Job ID = 6455271 SRX = SRX287651 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:59:55 prefetch.2.10.7: 1) Downloading 'SRR869838'... 2020-06-21T09:59:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:01:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:02:00 prefetch.2.10.7: 'SRR869838' is valid 2020-06-21T10:02:00 prefetch.2.10.7: 1) 'SRR869838' was downloaded successfully Read 16205141 spots for SRR869838/SRR869838.sra Written 16205141 spots for SRR869838/SRR869838.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: 00:04:20 16205141 reads; of these: 16205141 (100.00%) were unpaired; of these: 1385805 (8.55%) aligned 0 times 11374345 (70.19%) aligned exactly 1 time 3444991 (21.26%) aligned >1 times 91.45% overall alignment rate Time searching: 00:04:20 Overall time: 00:04:20 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1873879 / 14819336 = 0.1264 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 19:11:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.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 19:11:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:11:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:11:20: 1000000 INFO @ Sun, 21 Jun 2020 19:11:26: 2000000 INFO @ Sun, 21 Jun 2020 19:11:32: 3000000 INFO @ Sun, 21 Jun 2020 19:11:38: 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 @ Sun, 21 Jun 2020 19:11:44: 5000000 INFO @ Sun, 21 Jun 2020 19:11:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.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 19:11:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:11:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:11:51: 6000000 INFO @ Sun, 21 Jun 2020 19:11:51: 1000000 INFO @ Sun, 21 Jun 2020 19:11:57: 7000000 INFO @ Sun, 21 Jun 2020 19:11:58: 2000000 INFO @ Sun, 21 Jun 2020 19:12:04: 8000000 INFO @ Sun, 21 Jun 2020 19:12:05: 3000000 INFO @ Sun, 21 Jun 2020 19:12:11: 9000000 INFO @ Sun, 21 Jun 2020 19:12:11: 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 @ Sun, 21 Jun 2020 19:12:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.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 19:12:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:12:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:12:17: 10000000 INFO @ Sun, 21 Jun 2020 19:12:18: 5000000 INFO @ Sun, 21 Jun 2020 19:12:21: 1000000 INFO @ Sun, 21 Jun 2020 19:12:24: 11000000 INFO @ Sun, 21 Jun 2020 19:12:24: 6000000 INFO @ Sun, 21 Jun 2020 19:12:27: 2000000 INFO @ Sun, 21 Jun 2020 19:12:31: 12000000 INFO @ Sun, 21 Jun 2020 19:12:31: 7000000 INFO @ Sun, 21 Jun 2020 19:12:34: 3000000 INFO @ Sun, 21 Jun 2020 19:12:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:12:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:12:37: #1 total tags in treatment: 12945457 INFO @ Sun, 21 Jun 2020 19:12:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:12:37: #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 19:12:37: #1 tags after filtering in treatment: 12945457 INFO @ Sun, 21 Jun 2020 19:12:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:12:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:12:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:12:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:12:37: 8000000 INFO @ Sun, 21 Jun 2020 19:12:38: #2 number of paired peaks: 558 WARNING @ Sun, 21 Jun 2020 19:12:38: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Sun, 21 Jun 2020 19:12:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:12:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:12:38: end of X-cor INFO @ Sun, 21 Jun 2020 19:12:38: #2 finished! INFO @ Sun, 21 Jun 2020 19:12:38: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 19:12:38: #2 alternative fragment length(s) may be 3,39,48,538 bps INFO @ Sun, 21 Jun 2020 19:12:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.05_model.r WARNING @ Sun, 21 Jun 2020 19:12:38: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:12:38: #2 You may need to consider one of the other alternative d(s): 3,39,48,538 WARNING @ Sun, 21 Jun 2020 19:12:38: #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 19:12:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:12:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:12:40: 4000000 INFO @ Sun, 21 Jun 2020 19:12:44: 9000000 INFO @ Sun, 21 Jun 2020 19:12:47: 5000000 INFO @ Sun, 21 Jun 2020 19:12:50: 10000000 INFO @ Sun, 21 Jun 2020 19:12:53: 6000000 INFO @ Sun, 21 Jun 2020 19:12:57: 11000000 INFO @ Sun, 21 Jun 2020 19:13:00: 7000000 INFO @ Sun, 21 Jun 2020 19:13:04: 12000000 INFO @ Sun, 21 Jun 2020 19:13:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:13:06: 