Job ID = 6368491 SRX = SRX5020721 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:28:16 prefetch.2.10.7: 1) Downloading 'SRR8201344'... 2020-06-16T00:28:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:29:17 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:29:18 prefetch.2.10.7: 'SRR8201344' is valid 2020-06-16T00:29:18 prefetch.2.10.7: 1) 'SRR8201344' was downloaded successfully Read 7880897 spots for SRR8201344/SRR8201344.sra Written 7880897 spots for SRR8201344/SRR8201344.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: 00:01:44 7880897 reads; of these: 7880897 (100.00%) were unpaired; of these: 325078 (4.12%) aligned 0 times 6329043 (80.31%) aligned exactly 1 time 1226776 (15.57%) aligned >1 times 95.88% overall alignment rate Time searching: 00:01:44 Overall time: 00:01:44 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] 506702 / 7555819 = 0.0671 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 09:33:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.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 09:33:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:02: 1000000 INFO @ Tue, 16 Jun 2020 09:34:07: 2000000 INFO @ Tue, 16 Jun 2020 09:34:13: 3000000 INFO @ Tue, 16 Jun 2020 09:34:19: 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 09:34:24: 5000000 INFO @ Tue, 16 Jun 2020 09:34:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.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 09:34:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:30: 6000000 INFO @ Tue, 16 Jun 2020 09:34:32: 1000000 INFO @ Tue, 16 Jun 2020 09:34:36: 7000000 INFO @ Tue, 16 Jun 2020 09:34:36: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:34:36: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:34:36: #1 total tags in treatment: 7049117 INFO @ Tue, 16 Jun 2020 09:34:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:36: #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 09:34:36: #1 tags after filtering in treatment: 7049117 INFO @ Tue, 16 Jun 2020 09:34:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:36: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:37: #2 number of paired peaks: 349 WARNING @ Tue, 16 Jun 2020 09:34:37: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:37: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:37: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:37: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:37: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:37: #2 predicted fragment length is 69 bps INFO @ Tue, 16 Jun 2020 09:34:37: #2 alternative fragment length(s) may be 4,69 bps INFO @ Tue, 16 Jun 2020 09:34:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.05_model.r WARNING @ Tue, 16 Jun 2020 09:34:37: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:34:37: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Tue, 16 Jun 2020 09:34:37: #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 09:34:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:38: 2000000 INFO @ Tue, 16 Jun 2020 09:34:44: 3000000 INFO @ Tue, 16 Jun 2020 09:34:49: 4000000 INFO @ Tue, 16 Jun 2020 09:34:52: #3 Call peaks for each chromosome... 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 09:34:55: 5000000 INFO @ Tue, 16 Jun 2020 09:34:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.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 09:34:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.05_summits.bed INFO @ Tue, 16 Jun 2020 09:35:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (593 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:35:01: 6000000 INFO @ Tue, 16 Jun 2020 09:35:01: 1000000 INFO @ Tue, 16 Jun 2020 09:35:07: 2000000 INFO @ Tue, 16 Jun 2020 09:35:08: 7000000 INFO @ Tue, 16 Jun 2020 09:35:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:35:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:35:08: #1 total tags in treatment: 7049117 INFO @ Tue, 16 Jun 2020 09:35:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:08: #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 09:35:08: #1 tags after filtering in treatment: 7049117 INFO @ Tue, 16 Jun 2020 09:35:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:09: #2 number of paired peaks: 349 WARNING @ Tue, 16 Jun 2020 09:35:09: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:09: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:09: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:09: #2 predicted fragment length is 69 bps INFO @ Tue, 16 Jun 2020 09:35:09: #2 alternative fragment length(s) may be 4,69 bps INFO @ Tue, 16 Jun 2020 09:35:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.10_model.r WARNING @ Tue, 16 Jun 2020 09:35:09: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:09: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Tue, 16 Jun 2020 09:35:09: #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 09:35:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:12: 3000000 INFO @ Tue, 16 Jun 2020 09:35:17: 4000000 INFO @ Tue, 16 Jun 2020 09:35:22: 5000000 INFO @ Tue, 16 Jun 2020 09:35:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:28: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:35:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.10_summits.bed INFO @ Tue, 16 Jun 2020 09:35:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (302 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:35:33: 7000000 INFO @ Tue, 16 Jun 2020 09:35:33: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:35:33: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:35:33: #1 total tags in treatment: 7049117 INFO @ Tue, 16 Jun 2020 09:35:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:33: #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 09:35:33: #1 tags after filtering in treatment: 7049117 INFO @ Tue, 16 Jun 2020 09:35:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:34: #2 number of paired peaks: 349 WARNING @ Tue, 16 Jun 2020 09:35:34: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:34: #2 predicted fragment length is 69 bps INFO @ Tue, 16 Jun 2020 09:35:34: #2 alternative fragment length(s) may be 4,69 bps INFO @ Tue, 16 Jun 2020 09:35:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.20_model.r WARNING @ Tue, 16 Jun 2020 09:35:34: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:34: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Tue, 16 Jun 2020 09:35:34: #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 09:35:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:35:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020721/SRX5020721.20_summits.bed INFO @ Tue, 16 Jun 2020 09:35:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (146 records, 4 fields): 1 millis CompletedMACS2peakCalling