Job ID = 6498651 SRX = SRX661062 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T00:12:04 prefetch.2.10.7: 1) Downloading 'SRR1524297'... 2020-06-26T00:12:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:16:34 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:16:34 prefetch.2.10.7: 1) 'SRR1524297' was downloaded successfully Read 39501600 spots for SRR1524297/SRR1524297.sra Written 39501600 spots for SRR1524297/SRR1524297.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: 00:05:56 39501600 reads; of these: 39501600 (100.00%) were unpaired; of these: 31757364 (80.40%) aligned 0 times 5526279 (13.99%) aligned exactly 1 time 2217957 (5.61%) aligned >1 times 19.60% overall alignment rate Time searching: 00:05:56 Overall time: 00:05:56 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 3629759 / 7744236 = 0.4687 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 @ Fri, 26 Jun 2020 09:27:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 26 Jun 2020 09:27:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:27:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:27:18: 1000000 INFO @ Fri, 26 Jun 2020 09:27:24: 2000000 INFO @ Fri, 26 Jun 2020 09:27:31: 3000000 INFO @ Fri, 26 Jun 2020 09:27:37: 4000000 INFO @ Fri, 26 Jun 2020 09:27:38: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:27:38: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:27:38: #1 total tags in treatment: 4114477 INFO @ Fri, 26 Jun 2020 09:27:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:27:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:27:38: #1 tags after filtering in treatment: 4114477 INFO @ Fri, 26 Jun 2020 09:27:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:27:38: #1 finished! INFO @ Fri, 26 Jun 2020 09:27:38: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:27:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:27:38: #2 number of paired peaks: 415 WARNING @ Fri, 26 Jun 2020 09:27:38: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Fri, 26 Jun 2020 09:27:38: start model_add_line... INFO @ Fri, 26 Jun 2020 09:27:38: start X-correlation... INFO @ Fri, 26 Jun 2020 09:27:38: end of X-cor INFO @ Fri, 26 Jun 2020 09:27:38: #2 finished! INFO @ Fri, 26 Jun 2020 09:27:38: #2 predicted fragment length is 51 bps INFO @ Fri, 26 Jun 2020 09:27:38: #2 alternative fragment length(s) may be 51 bps INFO @ Fri, 26 Jun 2020 09:27:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.05_model.r WARNING @ Fri, 26 Jun 2020 09:27:38: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:27:38: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Fri, 26 Jun 2020 09:27:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:27:38: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:27:38: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 09:27:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 26 Jun 2020 09:27:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:27:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:27:48: 1000000 INFO @ Fri, 26 Jun 2020 09:27:48: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:27:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:27:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:27:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.05_summits.bed INFO @ Fri, 26 Jun 2020 09:27:54: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1207 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:27:54: 2000000 INFO @ Fri, 26 Jun 2020 09:28:00: 3000000 INFO @ Fri, 26 Jun 2020 09:28:06: 4000000 INFO @ Fri, 26 Jun 2020 09:28:07: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:28:07: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:28:07: #1 total tags in treatment: 4114477 INFO @ Fri, 26 Jun 2020 09:28:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:28:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:28:07: #1 tags after filtering in treatment: 4114477 INFO @ Fri, 26 Jun 2020 09:28:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:28:07: #1 finished! INFO @ Fri, 26 Jun 2020 09:28:07: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:28:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:28:07: #2 number of paired peaks: 415 WARNING @ Fri, 26 Jun 2020 09:28:07: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Fri, 26 Jun 2020 09:28:07: start model_add_line... INFO @ Fri, 26 Jun 2020 09:28:07: start X-correlation... INFO @ Fri, 26 Jun 2020 09:28:07: end of X-cor INFO @ Fri, 26 Jun 2020 09:28:07: #2 finished! INFO @ Fri, 26 Jun 2020 09:28:07: #2 predicted fragment length is 51 bps INFO @ Fri, 26 Jun 2020 09:28:07: #2 alternative fragment length(s) may be 51 bps INFO @ Fri, 26 Jun 2020 09:28:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.10_model.r WARNING @ Fri, 26 Jun 2020 09:28:07: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:28:07: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Fri, 26 Jun 2020 09:28:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:28:07: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:28:07: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 09:28:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 26 Jun 2020 09:28:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:28:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:28:17: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:28:19: 1000000 INFO @ Fri, 26 Jun 2020 09:28:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:28:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:28:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.10_summits.bed INFO @ Fri, 26 Jun 2020 09:28:22: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (854 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:28:25: 2000000 INFO @ Fri, 26 Jun 2020 09:28:32: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:28:39: 4000000 INFO @ Fri, 26 Jun 2020 09:28:39: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:28:39: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:28:39: #1 total tags in treatment: 4114477 INFO @ Fri, 26 Jun 2020 09:28:39: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:28:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:28:39: #1 tags after filtering in treatment: 4114477 INFO @ Fri, 26 Jun 2020 09:28:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:28:39: #1 finished! INFO @ Fri, 26 Jun 2020 09:28:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:28:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:28:40: #2 number of paired peaks: 415 WARNING @ Fri, 26 Jun 2020 09:28:40: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Fri, 26 Jun 2020 09:28:40: start model_add_line... INFO @ Fri, 26 Jun 2020 09:28:40: start X-correlation... INFO @ Fri, 26 Jun 2020 09:28:40: end of X-cor INFO @ Fri, 26 Jun 2020 09:28:40: #2 finished! INFO @ Fri, 26 Jun 2020 09:28:40: #2 predicted fragment length is 51 bps INFO @ Fri, 26 Jun 2020 09:28:40: #2 alternative fragment length(s) may be 51 bps INFO @ Fri, 26 Jun 2020 09:28:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.20_model.r WARNING @ Fri, 26 Jun 2020 09:28:40: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:28:40: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Fri, 26 Jun 2020 09:28:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:28:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:28:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:28:50: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:28:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:28:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:28:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX661062/SRX661062.20_summits.bed INFO @ Fri, 26 Jun 2020 09:28:55: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (449 records, 4 fields): 1 millis CompletedMACS2peakCalling