Job ID = 6368582 SRX = SRX5020808 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:23:18 prefetch.2.10.7: 1) Downloading 'SRR8201431'... 2020-06-16T00:23:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:25:13 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:25:13 prefetch.2.10.7: 1) 'SRR8201431' was downloaded successfully 2020-06-16T00:25:13 prefetch.2.10.7: 'SRR8201431' has 0 unresolved dependencies Read 20337357 spots for SRR8201431/SRR8201431.sra Written 20337357 spots for SRR8201431/SRR8201431.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: 00:06:36 20337357 reads; of these: 20337357 (100.00%) were unpaired; of these: 365391 (1.80%) aligned 0 times 16755301 (82.39%) aligned exactly 1 time 3216665 (15.82%) aligned >1 times 98.20% overall alignment rate Time searching: 00:06:36 Overall time: 00:06:36 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] 2093133 / 19971966 = 0.1048 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 09:38:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.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 09:38:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:31: 1000000 INFO @ Tue, 16 Jun 2020 09:38:37: 2000000 INFO @ Tue, 16 Jun 2020 09:38:44: 3000000 INFO @ Tue, 16 Jun 2020 09:38:50: 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 09:38:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.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 09:38:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:56: 5000000 INFO @ Tue, 16 Jun 2020 09:39:01: 1000000 INFO @ Tue, 16 Jun 2020 09:39:03: 6000000 INFO @ Tue, 16 Jun 2020 09:39:08: 2000000 INFO @ Tue, 16 Jun 2020 09:39:09: 7000000 INFO @ Tue, 16 Jun 2020 09:39:14: 3000000 INFO @ Tue, 16 Jun 2020 09:39:15: 8000000 INFO @ Tue, 16 Jun 2020 09:39:20: 4000000 INFO @ Tue, 16 Jun 2020 09:39:22: 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 09:39:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.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 09:39:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:26: 5000000 INFO @ Tue, 16 Jun 2020 09:39:28: 10000000 INFO @ Tue, 16 Jun 2020 09:39:31: 1000000 INFO @ Tue, 16 Jun 2020 09:39:33: 6000000 INFO @ Tue, 16 Jun 2020 09:39:34: 11000000 INFO @ Tue, 16 Jun 2020 09:39:36: 2000000 INFO @ Tue, 16 Jun 2020 09:39:39: 7000000 INFO @ Tue, 16 Jun 2020 09:39:41: 12000000 INFO @ Tue, 16 Jun 2020 09:39:42: 3000000 INFO @ Tue, 16 Jun 2020 09:39:46: 8000000 INFO @ Tue, 16 Jun 2020 09:39:47: 13000000 INFO @ Tue, 16 Jun 2020 09:39:47: 4000000 INFO @ Tue, 16 Jun 2020 09:39:52: 9000000 INFO @ Tue, 16 Jun 2020 09:39:53: 5000000 INFO @ Tue, 16 Jun 2020 09:39:53: 14000000 INFO @ Tue, 16 Jun 2020 09:39:58: 10000000 INFO @ Tue, 16 Jun 2020 09:39:58: 6000000 INFO @ Tue, 16 Jun 2020 09:40:00: 15000000 INFO @ Tue, 16 Jun 2020 09:40:04: 7000000 INFO @ Tue, 16 Jun 2020 09:40:04: 11000000 INFO @ Tue, 16 Jun 2020 09:40:06: 16000000 INFO @ Tue, 16 Jun 2020 09:40:09: 8000000 INFO @ Tue, 16 Jun 2020 09:40:11: 12000000 INFO @ Tue, 16 Jun 2020 09:40:12: 17000000 INFO @ Tue, 16 Jun 2020 09:40:15: 9000000 INFO @ Tue, 16 Jun 2020 09:40:17: 13000000 INFO @ Tue, 16 Jun 2020 09:40:18: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:40:18: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:40:18: #1 total tags in treatment: 17878833 INFO @ Tue, 16 Jun 2020 09:40:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:18: #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 09:40:18: #1 tags after filtering in treatment: 17878833 INFO @ Tue, 16 Jun 2020 09:40:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:19: #2 number of paired peaks: 210 WARNING @ Tue, 16 Jun 2020 09:40:19: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:19: #2 predicted fragment length is 69 bps INFO @ Tue, 16 Jun 2020 09:40:19: #2 alternative fragment length(s) may be 2,69 bps INFO @ Tue, 16 Jun 2020 09:40:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.05_model.r WARNING @ Tue, 16 Jun 2020 09:40:19: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:40:19: #2 You may need to consider one of the other alternative d(s): 2,69 WARNING @ Tue, 16 Jun 2020 09:40:19: #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 09:40:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:20: 10000000 INFO @ Tue, 16 Jun 2020 09:40:23: 14000000 INFO @ Tue, 16 Jun 2020 09:40:25: 11000000 INFO @ Tue, 16 Jun 2020 09:40:30: 15000000 INFO @ Tue, 16 Jun 2020 09:40:31: 12000000 INFO @ Tue, 16 Jun 2020 09:40:36: 13000000 INFO @ Tue, 16 Jun 2020 09:40:36: 16000000 INFO @ Tue, 16 Jun 2020 09:40:42: 14000000 INFO @ Tue, 16 Jun 2020 09:40:43: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:40:47: 15000000 INFO @ Tue, 16 Jun 2020 09:40:48: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:40:48: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:40:48: #1 total tags in treatment: 17878833 INFO @ Tue, 16 Jun 2020 09:40:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:48: #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 09:40:48: #1 tags after filtering in treatment: 17878833 INFO @ Tue, 16 Jun 2020 09:40:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:50: #2 number of paired peaks: 210 WARNING @ Tue, 16 Jun 2020 09:40:50: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:50: #2 predicted fragment length is 69 bps INFO @ Tue, 16 Jun 2020 09:40:50: #2 alternative fragment length(s) may be 2,69 bps INFO @ Tue, 16 Jun 2020 09:40:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.10_model.r WARNING @ Tue, 16 Jun 2020 09:40:50: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:40:50: #2 You may need to consider one of the other alternative d(s): 2,69 WARNING @ Tue, 16 Jun 2020 09:40:50: #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 09:40:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:52: 16000000 INFO @ Tue, 16 Jun 2020 09:40:58: 17000000 INFO @ Tue, 16 Jun 2020 09:41:02: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:41:02: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:41:02: #1 total tags in treatment: 17878833 INFO @ Tue, 16 Jun 2020 09:41:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:02: #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 09:41:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.05_summits.bed INFO @ Tue, 16 Jun 2020 09:41:03: Done! INFO @ Tue, 16 Jun 2020 09:41:03: #1 tags after filtering in treatment: 17878833 INFO @ Tue, 16 Jun 2020 09:41:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:03: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (607 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:41:04: #2 number of paired peaks: 210 WARNING @ Tue, 16 Jun 2020 09:41:04: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:04: #2 predicted fragment length is 69 bps INFO @ Tue, 16 Jun 2020 09:41:04: #2 alternative fragment length(s) may be 2,69 bps INFO @ Tue, 16 Jun 2020 09:41:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.20_model.r WARNING @ Tue, 16 Jun 2020 09:41:04: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:41:04: #2 You may need to consider one of the other alternative d(s): 2,69 WARNING @ Tue, 16 Jun 2020 09:41:04: #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 09:41:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:19: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:41:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.10_summits.bed INFO @ Tue, 16 Jun 2020 09:41:33: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (467 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:41:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020808/SRX5020808.20_summits.bed INFO @ Tue, 16 Jun 2020 09:41:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (229 records, 4 fields): 1 millis CompletedMACS2peakCalling