8000000 INFO @ Sun, 21 Jun 2020 19:13:10: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:13:10: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:13:10: #1 total tags in treatment: 12945457 INFO @ Sun, 21 Jun 2020 19:13:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:13:10: #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 19:13:11: #1 tags after filtering in treatment: 12945457 INFO @ Sun, 21 Jun 2020 19:13:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:13:11: #1 finished! INFO @ Sun, 21 Jun 2020 19:13:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:13:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:13:12: #2 number of paired peaks: 558 WARNING @ Sun, 21 Jun 2020 19:13:12: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Sun, 21 Jun 2020 19:13:12: start model_add_line... INFO @ Sun, 21 Jun 2020 19:13:12: start X-correlation... INFO @ Sun, 21 Jun 2020 19:13:12: end of X-cor INFO @ Sun, 21 Jun 2020 19:13:12: #2 finished! INFO @ Sun, 21 Jun 2020 19:13:12: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 19:13:12: #2 alternative fragment length(s) may be 3,39,48,538 bps INFO @ Sun, 21 Jun 2020 19:13:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.10_model.r WARNING @ Sun, 21 Jun 2020 19:13:12: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:13:12: #2 You may need to consider one of the other alternative d(s): 3,39,48,538 WARNING @ Sun, 21 Jun 2020 19:13:12: #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 19:13:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:13:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:13:13: 9000000 INFO @ Sun, 21 Jun 2020 19:13:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:13:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:13:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.05_summits.bed INFO @ Sun, 21 Jun 2020 19:13:17: Done! pass1 - making usageList (511 chroms): 1 millis pass2 - checking and writing primary data (2073 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:13:19: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:13:25: 11000000 INFO @ Sun, 21 Jun 2020 19:13:31: 12000000 INFO @ Sun, 21 Jun 2020 19:13:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:13:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:13:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:13:37: #1 total tags in treatment: 12945457 INFO @ Sun, 21 Jun 2020 19:13:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:13:37: #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 19:13:38: #1 tags after filtering in treatment: 12945457 INFO @ Sun, 21 Jun 2020 19:13:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:13:38: #1 finished! INFO @ Sun, 21 Jun 2020 19:13:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:13:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:13:39: #2 number of paired peaks: 558 WARNING @ Sun, 21 Jun 2020 19:13:39: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Sun, 21 Jun 2020 19:13:39: start model_add_line... INFO @ Sun, 21 Jun 2020 19:13:39: start X-correlation... INFO @ Sun, 21 Jun 2020 19:13:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:13:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:13:39: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 19:13:39: #2 alternative fragment length(s) may be 3,39,48,538 bps INFO @ Sun, 21 Jun 2020 19:13:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.20_model.r WARNING @ Sun, 21 Jun 2020 19:13:39: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:13:39: #2 You may need to consider one of the other alternative d(s): 3,39,48,538 WARNING @ Sun, 21 Jun 2020 19:13:39: #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 19:13:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:13:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:13:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:13:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:13:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.10_summits.bed INFO @ Sun, 21 Jun 2020 19:13:49: Done! pass1 - making usageList (446 chroms): 1 millis pass2 - checking and writing primary data (1520 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:14:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:14:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:14:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:14:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287651/SRX287651.20_summits.bed INFO @ Sun, 21 Jun 2020 19:14:20: Done! pass1 - making usageList (228 chroms): 1 millis pass2 - checking and writing primary data (434 records, 4 fields): 8 millis CompletedMACS2peakCalling