Job ID = 6366818 SRX = SRX234925 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:07:53 prefetch.2.10.7: 1) Downloading 'SRR707569'... 2020-06-15T23:07:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:08:26 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:08:26 prefetch.2.10.7: 'SRR707569' is valid 2020-06-15T23:08:26 prefetch.2.10.7: 1) 'SRR707569' was downloaded successfully Read 6438791 spots for SRR707569/SRR707569.sra Written 6438791 spots for SRR707569/SRR707569.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 6438791 reads; of these: 6438791 (100.00%) were unpaired; of these: 4595963 (71.38%) aligned 0 times 1529171 (23.75%) aligned exactly 1 time 313657 (4.87%) aligned >1 times 28.62% 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] 290194 / 1842828 = 0.1575 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 08:10:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.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 08:10:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:09: 1000000 INFO @ Tue, 16 Jun 2020 08:10:12: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:10:12: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:10:12: #1 total tags in treatment: 1552634 INFO @ Tue, 16 Jun 2020 08:10:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:12: #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 08:10:12: #1 tags after filtering in treatment: 1552634 INFO @ Tue, 16 Jun 2020 08:10:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:10:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:12: #2 number of paired peaks: 485 WARNING @ Tue, 16 Jun 2020 08:10:12: Fewer paired peaks (485) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 485 pairs to build model! INFO @ Tue, 16 Jun 2020 08:10:12: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:12: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:12: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:12: #2 predicted fragment length is 61 bps INFO @ Tue, 16 Jun 2020 08:10:12: #2 alternative fragment length(s) may be 61,105,566 bps INFO @ Tue, 16 Jun 2020 08:10:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.05_model.r WARNING @ Tue, 16 Jun 2020 08:10:12: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:10:12: #2 You may need to consider one of the other alternative d(s): 61,105,566 WARNING @ Tue, 16 Jun 2020 08:10:12: #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 08:10:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:10:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:10:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:10:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:10:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.05_summits.bed INFO @ Tue, 16 Jun 2020 08:10:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (396 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 08:10:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.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 08:10:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:39: 1000000 INFO @ Tue, 16 Jun 2020 08:10:42: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:10:42: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:10:42: #1 total tags in treatment: 1552634 INFO @ Tue, 16 Jun 2020 08:10:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:42: #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 08:10:42: #1 tags after filtering in treatment: 1552634 INFO @ Tue, 16 Jun 2020 08:10:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:10:42: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:42: #2 number of paired peaks: 485 WARNING @ Tue, 16 Jun 2020 08:10:42: Fewer paired peaks (485) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 485 pairs to build model! INFO @ Tue, 16 Jun 2020 08:10:42: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:42: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:42: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:42: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:42: #2 predicted fragment length is 61 bps INFO @ Tue, 16 Jun 2020 08:10:42: #2 alternative fragment length(s) may be 61,105,566 bps INFO @ Tue, 16 Jun 2020 08:10:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.10_model.r WARNING @ Tue, 16 Jun 2020 08:10:42: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:10:42: #2 You may need to consider one of the other alternative d(s): 61,105,566 WARNING @ Tue, 16 Jun 2020 08:10:42: #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 08:10:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:10:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:10:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:10:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:10:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.10_summits.bed INFO @ Tue, 16 Jun 2020 08:10:47: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (145 records, 4 fields): 2 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 08:11:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.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 08:11:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:09: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:11:12: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:11:12: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:11:12: #1 total tags in treatment: 1552634 INFO @ Tue, 16 Jun 2020 08:11:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:11:12: #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 08:11:12: #1 tags after filtering in treatment: 1552634 INFO @ Tue, 16 Jun 2020 08:11:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:11:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:11:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:11:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:12: #2 number of paired peaks: 485 WARNING @ Tue, 16 Jun 2020 08:11:12: Fewer paired peaks (485) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 485 pairs to build model! INFO @ Tue, 16 Jun 2020 08:11:12: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:12: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:12: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:12: #2 predicted fragment length is 61 bps INFO @ Tue, 16 Jun 2020 08:11:12: #2 alternative fragment length(s) may be 61,105,566 bps INFO @ Tue, 16 Jun 2020 08:11:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.20_model.r WARNING @ Tue, 16 Jun 2020 08:11:12: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:11:12: #2 You may need to consider one of the other alternative d(s): 61,105,566 WARNING @ Tue, 16 Jun 2020 08:11:12: #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 08:11:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:11:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX234925/SRX234925.20_summits.bed INFO @ Tue, 16 Jun 2020 08:11:18: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (35 records, 4 fields): 1 millis CompletedMACS2peakCalling