Job ID = 6368514 SRX = SRX5020743 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:18:51 prefetch.2.10.7: 1) Downloading 'SRR8201366'... 2020-06-16T00:18:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:21:36 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:21:36 prefetch.2.10.7: 1) 'SRR8201366' was downloaded successfully 2020-06-16T00:21:36 prefetch.2.10.7: 'SRR8201366' has 0 unresolved dependencies Read 21494488 spots for SRR8201366/SRR8201366.sra Written 21494488 spots for SRR8201366/SRR8201366.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: 00:07:27 21494488 reads; of these: 21494488 (100.00%) were unpaired; of these: 575075 (2.68%) aligned 0 times 15980721 (74.35%) aligned exactly 1 time 4938692 (22.98%) aligned >1 times 97.32% overall alignment rate Time searching: 00:07:27 Overall time: 00:07:27 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] 3671404 / 20919413 = 0.1755 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 09:35:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.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 09:35:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:00: 1000000 INFO @ Tue, 16 Jun 2020 09:36:06: 2000000 INFO @ Tue, 16 Jun 2020 09:36:11: 3000000 INFO @ Tue, 16 Jun 2020 09:36:17: 4000000 INFO @ Tue, 16 Jun 2020 09:36:22: 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 09:36:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.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 09:36:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:28: 6000000 INFO @ Tue, 16 Jun 2020 09:36:32: 1000000 INFO @ Tue, 16 Jun 2020 09:36:34: 7000000 INFO @ Tue, 16 Jun 2020 09:36:38: 2000000 INFO @ Tue, 16 Jun 2020 09:36:40: 8000000 INFO @ Tue, 16 Jun 2020 09:36:44: 3000000 INFO @ Tue, 16 Jun 2020 09:36:47: 9000000 INFO @ Tue, 16 Jun 2020 09:36:50: 4000000 INFO @ Tue, 16 Jun 2020 09:36:53: 10000000 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 09:36:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.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 09:36:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:57: 5000000 INFO @ Tue, 16 Jun 2020 09:36:59: 11000000 INFO @ Tue, 16 Jun 2020 09:37:02: 1000000 INFO @ Tue, 16 Jun 2020 09:37:03: 6000000 INFO @ Tue, 16 Jun 2020 09:37:06: 12000000 INFO @ Tue, 16 Jun 2020 09:37:10: 7000000 INFO @ Tue, 16 Jun 2020 09:37:10: 2000000 INFO @ Tue, 16 Jun 2020 09:37:12: 13000000 INFO @ Tue, 16 Jun 2020 09:37:16: 8000000 INFO @ Tue, 16 Jun 2020 09:37:17: 3000000 INFO @ Tue, 16 Jun 2020 09:37:19: 14000000 INFO @ Tue, 16 Jun 2020 09:37:23: 9000000 INFO @ Tue, 16 Jun 2020 09:37:24: 4000000 INFO @ Tue, 16 Jun 2020 09:37:26: 15000000 INFO @ Tue, 16 Jun 2020 09:37:30: 10000000 INFO @ Tue, 16 Jun 2020 09:37:32: 5000000 INFO @ Tue, 16 Jun 2020 09:37:33: 16000000 INFO @ Tue, 16 Jun 2020 09:37:37: 11000000 INFO @ Tue, 16 Jun 2020 09:37:39: 6000000 INFO @ Tue, 16 Jun 2020 09:37:39: 17000000 INFO @ Tue, 16 Jun 2020 09:37:41: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:37:41: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:37:41: #1 total tags in treatment: 17248009 INFO @ Tue, 16 Jun 2020 09:37:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:41: #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 09:37:41: #1 tags after filtering in treatment: 17248009 INFO @ Tue, 16 Jun 2020 09:37:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:43: #2 number of paired peaks: 770 WARNING @ Tue, 16 Jun 2020 09:37:43: Fewer paired peaks (770) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 770 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:43: #2 predicted fragment length is 108 bps INFO @ Tue, 16 Jun 2020 09:37:43: #2 alternative fragment length(s) may be 2,91,108,588 bps INFO @ Tue, 16 Jun 2020 09:37:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.05_model.r WARNING @ Tue, 16 Jun 2020 09:37:43: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:37:43: #2 You may need to consider one of the other alternative d(s): 2,91,108,588 WARNING @ Tue, 16 Jun 2020 09:37:43: #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 09:37:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:37:43: 12000000 INFO @ Tue, 16 Jun 2020 09:37:46: 7000000 INFO @ Tue, 16 Jun 2020 09:37:50: 13000000 INFO @ Tue, 16 Jun 2020 09:37:54: 8000000 INFO @ Tue, 16 Jun 2020 09:37:57: 14000000 INFO @ Tue, 16 Jun 2020 09:38:01: 9000000 INFO @ Tue, 16 Jun 2020 09:38:04: 15000000 INFO @ Tue, 16 Jun 2020 09:38:09: 10000000 INFO @ Tue, 16 Jun 2020 