Job ID = 6453362 SRX = SRX1120694 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:23:03 prefetch.2.10.7: 1) Downloading 'SRR2129926'... 2020-06-21T08:23:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:26:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:26:16 prefetch.2.10.7: 'SRR2129926' is valid 2020-06-21T08:26:16 prefetch.2.10.7: 1) 'SRR2129926' was downloaded successfully Read 6959058 spots for SRR2129926/SRR2129926.sra Written 6959058 spots for SRR2129926/SRR2129926.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: 00:01:55 6959058 reads; of these: 6959058 (100.00%) were unpaired; of these: 2709135 (38.93%) aligned 0 times 3653161 (52.50%) aligned exactly 1 time 596762 (8.58%) aligned >1 times 61.07% overall alignment rate Time searching: 00:01:55 Overall time: 00:01:55 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] 132611 / 4249923 = 0.0312 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 17:30:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.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 17:30:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:30:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:30:50: 1000000 INFO @ Sun, 21 Jun 2020 17:30:59: 2000000 INFO @ Sun, 21 Jun 2020 17:31:08: 3000000 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 17:31:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.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 17:31:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:31:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:31:18: 4000000 INFO @ Sun, 21 Jun 2020 17:31:19: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:31:19: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:31:19: #1 total tags in treatment: 4117312 INFO @ Sun, 21 Jun 2020 17:31:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:31:19: #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 17:31:19: #1 tags after filtering in treatment: 4117057 INFO @ Sun, 21 Jun 2020 17:31:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:31:19: #1 finished! INFO @ Sun, 21 Jun 2020 17:31:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:31:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:31:20: #2 number of paired peaks: 302 WARNING @ Sun, 21 Jun 2020 17:31:20: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Sun, 21 Jun 2020 17:31:20: start model_add_line... INFO @ Sun, 21 Jun 2020 17:31:20: start X-correlation... INFO @ Sun, 21 Jun 2020 17:31:20: end of X-cor INFO @ Sun, 21 Jun 2020 17:31:20: #2 finished! INFO @ Sun, 21 Jun 2020 17:31:20: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 17:31:20: #2 alternative fragment length(s) may be 4,91,540 bps INFO @ Sun, 21 Jun 2020 17:31:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.05_model.r WARNING @ Sun, 21 Jun 2020 17:31:20: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:31:20: #2 You may need to consider one of the other alternative d(s): 4,91,540 WARNING @ Sun, 21 Jun 2020 17:31:20: #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 17:31:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:31:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:31:20: 1000000 INFO @ Sun, 21 Jun 2020 17:31:29: 2000000 INFO @ Sun, 21 Jun 2020 17:31:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:31:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:31:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:31:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.05_summits.bed INFO @ Sun, 21 Jun 2020 17:31:34: Done! pass1 - making usageList (136 chroms): 1 millis pass2 - checking and writing primary data (277 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:31:38: 3000000 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 @ Sun, 21 Jun 2020 17:31:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.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 17:31:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:31:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:31:48: 4000000 INFO @ Sun, 21 Jun 2020 17:31:49: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:31:49: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:31:49: #1 total tags in treatment: 4117312 INFO @ Sun, 21 Jun 2020 17:31:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:31:49: #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 17:31:49: #1 tags after filtering in treatment: 4117057 INFO @ Sun, 21 Jun 2020 17:31:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:31:49: #1 finished! INFO @ Sun, 21 Jun 2020 17:31:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:31:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:31:49: #2 number of paired peaks: 302 WARNING @ Sun, 21 Jun 2020 17:31:49: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Sun, 21 Jun 2020 17:31:49: start model_add_line... INFO @ Sun, 21 Jun 2020 17:31:49: start X-correlation... INFO @ Sun, 21 Jun 2020 17:31:49: end of X-cor INFO @ Sun, 21 Jun 2020 17:31:49: #2 finished! INFO @ Sun, 21 Jun 2020 17:31:49: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 17:31:49: #2 alternative fragment length(s) may be 4,91,540 bps INFO @ Sun, 21 Jun 2020 17:31:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.10_model.r WARNING @ Sun, 21 Jun 2020 17:31:49: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:31:49: #2 You may need to consider one of the other alternative d(s): 4,91,540 WARNING @ Sun, 21 Jun 2020 17:31:49: #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 17:31:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:31:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:31:50: 1000000 INFO @ Sun, 21 Jun 2020 17:31:58: 2000000 INFO @ Sun, 21 Jun 2020 17:32:00: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:32:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:32:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:32:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.10_summits.bed INFO @ Sun, 21 Jun 2020 17:32:05: Done! pass1 - making usageList (76 chroms): 1 millis pass2 - checking and writing primary data (154 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:32:07: 3000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:32:16: 4000000 INFO @ Sun, 21 Jun 2020 17:32:17: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:32:17: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:32:17: #1 total tags in treatment: 4117312 INFO @ Sun, 21 Jun 2020 17:32:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:32:17: #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 17:32:17: #1 tags after filtering in treatment: 4117057 INFO @ Sun, 21 Jun 2020 17:32:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:32:17: #1 finished! INFO @ Sun, 21 Jun 2020 17:32:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:32:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:32:18: #2 number of paired peaks: 302 WARNING @ Sun, 21 Jun 2020 17:32:18: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Sun, 21 Jun 2020 17:32:18: start model_add_line... INFO @ Sun, 21 Jun 2020 17:32:18: start X-correlation... INFO @ Sun, 21 Jun 2020 17:32:18: end of X-cor INFO @ Sun, 21 Jun 2020 17:32:18: #2 finished! INFO @ Sun, 21 Jun 2020 17:32:18: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 17:32:18: #2 alternative fragment length(s) may be 4,91,540 bps INFO @ Sun, 21 Jun 2020 17:32:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.20_model.r WARNING @ Sun, 21 Jun 2020 17:32:18: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:32:18: #2 You may need to consider one of the other alternative d(s): 4,91,540 WARNING @ Sun, 21 Jun 2020 17:32:18: #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 17:32:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:32:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:32:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:32:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:32:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:32:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120694/SRX1120694.20_summits.bed INFO @ Sun, 21 Jun 2020 17:32:32: Done! pass1 - making usageList (56 chroms): 1 millis pass2 - checking and writing primary data (79 records, 4 fields): 4 millis CompletedMACS2peakCalling