, 16 Jun 2020 08:40:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:19: #2 predicted fragment length is 77 bps INFO @ Tue, 16 Jun 2020 08:40:19: #2 alternative fragment length(s) may be 2,77 bps INFO @ Tue, 16 Jun 2020 08:40:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.10_model.r WARNING @ Tue, 16 Jun 2020 08:40:19: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:40:19: #2 You may need to consider one of the other alternative d(s): 2,77 WARNING @ Tue, 16 Jun 2020 08:40:19: #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 08:40:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:19: 18000000 INFO @ Tue, 16 Jun 2020 08:40:27: 19000000 INFO @ Tue, 16 Jun 2020 08:40:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.05_summits.bed INFO @ Tue, 16 Jun 2020 08:40:33: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (20238 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:40:34: 20000000 INFO @ Tue, 16 Jun 2020 08:40:42: 21000000 INFO @ Tue, 16 Jun 2020 08:40:43: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:40:43: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:40:43: #1 total tags in treatment: 21253137 INFO @ Tue, 16 Jun 2020 08:40:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:43: #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 08:40:44: #1 tags after filtering in treatment: 21253137 INFO @ Tue, 16 Jun 2020 08:40:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:45: #2 number of paired peaks: 590 WARNING @ Tue, 16 Jun 2020 08:40:45: Fewer paired peaks (590) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 590 pairs to build model! INFO @ Tue, 16 Jun 2020 08:40:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:45: #2 predicted fragment length is 77 bps INFO @ Tue, 16 Jun 2020 08:40:45: #2 alternative fragment length(s) may be 2,77 bps INFO @ Tue, 16 Jun 2020 08:40:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.20_model.r WARNING @ Tue, 16 Jun 2020 08:40:45: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:40:45: #2 You may need to consider one of the other alternative d(s): 2,77 WARNING @ Tue, 16 Jun 2020 08:40:45: #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 08:40:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.10_summits.bed INFO @ Tue, 16 Jun 2020 08:41:18: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (11793 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:41:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710280/SRX2710280.20_summits.bed INFO @ Tue, 16 Jun 2020 08:41:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4751 records, 4 fields): 5 millis CompletedMACS2peakCalling