Job ID = 6368533 SRX = SRX5020761 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:18:21 prefetch.2.10.7: 1) Downloading 'SRR8201384'... 2020-06-16T00:18:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:20:00 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:20:01 prefetch.2.10.7: 'SRR8201384' is valid 2020-06-16T00:20:01 prefetch.2.10.7: 1) 'SRR8201384' was downloaded successfully 2020-06-16T00:20:01 prefetch.2.10.7: 'SRR8201384' has 0 unresolved dependencies Read 15276123 spots for SRR8201384/SRR8201384.sra Written 15276123 spots for SRR8201384/SRR8201384.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: 00:05:09 15276123 reads; of these: 15276123 (100.00%) were unpaired; of these: 3564470 (23.33%) aligned 0 times 9763623 (63.91%) aligned exactly 1 time 1948030 (12.75%) aligned >1 times 76.67% overall alignment rate Time searching: 00:05:09 Overall time: 00:05:09 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1520522 / 11711653 = 0.1298 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 09:29:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.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 09:29:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:27: 1000000 INFO @ Tue, 16 Jun 2020 09:29:33: 2000000 INFO @ Tue, 16 Jun 2020 09:29:39: 3000000 INFO @ Tue, 16 Jun 2020 09:29:45: 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 09:29:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.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 09:29:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:52: 5000000 INFO @ Tue, 16 Jun 2020 09:29:58: 1000000 INFO @ Tue, 16 Jun 2020 09:29:58: 6000000 INFO @ Tue, 16 Jun 2020 09:30:05: 2000000 INFO @ Tue, 16 Jun 2020 09:30:05: 7000000 INFO @ Tue, 16 Jun 2020 09:30:11: 3000000 INFO @ Tue, 16 Jun 2020 09:30:12: 8000000 INFO @ Tue, 16 Jun 2020 09:30:18: 4000000 INFO @ Tue, 16 Jun 2020 09:30:19: 9000000 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 09:30:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.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 09:30:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:30:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:30:25: 5000000 INFO @ Tue, 16 Jun 2020 09:30:26: 10000000 INFO @ Tue, 16 Jun 2020 09:30:27: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 09:30:27: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 09:30:27: #1 total tags in treatment: 10191131 INFO @ Tue, 16 Jun 2020 09:30:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:27: #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 09:30:27: #1 tags after filtering in treatment: 10191131 INFO @ Tue, 16 Jun 2020 09:30:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:30:27: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:28: #2 number of paired peaks: 461 WARNING @ Tue, 16 Jun 2020 09:30:28: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:28: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:28: 1000000 INFO @ Tue, 16 Jun 2020 09:30:28: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:28: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:28: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:28: #2 predicted fragment length is 93 bps INFO @ Tue, 16 Jun 2020 09:30:28: #2 alternative fragment length(s) may be 93 bps INFO @ Tue, 16 Jun 2020 09:30:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.05_model.r WARNING @ Tue, 16 Jun 2020 09:30:28: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:30:28: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Tue, 16 Jun 2020 09:30:28: #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 09:30:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:30:32: 6000000 INFO @ Tue, 16 Jun 2020 09:30:35: 2000000 INFO @ Tue, 16 Jun 2020 09:30:39: 7000000 INFO @ Tue, 16 Jun 2020 09:30:42: 3000000 INFO @ Tue, 16 Jun 2020 09:30:46: 8000000 INFO @ Tue, 16 Jun 2020 09:30:49: 4000000 INFO @ Tue, 16 Jun 2020 09:30:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:53: 9000000 INFO @ Tue, 16 Jun 2020 09:30:56: 5000000 INFO @ Tue, 16 Jun 2020 09:31:00: 10000000 INFO @ Tue, 16 Jun 2020 09:31:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.05_summits.bed INFO @ Tue, 16 Jun 2020 09:31:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1669 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:31:01: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 09:31:01: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 09:31:01: #1 total tags in treatment: 10191131 INFO @ Tue, 16 Jun 2020 09:31:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:01: #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 09:31:01: #1 tags after filtering in treatment: 10191131 INFO @ Tue, 16 Jun 2020 09:31:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:01: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:02: #2 number of paired peaks: 461 WARNING @ Tue, 16 Jun 2020 09:31:02: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:02: #2 predicted fragment length is 93 bps INFO @ Tue, 16 Jun 2020 09:31:02: #2 alternative fragment length(s) may be 93 bps INFO @ Tue, 16 Jun 2020 09:31:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.10_model.r WARNING @ Tue, 16 Jun 2020 09:31:02: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:31:02: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Tue, 16 Jun 2020 09:31:02: #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 09:31:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:03: 6000000 INFO @ Tue, 16 Jun 2020 09:31:09: 7000000 INFO @ Tue, 16 Jun 2020 09:31:15: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:31:21: 9000000 INFO @ Tue, 16 Jun 2020 09:31:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:31:28: 10000000 INFO @ Tue, 16 Jun 2020 09:31:29: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 09:31:29: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 09:31:29: #1 total tags in treatment: 10191131 INFO @ Tue, 16 Jun 2020 09:31:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:29: #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 09:31:29: #1 tags after filtering in treatment: 10191131 INFO @ Tue, 16 Jun 2020 09:31:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:30: #2 number of paired peaks: 461 WARNING @ Tue, 16 Jun 2020 09:31:30: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:30: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:30: #2 predicted fragment length is 93 bps INFO @ Tue, 16 Jun 2020 09:31:30: #2 alternative fragment length(s) may be 93 bps INFO @ Tue, 16 Jun 2020 09:31:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.20_model.r WARNING @ Tue, 16 Jun 2020 09:31:30: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:31:30: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Tue, 16 Jun 2020 09:31:30: #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 09:31:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.10_summits.bed INFO @ Tue, 16 Jun 2020 09:31:33: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1016 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:31:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020761/SRX5020761.20_summits.bed INFO @ Tue, 16 Jun 2020 09:32:00: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (578 records, 4 fields): 2 millis CompletedMACS2peakCalling