Job ID = 6365847 SRX = SRX002674 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:22:59 prefetch.2.10.7: 1) Downloading 'SRR013608'... 2020-06-15T22:22:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:23:20 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:23:21 prefetch.2.10.7: 'SRR013608' is valid 2020-06-15T22:23:21 prefetch.2.10.7: 1) 'SRR013608' was downloaded successfully Read 5588641 spots for SRR013608/SRR013608.sra Written 5588641 spots for SRR013608/SRR013608.sra 2020-06-15T22:23:45 prefetch.2.10.7: 1) Downloading 'SRR013609'... 2020-06-15T22:23:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:24:13 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:24:13 prefetch.2.10.7: 'SRR013609' is valid 2020-06-15T22:24:13 prefetch.2.10.7: 1) 'SRR013609' was downloaded successfully Read 4196074 spots for SRR013609/SRR013609.sra Written 4196074 spots for SRR013609/SRR013609.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: 00:01:31 9784715 reads; of these: 9784715 (100.00%) were unpaired; of these: 278830 (2.85%) aligned 0 times 7839784 (80.12%) aligned exactly 1 time 1666101 (17.03%) aligned >1 times 97.15% overall alignment rate Time searching: 00:01:31 Overall time: 00:01:31 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] 746406 / 9505885 = 0.0785 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 07:28:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.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 07:28:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:28:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:28:17: 1000000 INFO @ Tue, 16 Jun 2020 07:28:22: 2000000 INFO @ Tue, 16 Jun 2020 07:28:27: 3000000 INFO @ Tue, 16 Jun 2020 07:28:32: 4000000 INFO @ Tue, 16 Jun 2020 07:28:37: 5000000 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 07:28:41: 6000000 INFO @ Tue, 16 Jun 2020 07:28:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.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 07:28:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:28:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:28:46: 7000000 INFO @ Tue, 16 Jun 2020 07:28:47: 1000000 INFO @ Tue, 16 Jun 2020 07:28:51: 8000000 INFO @ Tue, 16 Jun 2020 07:28:52: 2000000 INFO @ Tue, 16 Jun 2020 07:28:55: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 07:28:55: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 07:28:55: #1 total tags in treatment: 8759479 INFO @ Tue, 16 Jun 2020 07:28:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:28:55: #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 07:28:55: #1 tags after filtering in treatment: 8759479 INFO @ Tue, 16 Jun 2020 07:28:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:28:55: #1 finished! INFO @ Tue, 16 Jun 2020 07:28:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:28:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:28:56: #2 number of paired peaks: 295 WARNING @ Tue, 16 Jun 2020 07:28:56: Fewer paired peaks (295) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 295 pairs to build model! INFO @ Tue, 16 Jun 2020 07:28:56: start model_add_line... INFO @ Tue, 16 Jun 2020 07:28:56: start X-correlation... INFO @ Tue, 16 Jun 2020 07:28:56: end of X-cor INFO @ Tue, 16 Jun 2020 07:28:56: #2 finished! INFO @ Tue, 16 Jun 2020 07:28:56: #2 predicted fragment length is 28 bps INFO @ Tue, 16 Jun 2020 07:28:56: #2 alternative fragment length(s) may be 2,28 bps INFO @ Tue, 16 Jun 2020 07:28:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.05_model.r WARNING @ Tue, 16 Jun 2020 07:28:56: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:28:56: #2 You may need to consider one of the other alternative d(s): 2,28 WARNING @ Tue, 16 Jun 2020 07:28:56: #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 07:28:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:28:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:28:57: 3000000 INFO @ Tue, 16 Jun 2020 07:29:02: 4000000 INFO @ Tue, 16 Jun 2020 07:29:07: 5000000 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 07:29:12: 6000000 INFO @ Tue, 16 Jun 2020 07:29:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.