Job ID = 6366554 SRX = SRX188620 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:02:38 prefetch.2.10.7: 1) Downloading 'SRR573733'... 2020-06-15T23:02:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:03:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:03:00 prefetch.2.10.7: 'SRR573733' is valid 2020-06-15T23:03:00 prefetch.2.10.7: 1) 'SRR573733' was downloaded successfully Read 2488882 spots for SRR573733/SRR573733.sra Written 2488882 spots for SRR573733/SRR573733.sra 2020-06-15T23:03:18 prefetch.2.10.7: 1) Downloading 'SRR573734'... 2020-06-15T23:03:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:03:48 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:03:48 prefetch.2.10.7: 'SRR573734' is valid 2020-06-15T23:03:48 prefetch.2.10.7: 1) 'SRR573734' was downloaded successfully Read 4693546 spots for SRR573734/SRR573734.sra Written 4693546 spots for SRR573734/SRR573734.sra 2020-06-15T23:04:11 prefetch.2.10.7: 1) Downloading 'SRR573735'... 2020-06-15T23:04:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:04:31 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:04:31 prefetch.2.10.7: 'SRR573735' is valid 2020-06-15T23:04:31 prefetch.2.10.7: 1) 'SRR573735' was downloaded successfully Read 3180657 spots for SRR573735/SRR573735.sra Written 3180657 spots for SRR573735/SRR573735.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: 00:00:41 10363085 reads; of these: 10363085 (100.00%) were unpaired; of these: 9554496 (92.20%) aligned 0 times 697719 (6.73%) aligned exactly 1 time 110870 (1.07%) aligned >1 times 7.80% overall alignment rate Time searching: 00:00:41 Overall time: 00:00:41 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] 25843 / 808589 = 0.0320 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 08:06:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.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 08:06:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:16: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:06:16: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:06:16: #1 total tags in treatment: 782746 INFO @ Tue, 16 Jun 2020 08:06:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:16: #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 08:06:16: #1 tags after filtering in treatment: 782746 INFO @ Tue, 16 Jun 2020 08:06:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:17: #2 number of paired peaks: 268 WARNING @ Tue, 16 Jun 2020 08:06:17: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:17: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:06:17: #2 alternative fragment length(s) may be 30,81,108,174,292,377,458,518,572 bps INFO @ Tue, 16 Jun 2020 08:06:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.05_model.r WARNING @ Tue, 16 Jun 2020 08:06:17: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:17: #2 You may need to consider one of the other alternative d(s): 30,81,108,174,292,377,458,518,572 WARNING @ Tue, 16 Jun 2020 08:06:17: #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 08:06:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.05_summits.bed INFO @ Tue, 16 Jun 2020 08:06:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (35 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 08:06:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.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 08:06:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:46: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:06:46: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:06:46: #1 total tags in treatment: 782746 INFO @ Tue, 16 Jun 2020 08:06:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:46: #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 08:06:46: #1 tags after filtering in treatment: 782746 INFO @ Tue, 16 Jun 2020 08:06:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:46: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:46: #2 number of paired peaks: 268 WARNING @ Tue, 16 Jun 2020 08:06:46: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:46: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:06:46: #2 alternative fragment length(s) may be 30,81,108,174,292,377,458,518,572 bps INFO @ Tue, 16 Jun 2020 08:06:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.10_model.r WARNING @ Tue, 16 Jun 2020 08:06:46: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:46: #2 You may need to consider one of the other alternative d(s): 30,81,108,174,292,377,458,518,572 WARNING @ Tue, 16 Jun 2020 08:06:46: #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 08:06:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.10_summits.bed INFO @ Tue, 16 Jun 2020 08:06:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (13 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 08:07:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.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 08:07:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:12: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:07:16: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:07:16: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:07:16: #1 total tags in treatment: 782746 INFO @ Tue, 16 Jun 2020 08:07:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:16: #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 08:07:16: #1 tags after filtering in treatment: 782746 INFO @ Tue, 16 Jun 2020 08:07:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:16: #2 number of paired peaks: 268 WARNING @ Tue, 16 Jun 2020 08:07:16: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:16: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:07:16: #2 alternative fragment length(s) may be 30,81,108,174,292,377,458,518,572 bps INFO @ Tue, 16 Jun 2020 08:07:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.20_model.r WARNING @ Tue, 16 Jun 2020 08:07:16: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:07:16: #2 You may need to consider one of the other alternative d(s): 30,81,108,174,292,377,458,518,572 WARNING @ Tue, 16 Jun 2020 08:07:16: #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 08:07:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX188620/SRX188620.20_summits.bed INFO @ Tue, 16 Jun 2020 08:07:19: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling