Job ID = 6508416 SRX = SRX287670 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:03:57 prefetch.2.10.7: 1) Downloading 'SRR869858'... 2020-06-26T14:03:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:05:24 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:05:25 prefetch.2.10.7: 'SRR869858' is valid 2020-06-26T14:05:25 prefetch.2.10.7: 1) 'SRR869858' was downloaded successfully Read 13389851 spots for SRR869858/SRR869858.sra Written 13389851 spots for SRR869858/SRR869858.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: 00:03:58 13389851 reads; of these: 13389851 (100.00%) were unpaired; of these: 961630 (7.18%) aligned 0 times 8386953 (62.64%) aligned exactly 1 time 4041268 (30.18%) aligned >1 times 92.82% overall alignment rate Time searching: 00:03:58 Overall time: 00:03:58 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] 2019815 / 12428221 = 0.1625 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 23:13:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.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 23:13:38: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:13:38: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:13:44: 1000000 INFO @ Fri, 26 Jun 2020 23:13:49: 2000000 INFO @ Fri, 26 Jun 2020 23:13:55: 3000000 INFO @ Fri, 26 Jun 2020 23:14:00: 4000000 INFO @ Fri, 26 Jun 2020 23:14:06: 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 @ Fri, 26 Jun 2020 23:14:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.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 23:14:08: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:14:08: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:14:12: 6000000 INFO @ Fri, 26 Jun 2020 23:14:14: 1000000 INFO @ Fri, 26 Jun 2020 23:14:17: 7000000 INFO @ Fri, 26 Jun 2020 23:14:20: 2000000 INFO @ Fri, 26 Jun 2020 23:14:23: 8000000 INFO @ Fri, 26 Jun 2020 23:14:26: 3000000 INFO @ Fri, 26 Jun 2020 23:14:29: 9000000 INFO @ Fri, 26 Jun 2020 23:14:31: 4000000 INFO @ Fri, 26 Jun 2020 23:14:35: 10000000 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 23:14:37: 5000000 INFO @ Fri, 26 Jun 2020 23:14:38: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:14:38: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:14:38: #1 total tags in treatment: 10408406 INFO @ Fri, 26 Jun 2020 23:14:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:14:38: #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 23:14:38: #1 tags after filtering in treatment: 10408406 INFO @ Fri, 26 Jun 2020 23:14:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:14:38: #1 finished! INFO @ Fri, 26 Jun 2020 23:14:38: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:14:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:14:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.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 23:14:38: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:14:38: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:14:39: #2 number of paired peaks: 864 WARNING @ Fri, 26 Jun 2020 23:14:39: Fewer paired peaks (864) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 864 pairs to build model! INFO @ Fri, 26 Jun 2020 23:14:39: start model_add_line... INFO @ Fri, 26 Jun 2020 23:14:39: start X-correlation... INFO @ Fri, 26 Jun 2020 23:14:39: end of X-cor INFO @ Fri, 26 Jun 2020 23:14:39: #2 finished! INFO @ Fri, 26 Jun 2020 23:14:39: #2 predicted fragment length is 42 bps INFO @ Fri, 26 Jun 2020 23:14:39: #2 alternative fragment length(s) may be 4,42 bps INFO @ Fri, 26 Jun 2020 23:14:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.05_model.r WARNING @ Fri, 26 Jun 2020 23:14:39: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:14:39: #2 You may need to consider one of the other alternative d(s): 4,42 WARNING @ Fri, 26 Jun 2020 23:14:39: #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 23:14:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:14:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:14:43: 6000000 INFO @ Fri, 26 Jun 2020 23:14:43: 1000000 INFO @ Fri, 26 Jun 2020 23:14:49: 2000000 INFO @ Fri, 26 Jun 2020 23:14:49: 7000000 INFO @ Fri, 26 Jun 2020 23:14:54: 3000000 INFO @ Fri, 26 Jun 2020 23:14:55: 8000000 INFO @ Fri, 26 Jun 2020 23:14:59: 4000000 INFO @ Fri, 26 Jun 2020 23:15:00: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:15:02: 9000000 INFO @ Fri, 26 Jun 2020 23:15:04: 5000000 INFO @ Fri, 26 Jun 2020 23:15:07: 10000000 INFO @ Fri, 26 Jun 2020 23:15:09: 6000000 INFO @ Fri, 26 Jun 2020 23:15:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:15:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:15:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.05_summits.bed INFO @ Fri, 26 Jun 2020 23:15:10: Done! INFO @ Fri, 26 Jun 2020 23:15:10: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:15:10: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:15:10: #1 total tags in treatment: 10408406 INFO @ Fri, 26 Jun 2020 23:15:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:15:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (612 chroms): 1 millis pass2 - checking and writing primary data (2220 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:15:10: #1 tags after filtering in treatment: 10408406 INFO @ Fri, 26 Jun 2020 23:15:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:15:10: #1 finished! INFO @ Fri, 26 Jun 2020 23:15:10: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:15:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:15:11: #2 number of paired peaks: 864 WARNING @ Fri, 26 Jun 2020 23:15:11: Fewer paired peaks (864) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 864 pairs to build model! INFO @ Fri, 26 Jun 2020 23:15:11: start model_add_line... INFO @ Fri, 26 Jun 2020 23:15:11: start X-correlation... INFO @ Fri, 26 Jun 2020 23:15:11: end of X-cor INFO @ Fri, 26 Jun 2020 23:15:11: #2 finished! INFO @ Fri, 26 Jun 2020 23:15:11: #2 predicted fragment length is 42 bps INFO @ Fri, 26 Jun 2020 23:15:11: #2 alternative fragment length(s) may be 4,42 bps INFO @ Fri, 26 Jun 2020 23:15:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.10_model.r WARNING @ Fri, 26 Jun 2020 23:15:11: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:15:11: #2 You may need to consider one of the other alternative d(s): 4,42 WARNING @ Fri, 26 Jun 2020 23:15:11: #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 23:15:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:15:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:15:15: 7000000 INFO @ Fri, 26 Jun 2020 23:15:20: 8000000 INFO @ Fri, 26 Jun 2020 23:15:25: 9000000 INFO @ Fri, 26 Jun 2020 23:15:30: 10000000 INFO @ Fri, 26 Jun 2020 23:15:32: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:15:33: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:15:33: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:15:33: #1 total tags in treatment: 10408406 INFO @ Fri, 26 Jun 2020 23:15:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:15:33: #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 23:15:33: #1 tags after filtering in treatment: 10408406 INFO @ Fri, 26 Jun 2020 23:15:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:15:33: #1 finished! INFO @ Fri, 26 Jun 2020 23:15:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:15:33: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:15:34: #2 number of paired peaks: 864 WARNING @ Fri, 26 Jun 2020 23:15:34: Fewer paired peaks (864) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 864 pairs to build model! INFO @ Fri, 26 Jun 2020 23:15:34: start model_add_line... INFO @ Fri, 26 Jun 2020 23:15:34: start X-correlation... INFO @ Fri, 26 Jun 2020 23:15:34: end of X-cor INFO @ Fri, 26 Jun 2020 23:15:34: #2 finished! INFO @ Fri, 26 Jun 2020 23:15:34: #2 predicted fragment length is 42 bps INFO @ Fri, 26 Jun 2020 23:15:34: #2 alternative fragment length(s) may be 4,42 bps INFO @ Fri, 26 Jun 2020 23:15:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.20_model.r WARNING @ Fri, 26 Jun 2020 23:15:34: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:15:34: #2 You may need to consider one of the other alternative d(s): 4,42 WARNING @ Fri, 26 Jun 2020 23:15:34: #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 23:15:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:15:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:15:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:15:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:15:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.10_summits.bed INFO @ Fri, 26 Jun 2020 23:15:42: Done! pass1 - making usageList (517 chroms): 2 millis pass2 - checking and writing primary data (1877 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:15:54: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:16:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:16:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:16:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287670/SRX287670.20_summits.bed INFO @ Fri, 26 Jun 2020 23:16:04: Done! pass1 - making usageList (367 chroms): 1 millis pass2 - checking and writing primary data (815 records, 4 fields): 12 millis CompletedMACS2peakCalling