Job ID = 6367460 SRX = SRX331217 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:25:36 prefetch.2.10.7: 1) Downloading 'SRR947449'... 2020-06-15T23:25:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:26:32 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:26:32 prefetch.2.10.7: 'SRR947449' is valid 2020-06-15T23:26:32 prefetch.2.10.7: 1) 'SRR947449' was downloaded successfully Read 5995904 spots for SRR947449/SRR947449.sra Written 5995904 spots for SRR947449/SRR947449.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: 00:00:31 5995904 reads; of these: 5995904 (100.00%) were unpaired; of these: 4778935 (79.70%) aligned 0 times 966746 (16.12%) aligned exactly 1 time 250223 (4.17%) aligned >1 times 20.30% overall alignment rate Time searching: 00:00:31 Overall time: 00:00:31 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] 46982 / 1216969 = 0.0386 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 08:28:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.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 08:28:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:12: 1000000 INFO @ Tue, 16 Jun 2020 08:28:12: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:28:12: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:28:12: #1 total tags in treatment: 1169987 INFO @ Tue, 16 Jun 2020 08:28:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:12: #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 08:28:12: #1 tags after filtering in treatment: 1169987 INFO @ Tue, 16 Jun 2020 08:28:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:13: #2 number of paired peaks: 472 WARNING @ Tue, 16 Jun 2020 08:28:13: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:13: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:28:13: #2 alternative fragment length(s) may be 31,97,583 bps INFO @ Tue, 16 Jun 2020 08:28:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.05_model.r WARNING @ Tue, 16 Jun 2020 08:28:13: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:28:13: #2 You may need to consider one of the other alternative d(s): 31,97,583 WARNING @ Tue, 16 Jun 2020 08:28:13: #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 08:28:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.05_summits.bed INFO @ Tue, 16 Jun 2020 08:28:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (274 records, 4 fields): 1 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 08:28:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.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 08:28:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:42: 1000000 INFO @ Tue, 16 Jun 2020 08:28:43: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:28:43: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:28:43: #1 total tags in treatment: 1169987 INFO @ Tue, 16 Jun 2020 08:28:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:43: #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 08:28:43: #1 tags after filtering in treatment: 1169987 INFO @ Tue, 16 Jun 2020 08:28:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:43: #2 number of paired peaks: 472 WARNING @ Tue, 16 Jun 2020 08:28:43: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:43: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:28:43: #2 alternative fragment length(s) may be 31,97,583 bps INFO @ Tue, 16 Jun 2020 08:28:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.10_model.r WARNING @ Tue, 16 Jun 2020 08:28:43: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:28:43: #2 You may need to consider one of the other alternative d(s): 31,97,583 WARNING @ Tue, 16 Jun 2020 08:28:43: #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 08:28:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.10_summits.bed INFO @ Tue, 16 Jun 2020 08:28:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (112 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 08:29:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.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 08:29:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:29:07: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:29:12: 1000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:29:13: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:29:13: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:29:13: #1 total tags in treatment: 1169987 INFO @ Tue, 16 Jun 2020 08:29:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:29:13: #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 08:29:13: #1 tags after filtering in treatment: 1169987 INFO @ Tue, 16 Jun 2020 08:29:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:29:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:29:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:29:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:29:13: #2 number of paired peaks: 472 WARNING @ Tue, 16 Jun 2020 08:29:13: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 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 31 bps INFO @ Tue, 16 Jun 2020 08:29:13: #2 alternative fragment length(s) may be 31,97,583 bps INFO @ Tue, 16 Jun 2020 08:29:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.20_model.r WARNING @ Tue, 16 Jun 2020 08:29:13: #2 Since the d (31) 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): 31,97,583 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 08:29:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331217/SRX331217.20_summits.bed INFO @ Tue, 16 Jun 2020 08:29:17: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (31 records, 4 fields): 1 millis CompletedMACS2peakCalling