Job ID = 6456876 SRX = SRX4047175 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:21:54 prefetch.2.10.7: 1) Downloading 'SRR7126156'... 2020-06-21T11:21:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:22:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:22:45 prefetch.2.10.7: 'SRR7126156' is valid 2020-06-21T11:22:45 prefetch.2.10.7: 1) 'SRR7126156' was downloaded successfully Read 8466741 spots for SRR7126156/SRR7126156.sra Written 8466741 spots for SRR7126156/SRR7126156.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: 00:01:36 8466741 reads; of these: 8466741 (100.00%) were unpaired; of these: 723991 (8.55%) aligned 0 times 6234246 (73.63%) aligned exactly 1 time 1508504 (17.82%) aligned >1 times 91.45% overall alignment rate Time searching: 00:01:36 Overall time: 00:01:36 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 725082 / 7742750 = 0.0936 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 @ Sun, 21 Jun 2020 20:26:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.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 @ Sun, 21 Jun 2020 20:26:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:26:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:26:51: 1000000 INFO @ Sun, 21 Jun 2020 20:26:56: 2000000 INFO @ Sun, 21 Jun 2020 20:27:02: 3000000 INFO @ Sun, 21 Jun 2020 20:27:07: 4000000 INFO @ Sun, 21 Jun 2020 20:27:12: 5000000 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 @ Sun, 21 Jun 2020 20:27:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.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 @ Sun, 21 Jun 2020 20:27:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:27:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:27:18: 6000000 INFO @ Sun, 21 Jun 2020 20:27:22: 1000000 INFO @ Sun, 21 Jun 2020 20:27:25: 7000000 INFO @ Sun, 21 Jun 2020 20:27:25: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:27:25: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:27:25: #1 total tags in treatment: 7017668 INFO @ Sun, 21 Jun 2020 20:27:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:27:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:27:25: #1 tags after filtering in treatment: 7017632 INFO @ Sun, 21 Jun 2020 20:27:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:27:25: #1 finished! INFO @ Sun, 21 Jun 2020 20:27:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:27:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:27:26: #2 number of paired peaks: 886 WARNING @ Sun, 21 Jun 2020 20:27:26: Fewer paired peaks (886) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 886 pairs to build model! INFO @ Sun, 21 Jun 2020 20:27:26: start model_add_line... INFO @ Sun, 21 Jun 2020 20:27:26: start X-correlation... INFO @ Sun, 21 Jun 2020 20:27:26: end of X-cor INFO @ Sun, 21 Jun 2020 20:27:26: #2 finished! INFO @ Sun, 21 Jun 2020 20:27:26: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 20:27:26: #2 alternative fragment length(s) may be 51,585 bps INFO @ Sun, 21 Jun 2020 20:27:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.05_model.r WARNING @ Sun, 21 Jun 2020 20:27:26: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:27:26: #2 You may need to consider one of the other alternative d(s): 51,585 WARNING @ Sun, 21 Jun 2020 20:27:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:27:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:27:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:27:27: 2000000 INFO @ Sun, 21 Jun 2020 20:27:33: 3000000 INFO @ Sun, 21 Jun 2020 20:27:38: 4000000 INFO @ Sun, 21 Jun 2020 20:27:41: #3 Call peaks for each chromosome... BedGraph に変換中... INFO @ Sun, 21 Jun 2020 20:27:44: 5000000 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 @ Sun, 21 Jun 2020 20:27:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.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 @ Sun, 21 Jun 2020 20:27:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:27:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:27:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:27:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:27:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.05_summits.bed INFO @ Sun, 21 Jun 2020 20:27:48: Done! pass1 - making usageList (593 chroms): 2 millis pass2 - checking and writing primary data (6190 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:27:50: 6000000 INFO @ Sun, 21 Jun 2020 20:27:51: 1000000 INFO @ Sun, 21 Jun 2020 20:27:56: 7000000 INFO @ Sun, 21 Jun 2020 20:27:56: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:27:56: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:27:56: #1 total tags in treatment: 7017668 INFO @ Sun, 21 Jun 2020 20:27:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:27:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:27:56: #1 tags after filtering in treatment: 7017632 INFO @ Sun, 21 Jun 2020 20:27:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:27:56: #1 finished! INFO @ Sun, 21 Jun 2020 20:27:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:27:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:27:57: #2 number of paired peaks: 886 WARNING @ Sun, 21 Jun 2020 20:27:57: Fewer paired peaks (886) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 886 pairs to build model! INFO @ Sun, 21 Jun 2020 20:27:57: start model_add_line... INFO @ Sun, 21 Jun 2020 20:27:57: start X-correlation... INFO @ Sun, 21 Jun 2020 20:27:57: end of X-cor INFO @ Sun, 21 Jun 2020 20:27:57: #2 finished! INFO @ Sun, 21 Jun 2020 20:27:57: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 20:27:57: #2 alternative fragment length(s) may be 51,585 bps INFO @ Sun, 21 Jun 2020 20:27:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.10_model.r WARNING @ Sun, 21 Jun 2020 20:27:57: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:27:57: #2 You may need to consider one of the other alternative d(s): 51,585 WARNING @ Sun, 21 Jun 2020 20:27:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:27:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:27:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:27:57: 2000000 INFO @ Sun, 21 Jun 2020 20:28:03: 3000000 INFO @ Sun, 21 Jun 2020 20:28:08: 4000000 INFO @ Sun, 21 Jun 2020 20:28:12: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:28:14: 5000000 INFO @ Sun, 21 Jun 2020 20:28:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:28:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:28:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.10_summits.bed INFO @ Sun, 21 Jun 2020 20:28:19: Done! INFO @ Sun, 21 Jun 2020 20:28:20: 6000000 pass1 - making usageList (484 chroms): 1 millis pass2 - checking and writing primary data (1628 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:28:25: 7000000 INFO @ Sun, 21 Jun 2020 20:28:25: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:28:25: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:28:25: #1 total tags in treatment: 7017668 INFO @ Sun, 21 Jun 2020 20:28:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:28:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:28:26: #1 tags after filtering in treatment: 7017632 INFO @ Sun, 21 Jun 2020 20:28:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:28:26: #1 finished! INFO @ Sun, 21 Jun 2020 20:28:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:28:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:28:26: #2 number of paired peaks: 886 WARNING @ Sun, 21 Jun 2020 20:28:26: Fewer paired peaks (886) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 886 pairs to build model! INFO @ Sun, 21 Jun 2020 20:28:26: start model_add_line... INFO @ Sun, 21 Jun 2020 20:28:26: start X-correlation... INFO @ Sun, 21 Jun 2020 20:28:26: end of X-cor INFO @ Sun, 21 Jun 2020 20:28:26: #2 finished! INFO @ Sun, 21 Jun 2020 20:28:26: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 20:28:26: #2 alternative fragment length(s) may be 51,585 bps INFO @ Sun, 21 Jun 2020 20:28:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.20_model.r WARNING @ Sun, 21 Jun 2020 20:28:26: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:28:26: #2 You may need to consider one of the other alternative d(s): 51,585 WARNING @ Sun, 21 Jun 2020 20:28:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:28:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:28:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:28:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:28:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:28:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:28:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4047175/SRX4047175.20_summits.bed INFO @ Sun, 21 Jun 2020 20:28:48: Done! pass1 - making usageList (186 chroms): 1 millis pass2 - checking and writing primary data (336 records, 4 fields): 6 millis CompletedMACS2peakCalling