09:38:10: 16000000 INFO @ Tue, 16 Jun 2020 09:38:16: 11000000 INFO @ Tue, 16 Jun 2020 09:38:17: 17000000 INFO @ Tue, 16 Jun 2020 09:38:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:38:19: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:38:19: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:38:19: #1 total tags in treatment: 17248009 INFO @ Tue, 16 Jun 2020 09:38:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:38:19: #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 09:38:19: #1 tags after filtering in treatment: 17248009 INFO @ Tue, 16 Jun 2020 09:38:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:38:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:38:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:38:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:38:21: #2 number of paired peaks: 770 WARNING @ Tue, 16 Jun 2020 09:38:21: Fewer paired peaks (770) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 770 pairs to build model! INFO @ Tue, 16 Jun 2020 09:38:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:38:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:38:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:38:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:38:21: #2 predicted fragment length is 108 bps INFO @ Tue, 16 Jun 2020 09:38:21: #2 alternative fragment length(s) may be 2,91,108,588 bps INFO @ Tue, 16 Jun 2020 09:38:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.10_model.r WARNING @ Tue, 16 Jun 2020 09:38:21: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:38:21: #2 You may need to consider one of the other alternative d(s): 2,91,108,588 WARNING @ Tue, 16 Jun 2020 09:38:21: #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 09:38:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:38:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:38:23: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:38:31: 13000000 INFO @ Tue, 16 Jun 2020 09:38:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:38:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:38:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.05_summits.bed INFO @ Tue, 16 Jun 2020 09:38:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2907 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:38:38: 14000000 INFO @ Tue, 16 Jun 2020 09:38:45: 15000000 INFO @ Tue, 16 Jun 2020 09:38:52: 16000000 INFO @ Tue, 16 Jun 2020 09:38:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:38:59: 17000000 INFO @ Tue, 16 Jun 2020 09:39:01: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:39:01: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:39:01: #1 total tags in treatment: 17248009 INFO @ Tue, 16 Jun 2020 09:39:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:01: #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 09:39:01: #1 tags after filtering in treatment: 17248009 INFO @ Tue, 16 Jun 2020 09:39:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:39:01: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:02: #2 number of paired peaks: 770 WARNING @ Tue, 16 Jun 2020 09:39:02: Fewer paired peaks (770) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 770 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:02: #2 predicted fragment length is 108 bps INFO @ Tue, 16 Jun 2020 09:39:02: #2 alternative fragment length(s) may be 2,91,108,588 bps INFO @ Tue, 16 Jun 2020 09:39:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.20_model.r WARNING @ Tue, 16 Jun 2020 09:39:02: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:39:02: #2 You may need to consider one of the other alternative d(s): 2,91,108,588 WARNING @ Tue, 16 Jun 2020 09:39:02: #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 09:39:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:39:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:39:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:39:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.10_summits.bed INFO @ Tue, 16 Jun 2020 09:39:12: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (960 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:39:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:39:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:39:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:39:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020743/SRX5020743.20_summits.bed INFO @ Tue, 16 Jun 2020 09:39:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (311 records, 4 fields): 1 millis CompletedMACS2peakCalling