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 07:29:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:29:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:29:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:29:17: 1000000 INFO @ Tue, 16 Jun 2020 07:29:17: 7000000 INFO @ Tue, 16 Jun 2020 07:29:22: 2000000 INFO @ Tue, 16 Jun 2020 07:29:22: 8000000 INFO @ Tue, 16 Jun 2020 07:29:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:29:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:29:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.05_summits.bed INFO @ Tue, 16 Jun 2020 07:29:22: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (486 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:29:26: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 07:29:26: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 07:29:26: #1 total tags in treatment: 8759479 INFO @ Tue, 16 Jun 2020 07:29:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:29:26: #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 07:29:26: #1 tags after filtering in treatment: 8759479 INFO @ Tue, 16 Jun 2020 07:29:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:29:26: #1 finished! INFO @ Tue, 16 Jun 2020 07:29:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:29:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:29:27: #2 number of paired peaks: 295 WARNING @ Tue, 16 Jun 2020 07:29:27: Fewer paired peaks (295) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 295 pairs to build model! INFO @ Tue, 16 Jun 2020 07:29:27: start model_add_line... INFO @ Tue, 16 Jun 2020 07:29:27: start X-correlation... INFO @ Tue, 16 Jun 2020 07:29:27: end of X-cor INFO @ Tue, 16 Jun 2020 07:29:27: #2 finished! INFO @ Tue, 16 Jun 2020 07:29:27: #2 predicted fragment length is 28 bps INFO @ Tue, 16 Jun 2020 07:29:27: #2 alternative fragment length(s) may be 2,28 bps INFO @ Tue, 16 Jun 2020 07:29:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.10_model.r WARNING @ Tue, 16 Jun 2020 07:29:27: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:29:27: #2 You may need to consider one of the other alternative d(s): 2,28 WARNING @ Tue, 16 Jun 2020 07:29:27: #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 07:29:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:29:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:29:27: 3000000 INFO @ Tue, 16 Jun 2020 07:29:32: 4000000 INFO @ Tue, 16 Jun 2020 07:29:37: 5000000 INFO @ Tue, 16 Jun 2020 07:29:42: 6000000 INFO @ Tue, 16 Jun 2020 07:29:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:29:47: 7000000 INFO @ Tue, 16 Jun 2020 07:29:52: 8000000 INFO @ Tue, 16 Jun 2020 07:29:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:29:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:29:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.10_summits.bed INFO @ Tue, 16 Jun 2020 07:29:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (224 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:29:55: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 07:29:55: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 07:29:55: #1 total tags in treatment: 8759479 INFO @ Tue, 16 Jun 2020 07:29:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:29:55: #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 07:29:56: #1 tags after filtering in treatment: 8759479 INFO @ Tue, 16 Jun 2020 07:29:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:29:56: #1 finished! INFO @ Tue, 16 Jun 2020 07:29:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:29:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:29:56: #2 number of paired peaks: 295 WARNING @ Tue, 16 Jun 2020 07:29:56: Fewer paired peaks (295) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 295 pairs to build model! INFO @ Tue, 16 Jun 2020 07:29:56: start model_add_line... INFO @ Tue, 16 Jun 2020 07:29:56: start X-correlation... INFO @ Tue, 16 Jun 2020 07:29:56: end of X-cor INFO @ Tue, 16 Jun 2020 07:29:56: #2 finished! INFO @ Tue, 16 Jun 2020 07:29:56: #2 predicted fragment length is 28 bps INFO @ Tue, 16 Jun 2020 07:29:56: #2 alternative fragment length(s) may be 2,28 bps INFO @ Tue, 16 Jun 2020 07:29:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.20_model.r WARNING @ Tue, 16 Jun 2020 07:29:56: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:29:56: #2 You may need to consider one of the other alternative d(s): 2,28 WARNING @ Tue, 16 Jun 2020 07:29:56: #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 07:29:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:29:56: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:30:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:30:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:30:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:30:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX002674/SRX002674.20_summits.bed INFO @ Tue, 16 Jun 2020 07:30:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (62 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。