Job ID = 6368668 SRX = SRX529228 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:29:31 prefetch.2.10.7: 1) Downloading 'SRR1265832'... 2020-06-16T00:29:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:31:12 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:31:13 prefetch.2.10.7: 'SRR1265832' is valid 2020-06-16T00:31:13 prefetch.2.10.7: 1) 'SRR1265832' was downloaded successfully Read 14054183 spots for SRR1265832/SRR1265832.sra Written 14054183 spots for SRR1265832/SRR1265832.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: 00:03:36 14054183 reads; of these: 14054183 (100.00%) were unpaired; of these: 231703 (1.65%) aligned 0 times 11969028 (85.16%) aligned exactly 1 time 1853452 (13.19%) aligned >1 times 98.35% overall alignment rate Time searching: 00:03:36 Overall time: 00:03:36 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 8 files... [bam_rmdupse_core] 1519564 / 13822480 = 0.1099 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 09:39:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.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 09:39:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:13: 1000000 INFO @ Tue, 16 Jun 2020 09:39:19: 2000000 INFO @ Tue, 16 Jun 2020 09:39:24: 3000000 INFO @ Tue, 16 Jun 2020 09:39:30: 4000000 INFO @ Tue, 16 Jun 2020 09:39:35: 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 09:39:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.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 09:39:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:41: 6000000 INFO @ Tue, 16 Jun 2020 09:39:43: 1000000 INFO @ Tue, 16 Jun 2020 09:39:46: 7000000 INFO @ Tue, 16 Jun 2020 09:39:48: 2000000 INFO @ Tue, 16 Jun 2020 09:39:52: 8000000 INFO @ Tue, 16 Jun 2020 09:39:53: 3000000 INFO @ Tue, 16 Jun 2020 09:39:57: 9000000 INFO @ Tue, 16 Jun 2020 09:39:58: 4000000 INFO @ Tue, 16 Jun 2020 09:40:03: 5000000 INFO @ Tue, 16 Jun 2020 09:40:03: 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 09:40:08: 6000000 INFO @ Tue, 16 Jun 2020 09:40:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.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 09:40:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:08: 11000000 INFO @ Tue, 16 Jun 2020 09:40:13: 7000000 INFO @ Tue, 16 Jun 2020 09:40:14: 1000000 INFO @ Tue, 16 Jun 2020 09:40:14: 12000000 INFO @ Tue, 16 Jun 2020 09:40:16: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:40:16: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:40:16: #1 total tags in treatment: 12302916 INFO @ Tue, 16 Jun 2020 09:40:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:16: #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 09:40:16: #1 tags after filtering in treatment: 12302916 INFO @ Tue, 16 Jun 2020 09:40:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:16: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:17: #2 number of paired peaks: 127 WARNING @ Tue, 16 Jun 2020 09:40:17: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:17: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:40:17: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 16 Jun 2020 09:40:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.05_model.r WARNING @ Tue, 16 Jun 2020 09:40:17: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:40:17: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 16 Jun 2020 09:40:17: #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 09:40:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:18: 8000000 INFO @ Tue, 16 Jun 2020 09:40:19: 2000000 INFO @ Tue, 16 Jun 2020 09:40:23: 9000000 INFO @ Tue, 16 Jun 2020 09:40:25: 3000000 INFO @ Tue, 16 Jun 2020 09:40:28: 10000000 INFO @ Tue, 16 Jun 2020 09:40:31: 4000000 INFO @ Tue, 16 Jun 2020 09:40:33: 11000000 INFO @ Tue, 16 Jun 2020 09:40:36: 5000000 INFO @ Tue, 16 Jun 2020 09:40:38: 12000000 INFO @ Tue, 16 Jun 2020 09:40:39: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:40:39: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:40:39: #1 total tags in treatment: 12302916 INFO @ Tue, 16 Jun 2020 09:40:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:39: #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 09:40:40: #1 tags after filtering in treatment: 12302916 INFO @ Tue, 16 Jun 2020 09:40:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:40: #2 number of paired peaks: 127 WARNING @ Tue, 16 Jun 2020 09:40:40: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:40: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:40: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:40: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:40: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:40:40: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 16 Jun 2020 09:40:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.10_model.r WARNING @ Tue, 16 Jun 2020 09:40:40: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:40:40: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 16 Jun 2020 09:40:40: #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 09:40:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:42: 6000000 INFO @ Tue, 16 Jun 2020 09:40:47: 7000000 INFO @ Tue, 16 Jun 2020 09:40:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.05_summits.bed INFO @ Tue, 16 Jun 2020 09:40:51: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (442 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:40:53: 8000000 INFO @ Tue, 16 Jun 2020 09:40:58: 9000000 INFO @ Tue, 16 Jun 2020 09:41:02: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:41:04: 10000000 INFO @ Tue, 16 Jun 2020 09:41:09: 11000000 INFO @ Tue, 16 Jun 2020 09:41:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.10_summits.bed INFO @ Tue, 16 Jun 2020 09:41:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (246 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:41:15: 12000000 INFO @ Tue, 16 Jun 2020 09:41:17: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:41:17: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:41:17: #1 total tags in treatment: 12302916 INFO @ Tue, 16 Jun 2020 09:41:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:17: #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 09:41:17: #1 tags after filtering in treatment: 12302916 INFO @ Tue, 16 Jun 2020 09:41:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:18: #2 number of paired peaks: 127 WARNING @ Tue, 16 Jun 2020 09:41:18: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:18: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:41:18: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 16 Jun 2020 09:41:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.20_model.r WARNING @ Tue, 16 Jun 2020 09:41:18: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:41:18: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 16 Jun 2020 09:41:18: #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 09:41:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:41:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529228/SRX529228.20_summits.bed INFO @ Tue, 16 Jun 2020 09:41:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (100 records, 4 fields): 1 millis CompletedMACS2peakCalling