Job ID = 6367469 SRX = SRX331226 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:26:06 prefetch.2.10.7: 1) Downloading 'SRR947458'... 2020-06-15T23:26:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:26:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:26:52 prefetch.2.10.7: 'SRR947458' is valid 2020-06-15T23:26:52 prefetch.2.10.7: 1) 'SRR947458' was downloaded successfully Read 8214334 spots for SRR947458/SRR947458.sra Written 8214334 spots for SRR947458/SRR947458.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: 00:01:12 8214334 reads; of these: 8214334 (100.00%) were unpaired; of these: 1720733 (20.95%) aligned 0 times 5332600 (64.92%) aligned exactly 1 time 1161001 (14.13%) aligned >1 times 79.05% overall alignment rate Time searching: 00:01:12 Overall time: 00:01:12 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_rmdupse_core] 633885 / 6493601 = 0.0976 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 08:30:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.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 08:30:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:20: 1000000 INFO @ Tue, 16 Jun 2020 08:30:25: 2000000 INFO @ Tue, 16 Jun 2020 08:30:29: 3000000 INFO @ Tue, 16 Jun 2020 08:30:34: 4000000 INFO @ Tue, 16 Jun 2020 08:30:39: 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 08:30:43: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:30:43: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:30:43: #1 total tags in treatment: 5859716 INFO @ Tue, 16 Jun 2020 08:30:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:43: #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 08:30:43: #1 tags after filtering in treatment: 5859716 INFO @ Tue, 16 Jun 2020 08:30:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:30:44: #2 number of paired peaks: 461 WARNING @ Tue, 16 Jun 2020 08:30:44: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Tue, 16 Jun 2020 08:30:44: start model_add_line... INFO @ Tue, 16 Jun 2020 08:30:44: start X-correlation... INFO @ Tue, 16 Jun 2020 08:30:44: end of X-cor INFO @ Tue, 16 Jun 2020 08:30:44: #2 finished! INFO @ Tue, 16 Jun 2020 08:30:44: #2 predicted fragment length is 32 bps INFO @ Tue, 16 Jun 2020 08:30:44: #2 alternative fragment length(s) may be 2,32,544,560,576 bps INFO @ Tue, 16 Jun 2020 08:30:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.05_model.r WARNING @ Tue, 16 Jun 2020 08:30:44: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:30:44: #2 You may need to consider one of the other alternative d(s): 2,32,544,560,576 WARNING @ Tue, 16 Jun 2020 08:30:44: #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 08:30:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:30:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:30:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.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 08:30:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:50: 1000000 INFO @ Tue, 16 Jun 2020 08:30:55: 2000000 INFO @ Tue, 16 Jun 2020 08:30:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:30:59: 3000000 INFO @ Tue, 16 Jun 2020 08:31:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.05_summits.bed INFO @ Tue, 16 Jun 2020 08:31:01: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (645 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:31:04: 4000000 INFO @ Tue, 16 Jun 2020 08:31:09: 5000000 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 08:31:13: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:31:13: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:31:13: #1 total tags in treatment: 5859716 INFO @ Tue, 16 Jun 2020 08:31:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:13: #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 08:31:14: #1 tags after filtering in treatment: 5859716 INFO @ Tue, 16 Jun 2020 08:31:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:14: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:14: #2 number of paired peaks: 461 WARNING @ Tue, 16 Jun 2020 08:31:14: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:14: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:14: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:14: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:14: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:14: #2 predicted fragment length is 32 bps INFO @ Tue, 16 Jun 2020 08:31:14: #2 alternative fragment length(s) may be 2,32,544,560,576 bps INFO @ Tue, 16 Jun 2020 08:31:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.10_model.r WARNING @ Tue, 16 Jun 2020 08:31:14: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:31:14: #2 You may need to consider one of the other alternative d(s): 2,32,544,560,576 WARNING @ Tue, 16 Jun 2020 08:31:14: #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 08:31:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:31:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.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 08:31:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:20: 1000000 INFO @ Tue, 16 Jun 2020 08:31:25: 2000000 INFO @ Tue, 16 Jun 2020 08:31:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:30: 3000000 INFO @ Tue, 16 Jun 2020 08:31:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.10_summits.bed INFO @ Tue, 16 Jun 2020 08:31:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (313 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:31:35: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:31:40: 5000000 INFO @ Tue, 16 Jun 2020 08:31:44: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:31:44: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:31:44: #1 total tags in treatment: 5859716 INFO @ Tue, 16 Jun 2020 08:31:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:44: #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 08:31:44: #1 tags after filtering in treatment: 5859716 INFO @ Tue, 16 Jun 2020 08:31:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:45: #2 number of paired peaks: 461 WARNING @ Tue, 16 Jun 2020 08:31:45: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:45: #2 predicted fragment length is 32 bps INFO @ Tue, 16 Jun 2020 08:31:45: #2 alternative fragment length(s) may be 2,32,544,560,576 bps INFO @ Tue, 16 Jun 2020 08:31:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.20_model.r WARNING @ Tue, 16 Jun 2020 08:31:45: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:31:45: #2 You may need to consider one of the other alternative d(s): 2,32,544,560,576 WARNING @ Tue, 16 Jun 2020 08:31:45: #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 08:31:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:31:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331226/SRX331226.20_summits.bed INFO @ Tue, 16 Jun 2020 08:32:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (99 records, 4 fields): 1 millis CompletedMACS2peakCalling