Job ID = 6368039 SRX = SRX466502 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:04:00 prefetch.2.10.7: 1) Downloading 'SRR1163568'... 2020-06-16T00:04:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:05:51 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:05:51 prefetch.2.10.7: 1) 'SRR1163568' was downloaded successfully Read 11726087 spots for SRR1163568/SRR1163568.sra Written 11726087 spots for SRR1163568/SRR1163568.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: 00:02:13 11726087 reads; of these: 11726087 (100.00%) were unpaired; of these: 482473 (4.11%) aligned 0 times 9733246 (83.01%) aligned exactly 1 time 1510368 (12.88%) aligned >1 times 95.89% overall alignment rate Time searching: 00:02:13 Overall time: 00:02:13 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] 7097903 / 11243614 = 0.6313 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 09:11:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.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 09:11:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:15: 1000000 INFO @ Tue, 16 Jun 2020 09:11:21: 2000000 INFO @ Tue, 16 Jun 2020 09:11:27: 3000000 INFO @ Tue, 16 Jun 2020 09:11:33: 4000000 INFO @ Tue, 16 Jun 2020 09:11:34: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:11:34: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:11:34: #1 total tags in treatment: 4145711 INFO @ Tue, 16 Jun 2020 09:11:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:34: #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 09:11:34: #1 tags after filtering in treatment: 4145711 INFO @ Tue, 16 Jun 2020 09:11:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:34: #2 number of paired peaks: 508 WARNING @ Tue, 16 Jun 2020 09:11:34: Fewer paired peaks (508) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 508 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:34: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 09:11:34: #2 alternative fragment length(s) may be 4,43 bps INFO @ Tue, 16 Jun 2020 09:11:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.05_model.r WARNING @ Tue, 16 Jun 2020 09:11:34: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:34: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Tue, 16 Jun 2020 09:11:34: #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 09:11:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:34: #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 09:11:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.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 09:11:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:46: 1000000 INFO @ Tue, 16 Jun 2020 09:11:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.05_summits.bed INFO @ Tue, 16 Jun 2020 09:11:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (616 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:52: 2000000 INFO @ Tue, 16 Jun 2020 09:11:58: 3000000 INFO @ Tue, 16 Jun 2020 09:12:04: 4000000 INFO @ Tue, 16 Jun 2020 09:12:04: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:12:04: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:12:04: #1 total tags in treatment: 4145711 INFO @ Tue, 16 Jun 2020 09:12:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:04: #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 09:12:05: #1 tags after filtering in treatment: 4145711 INFO @ Tue, 16 Jun 2020 09:12:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:05: #2 number of paired peaks: 508 WARNING @ Tue, 16 Jun 2020 09:12:05: Fewer paired peaks (508) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 508 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:05: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:05: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 09:12:05: #2 alternative fragment length(s) may be 4,43 bps INFO @ Tue, 16 Jun 2020 09:12:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.10_model.r WARNING @ Tue, 16 Jun 2020 09:12:05: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:05: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Tue, 16 Jun 2020 09:12:05: #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 09:12:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:05: #3 Pre-compute pvalue-qvalue table... 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 09:12:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.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 09:12:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:15: 1000000 INFO @ Tue, 16 Jun 2020 09:12:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.10_summits.bed INFO @ Tue, 16 Jun 2020 09:12:19: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (306 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:21: 2000000 INFO @ Tue, 16 Jun 2020 09:12:28: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:12:33: 4000000 INFO @ Tue, 16 Jun 2020 09:12:34: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:12:34: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:12:34: #1 total tags in treatment: 4145711 INFO @ Tue, 16 Jun 2020 09:12:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:34: #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 09:12:34: #1 tags after filtering in treatment: 4145711 INFO @ Tue, 16 Jun 2020 09:12:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:35: #2 number of paired peaks: 508 WARNING @ Tue, 16 Jun 2020 09:12:35: Fewer paired peaks (508) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 508 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:35: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:35: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:35: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:35: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 09:12:35: #2 alternative fragment length(s) may be 4,43 bps INFO @ Tue, 16 Jun 2020 09:12:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.20_model.r WARNING @ Tue, 16 Jun 2020 09:12:35: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:35: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Tue, 16 Jun 2020 09:12:35: #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 09:12:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:12:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466502/SRX466502.20_summits.bed INFO @ Tue, 16 Jun 2020 09:12:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (100 records, 4 fields): 1 millis CompletedMACS2peakCalling