Job ID = 6368508 SRX = SRX5020738 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:25:46 prefetch.2.10.7: 1) Downloading 'SRR8201361'... 2020-06-16T00:25:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:26:51 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:26:51 prefetch.2.10.7: 'SRR8201361' is valid 2020-06-16T00:26:51 prefetch.2.10.7: 1) 'SRR8201361' was downloaded successfully Read 5742321 spots for SRR8201361/SRR8201361.sra Written 5742321 spots for SRR8201361/SRR8201361.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: 00:01:06 5742321 reads; of these: 5742321 (100.00%) were unpaired; of these: 839532 (14.62%) aligned 0 times 3997937 (69.62%) aligned exactly 1 time 904852 (15.76%) aligned >1 times 85.38% overall alignment rate Time searching: 00:01:06 Overall time: 00:01:06 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] 426738 / 4902789 = 0.0870 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 09:30:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.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 09:30:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:30:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:30:32: 1000000 INFO @ Tue, 16 Jun 2020 09:30:38: 2000000 INFO @ Tue, 16 Jun 2020 09:30:45: 3000000 INFO @ Tue, 16 Jun 2020 09:30:51: 4000000 INFO @ Tue, 16 Jun 2020 09:30:54: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:30:54: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:30:54: #1 total tags in treatment: 4476051 INFO @ Tue, 16 Jun 2020 09:30:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:54: #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 09:30:54: #1 tags after filtering in treatment: 4476051 INFO @ Tue, 16 Jun 2020 09:30:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:30:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:54: #2 number of paired peaks: 425 WARNING @ Tue, 16 Jun 2020 09:30:54: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:54: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:54: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:54: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:54: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:54: #2 predicted fragment length is 56 bps INFO @ Tue, 16 Jun 2020 09:30:54: #2 alternative fragment length(s) may be 56 bps INFO @ Tue, 16 Jun 2020 09:30:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.05_model.r WARNING @ Tue, 16 Jun 2020 09:30:54: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:30:54: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Tue, 16 Jun 2020 09:30:54: #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 09:30:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:54: #3 Pre-compute pvalue-qvalue table... 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 09:30:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.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 09:30:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:30:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:31:03: 1000000 INFO @ Tue, 16 Jun 2020 09:31:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.05_summits.bed INFO @ Tue, 16 Jun 2020 09:31:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (435 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:31:11: 2000000 INFO @ Tue, 16 Jun 2020 09:31:18: 3000000 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 09:31:25: 4000000 INFO @ Tue, 16 Jun 2020 09:31:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.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 09:31:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:28: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:31:28: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:31:28: #1 total tags in treatment: 4476051 INFO @ Tue, 16 Jun 2020 09:31:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:28: #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 09:31:28: #1 tags after filtering in treatment: 4476051 INFO @ Tue, 16 Jun 2020 09:31:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:28: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:29: #2 number of paired peaks: 425 WARNING @ Tue, 16 Jun 2020 09:31:29: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:29: #2 predicted fragment length is 56 bps INFO @ Tue, 16 Jun 2020 09:31:29: #2 alternative fragment length(s) may be 56 bps INFO @ Tue, 16 Jun 2020 09:31:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.10_model.r WARNING @ Tue, 16 Jun 2020 09:31:29: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:31:29: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Tue, 16 Jun 2020 09:31:29: #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 09:31:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:33: 1000000 INFO @ Tue, 16 Jun 2020 09:31:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:31:40: 2000000 INFO @ Tue, 16 Jun 2020 09:31:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.10_summits.bed INFO @ Tue, 16 Jun 2020 09:31:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (249 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:31:46: 3000000 INFO @ Tue, 16 Jun 2020 09:31:52: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:31:55: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:31:55: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:31:55: #1 total tags in treatment: 4476051 INFO @ Tue, 16 Jun 2020 09:31:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:55: #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 09:31:55: #1 tags after filtering in treatment: 4476051 INFO @ Tue, 16 Jun 2020 09:31:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:56: #2 number of paired peaks: 425 WARNING @ Tue, 16 Jun 2020 09:31:56: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:56: #2 predicted fragment length is 56 bps INFO @ Tue, 16 Jun 2020 09:31:56: #2 alternative fragment length(s) may be 56 bps INFO @ Tue, 16 Jun 2020 09:31:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.20_model.r WARNING @ Tue, 16 Jun 2020 09:31:56: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:31:56: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Tue, 16 Jun 2020 09:31:56: #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 09:31:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:05: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:32:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020738/SRX5020738.20_summits.bed INFO @ Tue, 16 Jun 2020 09:32:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (120 records, 4 fields): 1 millis CompletedMACS2peakCalling