Job ID = 6366632 SRX = SRX2144179 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:55:14 prefetch.2.10.7: 1) Downloading 'SRR4188783'... 2020-06-15T22:55:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:56:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:56:04 prefetch.2.10.7: 'SRR4188783' is valid 2020-06-15T22:56:04 prefetch.2.10.7: 1) 'SRR4188783' was downloaded successfully Read 6820219 spots for SRR4188783/SRR4188783.sra Written 6820219 spots for SRR4188783/SRR4188783.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: 00:01:25 6820219 reads; of these: 6820219 (100.00%) were unpaired; of these: 979380 (14.36%) aligned 0 times 4462291 (65.43%) aligned exactly 1 time 1378548 (20.21%) aligned >1 times 85.64% overall alignment rate Time searching: 00:01:25 Overall time: 00:01:25 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] 491993 / 5840839 = 0.0842 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 07:59:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.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 07:59:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:59:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:59:44: 1000000 INFO @ Tue, 16 Jun 2020 07:59:51: 2000000 INFO @ Tue, 16 Jun 2020 07:59:58: 3000000 INFO @ Tue, 16 Jun 2020 08:00:05: 4000000 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 08:00:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.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 08:00:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:00:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:00:12: 5000000 INFO @ Tue, 16 Jun 2020 08:00:15: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:00:15: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:00:15: #1 total tags in treatment: 5348846 INFO @ Tue, 16 Jun 2020 08:00:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:00:15: #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 08:00:15: #1 tags after filtering in treatment: 5348846 INFO @ Tue, 16 Jun 2020 08:00:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:00:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:00:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:00:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:00:15: 1000000 INFO @ Tue, 16 Jun 2020 08:00:15: #2 number of paired peaks: 553 WARNING @ Tue, 16 Jun 2020 08:00:15: Fewer paired peaks (553) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 553 pairs to build model! INFO @ Tue, 16 Jun 2020 08:00:15: start model_add_line... INFO @ Tue, 16 Jun 2020 08:00:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:00:15: end of X-cor INFO @ Tue, 16 Jun 2020 08:00:15: #2 finished! INFO @ Tue, 16 Jun 2020 08:00:15: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:00:15: #2 alternative fragment length(s) may be 4,48 bps INFO @ Tue, 16 Jun 2020 08:00:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.05_model.r WARNING @ Tue, 16 Jun 2020 08:00:15: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:00:15: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Tue, 16 Jun 2020 08:00:15: #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 08:00:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:00:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:00:24: 2000000 INFO @ Tue, 16 Jun 2020 08:00:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:00:30: 3000000 INFO @ Tue, 16 Jun 2020 08:00:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:00:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:00:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.05_summits.bed INFO @ Tue, 16 Jun 2020 08:00:31: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (586 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 08:00:37: 4000000 INFO @ Tue, 16 Jun 2020 08:00:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.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 08:00:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:00:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:00:45: 5000000 INFO @ Tue, 16 Jun 2020 08:00:45: 1000000 INFO @ Tue, 16 Jun 2020 08:00:47: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:00:47: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:00:47: #1 total tags in treatment: 5348846 INFO @ Tue, 16 Jun 2020 08:00:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:00:47: #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 08:00:47: #1 tags after filtering in treatment: 5348846 INFO @ Tue, 16 Jun 2020 08:00:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:00:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:00:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:00:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:00:48: #2 number of paired peaks: 553 WARNING @ Tue, 16 Jun 2020 08:00:48: Fewer paired peaks (553) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 553 pairs to build model! INFO @ Tue, 16 Jun 2020 08:00:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:00:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:00:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:00:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:00:48: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:00:48: #2 alternative fragment length(s) may be 4,48 bps INFO @ Tue, 16 Jun 2020 08:00:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.10_model.r WARNING @ Tue, 16 Jun 2020 08:00:48: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:00:48: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Tue, 16 Jun 2020 08:00:48: #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 08:00:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:00:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:00:52: 2000000 INFO @ Tue, 16 Jun 2020 08:00:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:00:59: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:01:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.10_summits.bed INFO @ Tue, 16 Jun 2020 08:01:04: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (392 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:01:06: 4000000 INFO @ Tue, 16 Jun 2020 08:01:12: 5000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:01:15: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:01:15: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:01:15: #1 total tags in treatment: 5348846 INFO @ Tue, 16 Jun 2020 08:01:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:01:15: #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 08:01:15: #1 tags after filtering in treatment: 5348846 INFO @ Tue, 16 Jun 2020 08:01:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:01:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:01:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:01:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:01:15: #2 number of paired peaks: 553 WARNING @ Tue, 16 Jun 2020 08:01:15: Fewer paired peaks (553) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 553 pairs to build model! INFO @ Tue, 16 Jun 2020 08:01:15: start model_add_line... INFO @ Tue, 16 Jun 2020 08:01:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:01:15: end of X-cor INFO @ Tue, 16 Jun 2020 08:01:15: #2 finished! INFO @ Tue, 16 Jun 2020 08:01:15: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:01:15: #2 alternative fragment length(s) may be 4,48 bps INFO @ Tue, 16 Jun 2020 08:01:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.20_model.r WARNING @ Tue, 16 Jun 2020 08:01:15: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:01:15: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Tue, 16 Jun 2020 08:01:15: #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 08:01:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:01:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:01:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:01:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144179/SRX2144179.20_summits.bed INFO @ Tue, 16 Jun 2020 08:01:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (156 records, 4 fields): 1 millis CompletedMACS2peakCalling