Job ID = 6367510 SRX = SRX331266 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:25:51 prefetch.2.10.7: 1) Downloading 'SRR947498'... 2020-06-15T23:25:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:26:36 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:26:37 prefetch.2.10.7: 'SRR947498' is valid 2020-06-15T23:26:37 prefetch.2.10.7: 1) 'SRR947498' was downloaded successfully Read 5635785 spots for SRR947498/SRR947498.sra Written 5635785 spots for SRR947498/SRR947498.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: 00:00:01 Multiseed full-index search: 00:00:37 5635785 reads; of these: 5635785 (100.00%) were unpaired; of these: 2792499 (49.55%) aligned 0 times 2429154 (43.10%) aligned exactly 1 time 414132 (7.35%) aligned >1 times 50.45% overall alignment rate Time searching: 00:00:38 Overall time: 00:00:38 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] 873817 / 2843286 = 0.3073 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 08:28:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.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 08:28:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:35: 1000000 INFO @ Tue, 16 Jun 2020 08:28:40: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:28:40: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:28:40: #1 total tags in treatment: 1969469 INFO @ Tue, 16 Jun 2020 08:28:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:40: #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 08:28:40: #1 tags after filtering in treatment: 1969469 INFO @ Tue, 16 Jun 2020 08:28:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:40: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:40: #2 number of paired peaks: 546 WARNING @ Tue, 16 Jun 2020 08:28:40: Fewer paired peaks (546) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 546 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:40: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 08:28:40: #2 alternative fragment length(s) may be 38,64,89 bps INFO @ Tue, 16 Jun 2020 08:28:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.05_model.r WARNING @ Tue, 16 Jun 2020 08:28:40: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:28:40: #2 You may need to consider one of the other alternative d(s): 38,64,89 WARNING @ Tue, 16 Jun 2020 08:28:40: #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 08:28:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.05_summits.bed INFO @ Tue, 16 Jun 2020 08:28:46: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (336 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 08:29:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.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 08:29:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:29:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:29:06: 1000000 INFO @ Tue, 16 Jun 2020 08:29:12: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:29:12: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:29:12: #1 total tags in treatment: 1969469 INFO @ Tue, 16 Jun 2020 08:29:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:29:12: #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 08:29:12: #1 tags after filtering in treatment: 1969469 INFO @ Tue, 16 Jun 2020 08:29:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:29:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:29:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:29:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:29:13: #2 number of paired peaks: 546 WARNING @ Tue, 16 Jun 2020 08:29:13: Fewer paired peaks (546) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 546 pairs to build model! INFO @ Tue, 16 Jun 2020 08:29:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:29:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:29:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:29:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:29:13: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 08:29:13: #2 alternative fragment length(s) may be 38,64,89 bps INFO @ Tue, 16 Jun 2020 08:29:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.10_model.r WARNING @ Tue, 16 Jun 2020 08:29:13: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:29:13: #2 You may need to consider one of the other alternative d(s): 38,64,89 WARNING @ Tue, 16 Jun 2020 08:29:13: #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 08:29:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:29:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:29:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.10_summits.bed INFO @ Tue, 16 Jun 2020 08:29:19: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (118 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 08:29:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.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 08:29:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:29:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:29:35: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:29:40: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:29:40: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:29:40: #1 total tags in treatment: 1969469 INFO @ Tue, 16 Jun 2020 08:29:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:29:40: #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 08:29:40: #1 tags after filtering in treatment: 1969469 INFO @ Tue, 16 Jun 2020 08:29:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:29:40: #1 finished! INFO @ Tue, 16 Jun 2020 08:29:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:29:40: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:29:40: #2 number of paired peaks: 546 WARNING @ Tue, 16 Jun 2020 08:29:40: Fewer paired peaks (546) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 546 pairs to build model! INFO @ Tue, 16 Jun 2020 08:29:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:29:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:29:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:29:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:29:40: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 08:29:40: #2 alternative fragment length(s) may be 38,64,89 bps INFO @ Tue, 16 Jun 2020 08:29:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.20_model.r WARNING @ Tue, 16 Jun 2020 08:29:40: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:29:40: #2 You may need to consider one of the other alternative d(s): 38,64,89 WARNING @ Tue, 16 Jun 2020 08:29:40: #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 08:29:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:29:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:29:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331266/SRX331266.20_summits.bed INFO @ Tue, 16 Jun 2020 08:29:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (20 records, 4 fields): 1 millis CompletedMACS2peakCalling