Job ID = 6368008 SRX = SRX466471 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:57:50 prefetch.2.10.7: 1) Downloading 'SRR1163537'... 2020-06-15T23:57:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:58:23 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:58:23 prefetch.2.10.7: 'SRR1163537' is valid 2020-06-15T23:58:23 prefetch.2.10.7: 1) 'SRR1163537' was downloaded successfully Read 2533543 spots for SRR1163537/SRR1163537.sra Written 2533543 spots for SRR1163537/SRR1163537.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: 00:00:38 2533543 reads; of these: 2533543 (100.00%) were unpaired; of these: 215128 (8.49%) aligned 0 times 1800072 (71.05%) aligned exactly 1 time 518343 (20.46%) aligned >1 times 91.51% overall alignment rate Time searching: 00:00:38 Overall time: 00:00:38 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] 390818 / 2318415 = 0.1686 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 09:00:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.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 09:00:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:00:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:00:24: 1000000 INFO @ Tue, 16 Jun 2020 09:00:31: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:00:31: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:00:31: #1 total tags in treatment: 1927597 INFO @ Tue, 16 Jun 2020 09:00:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:00:31: #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 09:00:31: #1 tags after filtering in treatment: 1927597 INFO @ Tue, 16 Jun 2020 09:00:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:00:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:00:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:00:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:00:32: #2 number of paired peaks: 603 WARNING @ Tue, 16 Jun 2020 09:00:32: Fewer paired peaks (603) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 603 pairs to build model! INFO @ Tue, 16 Jun 2020 09:00:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:00:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:00:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:00:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:00:32: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:00:32: #2 alternative fragment length(s) may be 49,447,495,595 bps INFO @ Tue, 16 Jun 2020 09:00:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.05_model.r WARNING @ Tue, 16 Jun 2020 09:00:32: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:00:32: #2 You may need to consider one of the other alternative d(s): 49,447,495,595 WARNING @ Tue, 16 Jun 2020 09:00:32: #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 09:00:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:00:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:00:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:00:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:00:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:00:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.05_summits.bed INFO @ Tue, 16 Jun 2020 09:00:39: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (484 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 09:00:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.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 09:00:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:00:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:00:53: 1000000 INFO @ Tue, 16 Jun 2020 09:01:00: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:01:00: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:01:00: #1 total tags in treatment: 1927597 INFO @ Tue, 16 Jun 2020 09:01:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:01:00: #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 09:01:00: #1 tags after filtering in treatment: 1927597 INFO @ Tue, 16 Jun 2020 09:01:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:01:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:01:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:01:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:01:00: #2 number of paired peaks: 603 WARNING @ Tue, 16 Jun 2020 09:01:00: Fewer paired peaks (603) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 603 pairs to build model! INFO @ Tue, 16 Jun 2020 09:01:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:01:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:01:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:01:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:01:00: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:01:00: #2 alternative fragment length(s) may be 49,447,495,595 bps INFO @ Tue, 16 Jun 2020 09:01:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.10_model.r WARNING @ Tue, 16 Jun 2020 09:01:00: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:01:00: #2 You may need to consider one of the other alternative d(s): 49,447,495,595 WARNING @ Tue, 16 Jun 2020 09:01:00: #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 09:01:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:01:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:01:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:01:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:01:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:01:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.10_summits.bed INFO @ Tue, 16 Jun 2020 09:01:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (284 records, 4 fields): 1 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 09:01:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.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 09:01:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:16: #1 read treatment tags... BedGraph に変換しました。 INFO @ Tue, 16 Jun 2020 09:01:25: 1000000 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:01:34: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:01:34: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:01:34: #1 total tags in treatment: 1927597 INFO @ Tue, 16 Jun 2020 09:01:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:01:34: #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 09:01:34: #1 tags after filtering in treatment: 1927597 INFO @ Tue, 16 Jun 2020 09:01:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:01:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:01:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:01:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:01:34: #2 number of paired peaks: 603 WARNING @ Tue, 16 Jun 2020 09:01:34: Fewer paired peaks (603) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 603 pairs to build model! INFO @ Tue, 16 Jun 2020 09:01:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:01:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:01:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:01:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:01:34: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:01:34: #2 alternative fragment length(s) may be 49,447,495,595 bps INFO @ Tue, 16 Jun 2020 09:01:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.20_model.r WARNING @ Tue, 16 Jun 2020 09:01:34: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:01:34: #2 You may need to consider one of the other alternative d(s): 49,447,495,595 WARNING @ Tue, 16 Jun 2020 09:01:34: #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 09:01:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:01:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:01:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:01:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:01:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:01:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466471/SRX466471.20_summits.bed INFO @ Tue, 16 Jun 2020 09:01:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (106 records, 4 fields): 3 millis CompletedMACS2peakCalling