Job ID = 6366822 SRX = SRX2350721 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:06:23 prefetch.2.10.7: 1) Downloading 'SRR5024030'... 2020-06-15T23:06:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:07:39 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:07:39 prefetch.2.10.7: 'SRR5024030' is valid 2020-06-15T23:07:39 prefetch.2.10.7: 1) 'SRR5024030' was downloaded successfully Read 9815437 spots for SRR5024030/SRR5024030.sra Written 9815437 spots for SRR5024030/SRR5024030.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: 00:02:20 9815437 reads; of these: 9815437 (100.00%) were unpaired; of these: 540117 (5.50%) aligned 0 times 6730535 (68.57%) aligned exactly 1 time 2544785 (25.93%) aligned >1 times 94.50% overall alignment rate Time searching: 00:02:20 Overall time: 00:02:20 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] 1659936 / 9275320 = 0.1790 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 08:13:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.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 08:13:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:08: 1000000 INFO @ Tue, 16 Jun 2020 08:13:14: 2000000 INFO @ Tue, 16 Jun 2020 08:13:21: 3000000 INFO @ Tue, 16 Jun 2020 08:13:27: 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 08:13:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.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 08:13:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:33: 5000000 INFO @ Tue, 16 Jun 2020 08:13:38: 1000000 INFO @ Tue, 16 Jun 2020 08:13:40: 6000000 INFO @ Tue, 16 Jun 2020 08:13:45: 2000000 INFO @ Tue, 16 Jun 2020 08:13:46: 7000000 INFO @ Tue, 16 Jun 2020 08:13:51: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:13:51: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:13:51: #1 total tags in treatment: 7615384 INFO @ Tue, 16 Jun 2020 08:13:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:51: #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 08:13:51: 3000000 INFO @ Tue, 16 Jun 2020 08:13:51: #1 tags after filtering in treatment: 7615384 INFO @ Tue, 16 Jun 2020 08:13:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:51: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:51: #2 number of paired peaks: 647 WARNING @ Tue, 16 Jun 2020 08:13:51: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:51: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:51: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:13:51: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 08:13:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.05_model.r WARNING @ Tue, 16 Jun 2020 08:13:51: #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 08:13:51: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 08:13:51: #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 08:13:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:13:57: 4000000 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 08:14:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.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 08:14:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:03: 5000000 INFO @ Tue, 16 Jun 2020 08:14:08: 1000000 INFO @ Tue, 16 Jun 2020 08:14:09: 6000000 INFO @ Tue, 16 Jun 2020 08:14:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:15: 2000000 INFO @ Tue, 16 Jun 2020 08:14:15: 7000000 INFO @ Tue, 16 Jun 2020 08:14:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.05_summits.bed INFO @ Tue, 16 Jun 2020 08:14:17: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (695 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:14:19: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:14:19: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:14:19: #1 total tags in treatment: 7615384 INFO @ Tue, 16 Jun 2020 08:14:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:19: #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 08:14:19: #1 tags after filtering in treatment: 7615384 INFO @ Tue, 16 Jun 2020 08:14:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:20: #2 number of paired peaks: 647 WARNING @ Tue, 16 Jun 2020 08:14:20: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:20: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:14:20: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 08:14:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.10_model.r WARNING @ Tue, 16 Jun 2020 08:14:20: #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 08:14:20: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 08:14:20: #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 08:14:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:21: 3000000 INFO @ Tue, 16 Jun 2020 08:14:27: 4000000 INFO @ Tue, 16 Jun 2020 08:14:33: 5000000 INFO @ Tue, 16 Jun 2020 08:14:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:39: 6000000 INFO @ Tue, 16 Jun 2020 08:14:45: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:14:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.10_summits.bed INFO @ Tue, 16 Jun 2020 08:14:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (415 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:14:48: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:14:48: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:14:48: #1 total tags in treatment: 7615384 INFO @ Tue, 16 Jun 2020 08:14:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:48: #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 08:14:49: #1 tags after filtering in treatment: 7615384 INFO @ Tue, 16 Jun 2020 08:14:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:49: #2 number of paired peaks: 647 WARNING @ Tue, 16 Jun 2020 08:14:49: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:49: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:14:49: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 08:14:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.20_model.r WARNING @ Tue, 16 Jun 2020 08:14:49: #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 08:14:49: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 08:14:49: #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 08:14:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:15:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350721/SRX2350721.20_summits.bed INFO @ Tue, 16 Jun 2020 08:15:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (171 records, 4 fields): 1 millis CompletedMACS2peakCalling