Job ID = 6367762 SRX = SRX4082376 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:19:51 prefetch.2.10.7: 1) Downloading 'SRR7164194'... 2020-06-16T00:19:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:20:46 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:20:46 prefetch.2.10.7: 'SRR7164194' is valid 2020-06-16T00:20:46 prefetch.2.10.7: 1) 'SRR7164194' was downloaded successfully Read 6486000 spots for SRR7164194/SRR7164194.sra Written 6486000 spots for SRR7164194/SRR7164194.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: 00:01:55 6486000 reads; of these: 6486000 (100.00%) were unpaired; of these: 588855 (9.08%) aligned 0 times 4494164 (69.29%) aligned exactly 1 time 1402981 (21.63%) aligned >1 times 90.92% overall alignment rate Time searching: 00:01:55 Overall time: 00:01:55 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] 1311479 / 5897145 = 0.2224 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 09:25:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.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 09:25:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:25:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:25:24: 1000000 INFO @ Tue, 16 Jun 2020 09:25:31: 2000000 INFO @ Tue, 16 Jun 2020 09:25:38: 3000000 INFO @ Tue, 16 Jun 2020 09:25:45: 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 09:25:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.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 09:25:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:25:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:25:48: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:25:48: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:25:48: #1 total tags in treatment: 4585666 INFO @ Tue, 16 Jun 2020 09:25:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:48: #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 09:25:49: #1 tags after filtering in treatment: 4585666 INFO @ Tue, 16 Jun 2020 09:25:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:49: #2 number of paired peaks: 608 WARNING @ Tue, 16 Jun 2020 09:25:49: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Tue, 16 Jun 2020 09:25:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:49: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:25:49: #2 alternative fragment length(s) may be 4,50,546 bps INFO @ Tue, 16 Jun 2020 09:25:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.05_model.r WARNING @ Tue, 16 Jun 2020 09:25:49: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:25:49: #2 You may need to consider one of the other alternative d(s): 4,50,546 WARNING @ Tue, 16 Jun 2020 09:25:49: #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 09:25:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:25:54: 1000000 INFO @ Tue, 16 Jun 2020 09:25:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:01: 2000000 INFO @ Tue, 16 Jun 2020 09:26:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.05_summits.bed INFO @ Tue, 16 Jun 2020 09:26:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (653 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:26:08: 3000000 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 09:26:15: 4000000 INFO @ Tue, 16 Jun 2020 09:26:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.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 09:26:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:26:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:19: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:26:19: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:26:19: #1 total tags in treatment: 4585666 INFO @ Tue, 16 Jun 2020 09:26:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:19: #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 09:26:19: #1 tags after filtering in treatment: 4585666 INFO @ Tue, 16 Jun 2020 09:26:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:19: #2 number of paired peaks: 608 WARNING @ Tue, 16 Jun 2020 09:26:19: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:19: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:26:19: #2 alternative fragment length(s) may be 4,50,546 bps INFO @ Tue, 16 Jun 2020 09:26:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.10_model.r WARNING @ Tue, 16 Jun 2020 09:26:19: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:26:19: #2 You may need to consider one of the other alternative d(s): 4,50,546 WARNING @ Tue, 16 Jun 2020 09:26:19: #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 09:26:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:25: 1000000 INFO @ Tue, 16 Jun 2020 09:26:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:32: 2000000 INFO @ Tue, 16 Jun 2020 09:26:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.10_summits.bed INFO @ Tue, 16 Jun 2020 09:26:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (429 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:26:39: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:26:46: 4000000 INFO @ Tue, 16 Jun 2020 09:26:50: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:26:50: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:26:50: #1 total tags in treatment: 4585666 INFO @ Tue, 16 Jun 2020 09:26:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:50: #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 09:26:50: #1 tags after filtering in treatment: 4585666 INFO @ Tue, 16 Jun 2020 09:26:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:50: #2 number of paired peaks: 608 WARNING @ Tue, 16 Jun 2020 09:26:50: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:51: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:26:51: #2 alternative fragment length(s) may be 4,50,546 bps INFO @ Tue, 16 Jun 2020 09:26:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.20_model.r WARNING @ Tue, 16 Jun 2020 09:26:51: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:26:51: #2 You may need to consider one of the other alternative d(s): 4,50,546 WARNING @ Tue, 16 Jun 2020 09:26:51: #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 09:26:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:27:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082376/SRX4082376.20_summits.bed INFO @ Tue, 16 Jun 2020 09:27:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (183 records, 4 fields): 1 millis CompletedMACS2peakCalling