Job ID = 6367974 SRX = SRX4626826 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:41:44 prefetch.2.10.7: 1) Downloading 'SRR7771409'... 2020-06-15T23:41:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:44:35 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:44:35 prefetch.2.10.7: 'SRR7771409' is valid 2020-06-15T23:44:35 prefetch.2.10.7: 1) 'SRR7771409' was downloaded successfully Read 13986632 spots for SRR7771409/SRR7771409.sra Written 13986632 spots for SRR7771409/SRR7771409.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: 00:02:17 13986632 reads; of these: 13986632 (100.00%) were unpaired; of these: 3652149 (26.11%) aligned 0 times 8609592 (61.56%) aligned exactly 1 time 1724891 (12.33%) aligned >1 times 73.89% overall alignment rate Time searching: 00:02:17 Overall time: 00:02:17 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] 8071114 / 10334483 = 0.7810 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 08:49:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.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 08:49:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:32: 1000000 INFO @ Tue, 16 Jun 2020 08:49:37: 2000000 INFO @ Tue, 16 Jun 2020 08:49:38: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 08:49:38: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 08:49:38: #1 total tags in treatment: 2263369 INFO @ Tue, 16 Jun 2020 08:49:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:49:38: #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 08:49:38: #1 tags after filtering in treatment: 2263369 INFO @ Tue, 16 Jun 2020 08:49:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:49:38: #2 number of paired peaks: 1016 INFO @ Tue, 16 Jun 2020 08:49:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:49:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:49:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:49:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:49:38: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 08:49:38: #2 alternative fragment length(s) may be 38,576 bps INFO @ Tue, 16 Jun 2020 08:49:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.05_model.r WARNING @ Tue, 16 Jun 2020 08:49:38: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:49:38: #2 You may need to consider one of the other alternative d(s): 38,576 WARNING @ Tue, 16 Jun 2020 08:49:38: #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 08:49:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:49:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:49:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:49:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.05_summits.bed INFO @ Tue, 16 Jun 2020 08:49:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (864 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 08:49:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.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 08:49:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:01: 1000000 INFO @ Tue, 16 Jun 2020 08:50:05: 2000000 INFO @ Tue, 16 Jun 2020 08:50:07: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 08:50:07: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 08:50:07: #1 total tags in treatment: 2263369 INFO @ Tue, 16 Jun 2020 08:50:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:07: #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 08:50:07: #1 tags after filtering in treatment: 2263369 INFO @ Tue, 16 Jun 2020 08:50:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:07: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:07: #2 number of paired peaks: 1016 INFO @ Tue, 16 Jun 2020 08:50:07: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:07: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:07: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:07: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:07: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 08:50:07: #2 alternative fragment length(s) may be 38,576 bps INFO @ Tue, 16 Jun 2020 08:50:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.10_model.r WARNING @ Tue, 16 Jun 2020 08:50:07: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:50:07: #2 You may need to consider one of the other alternative d(s): 38,576 WARNING @ Tue, 16 Jun 2020 08:50:07: #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 08:50:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.10_summits.bed INFO @ Tue, 16 Jun 2020 08:50:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (445 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 08:50:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.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 08:50:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:31: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:50:36: 2000000 INFO @ Tue, 16 Jun 2020 08:50:37: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 08:50:37: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 08:50:37: #1 total tags in treatment: 2263369 INFO @ Tue, 16 Jun 2020 08:50:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:37: #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 08:50:38: #1 tags after filtering in treatment: 2263369 INFO @ Tue, 16 Jun 2020 08:50:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:38: #2 number of paired peaks: 1016 INFO @ Tue, 16 Jun 2020 08:50:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:38: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 08:50:38: #2 alternative fragment length(s) may be 38,576 bps INFO @ Tue, 16 Jun 2020 08:50:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.20_model.r WARNING @ Tue, 16 Jun 2020 08:50:38: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:50:38: #2 You may need to consider one of the other alternative d(s): 38,576 WARNING @ Tue, 16 Jun 2020 08:50:38: #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 08:50:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:50:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4626826/SRX4626826.20_summits.bed INFO @ Tue, 16 Jun 2020 08:50:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (138 records, 4 fields): 1 millis CompletedMACS2peakCalling