Job ID = 6459744 SRX = SRX7672885 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:30:02 prefetch.2.10.7: 1) Downloading 'SRR11017732'... 2020-06-21T13:30:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:33:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:33:29 prefetch.2.10.7: 1) 'SRR11017732' was downloaded successfully Read 18580671 spots for SRR11017732/SRR11017732.sra Written 18580671 spots for SRR11017732/SRR11017732.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: 00:02:25 18580671 reads; of these: 18580671 (100.00%) were unpaired; of these: 15416532 (82.97%) aligned 0 times 2334575 (12.56%) aligned exactly 1 time 829564 (4.46%) aligned >1 times 17.03% overall alignment rate Time searching: 00:02:25 Overall time: 00:02:25 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] 410840 / 3164139 = 0.1298 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 22:38:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.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 22:38:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:38:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:38:26: 1000000 INFO @ Sun, 21 Jun 2020 22:38:32: 2000000 INFO @ Sun, 21 Jun 2020 22:38:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:38:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:38:37: #1 total tags in treatment: 2753299 INFO @ Sun, 21 Jun 2020 22:38:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:38:37: #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 22:38:37: #1 tags after filtering in treatment: 2753231 INFO @ Sun, 21 Jun 2020 22:38:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:38:37: #1 finished! INFO @ Sun, 21 Jun 2020 22:38:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:38:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:38:37: #2 number of paired peaks: 584 WARNING @ Sun, 21 Jun 2020 22:38:37: Fewer paired peaks (584) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 584 pairs to build model! INFO @ Sun, 21 Jun 2020 22:38:37: start model_add_line... INFO @ Sun, 21 Jun 2020 22:38:37: start X-correlation... INFO @ Sun, 21 Jun 2020 22:38:37: end of X-cor INFO @ Sun, 21 Jun 2020 22:38:37: #2 finished! INFO @ Sun, 21 Jun 2020 22:38:37: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 22:38:37: #2 alternative fragment length(s) may be 55 bps INFO @ Sun, 21 Jun 2020 22:38:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.05_model.r WARNING @ Sun, 21 Jun 2020 22:38:37: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:38:37: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sun, 21 Jun 2020 22:38:37: #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 22:38:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:38:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:38:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:38:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:38:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:38:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.05_summits.bed INFO @ Sun, 21 Jun 2020 22:38:47: Done! pass1 - making usageList (301 chroms): 1 millis pass2 - checking and writing primary data (676 records, 4 fields): 11 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 @ Sun, 21 Jun 2020 22:38:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.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 22:38:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:38:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:38:56: 1000000 INFO @ Sun, 21 Jun 2020 22:39:01: 2000000 INFO @ Sun, 21 Jun 2020 22:39:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:39:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:39:06: #1 total tags in treatment: 2753299 INFO @ Sun, 21 Jun 2020 22:39:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:39:06: #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 22:39:07: #1 tags after filtering in treatment: 2753231 INFO @ Sun, 21 Jun 2020 22:39:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:39:07: #1 finished! INFO @ Sun, 21 Jun 2020 22:39:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:39:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:39:07: #2 number of paired peaks: 584 WARNING @ Sun, 21 Jun 2020 22:39:07: Fewer paired peaks (584) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 584 pairs to build model! INFO @ Sun, 21 Jun 2020 22:39:07: start model_add_line... INFO @ Sun, 21 Jun 2020 22:39:07: start X-correlation... INFO @ Sun, 21 Jun 2020 22:39:07: end of X-cor INFO @ Sun, 21 Jun 2020 22:39:07: #2 finished! INFO @ Sun, 21 Jun 2020 22:39:07: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 22:39:07: #2 alternative fragment length(s) may be 55 bps INFO @ Sun, 21 Jun 2020 22:39:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.10_model.r WARNING @ Sun, 21 Jun 2020 22:39:07: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:39:07: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sun, 21 Jun 2020 22:39:07: #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 22:39:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:39:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:39:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:39:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:39:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:39:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.10_summits.bed INFO @ Sun, 21 Jun 2020 22:39:17: Done! pass1 - making usageList (165 chroms): 0 millis pass2 - checking and writing primary data (362 records, 4 fields): 6 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 @ Sun, 21 Jun 2020 22:39:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.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 22:39:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:39:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:39:27: 1000000 INFO @ Sun, 21 Jun 2020 22:39:34: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:39:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:39:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:39:40: #1 total tags in treatment: 2753299 INFO @ Sun, 21 Jun 2020 22:39:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:39:40: #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 22:39:40: #1 tags after filtering in treatment: 2753231 INFO @ Sun, 21 Jun 2020 22:39:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:39:40: #1 finished! INFO @ Sun, 21 Jun 2020 22:39:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:39:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:39:40: #2 number of paired peaks: 584 WARNING @ Sun, 21 Jun 2020 22:39:40: Fewer paired peaks (584) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 584 pairs to build model! INFO @ Sun, 21 Jun 2020 22:39:40: start model_add_line... INFO @ Sun, 21 Jun 2020 22:39:40: start X-correlation... INFO @ Sun, 21 Jun 2020 22:39:40: end of X-cor INFO @ Sun, 21 Jun 2020 22:39:40: #2 finished! INFO @ Sun, 21 Jun 2020 22:39:40: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 22:39:40: #2 alternative fragment length(s) may be 55 bps INFO @ Sun, 21 Jun 2020 22:39:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.20_model.r WARNING @ Sun, 21 Jun 2020 22:39:40: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:39:40: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sun, 21 Jun 2020 22:39:40: #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 22:39:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:39:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:39:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:39:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:39:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:39:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7672885/SRX7672885.20_summits.bed INFO @ Sun, 21 Jun 2020 22:39:51: Done! pass1 - making usageList (116 chroms): 1 millis pass2 - checking and writing primary data (210 records, 4 fields): 6 millis CompletedMACS2peakCalling