Job ID = 6455390 SRX = SRX287750 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:02:59 prefetch.2.10.7: 1) Downloading 'SRR869939'... 2020-06-21T10:02:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:04:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:04:44 prefetch.2.10.7: 'SRR869939' is valid 2020-06-21T10:04:44 prefetch.2.10.7: 1) 'SRR869939' was downloaded successfully Read 15325380 spots for SRR869939/SRR869939.sra Written 15325380 spots for SRR869939/SRR869939.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: 00:04:59 15325380 reads; of these: 15325380 (100.00%) were unpaired; of these: 1013686 (6.61%) aligned 0 times 9393762 (61.30%) aligned exactly 1 time 4917932 (32.09%) aligned >1 times 93.39% overall alignment rate Time searching: 00:04:59 Overall time: 00:04:59 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] 2936835 / 14311694 = 0.2052 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 19:14:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.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 19:14:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:28: 1000000 INFO @ Sun, 21 Jun 2020 19:14:33: 2000000 INFO @ Sun, 21 Jun 2020 19:14:38: 3000000 INFO @ Sun, 21 Jun 2020 19:14:44: 4000000 INFO @ Sun, 21 Jun 2020 19:14:49: 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 19:14:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.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 19:14:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:54: 6000000 INFO @ Sun, 21 Jun 2020 19:14:58: 1000000 INFO @ Sun, 21 Jun 2020 19:14:59: 7000000 INFO @ Sun, 21 Jun 2020 19:15:03: 2000000 INFO @ Sun, 21 Jun 2020 19:15:05: 8000000 INFO @ Sun, 21 Jun 2020 19:15:09: 3000000 INFO @ Sun, 21 Jun 2020 19:15:10: 9000000 INFO @ Sun, 21 Jun 2020 19:15:14: 4000000 INFO @ Sun, 21 Jun 2020 19:15:16: 10000000 INFO @ Sun, 21 Jun 2020 19:15:20: 5000000 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 19:15:21: 11000000 INFO @ Sun, 21 Jun 2020 19:15:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.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 19:15:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:15:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:15:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:24: #1 total tags in treatment: 11374859 INFO @ Sun, 21 Jun 2020 19:15:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:24: #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 19:15:24: #1 tags after filtering in treatment: 11374859 INFO @ Sun, 21 Jun 2020 19:15:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:24: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:25: #2 number of paired peaks: 873 WARNING @ Sun, 21 Jun 2020 19:15:25: Fewer paired peaks (873) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 873 pairs to build model! INFO @ Sun, 21 Jun 2020 19:15:25: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:25: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:25: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:25: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:25: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 19:15:25: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sun, 21 Jun 2020 19:15:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.05_model.r INFO @ Sun, 21 Jun 2020 19:15:25: 6000000 WARNING @ Sun, 21 Jun 2020 19:15:25: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:15:25: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sun, 21 Jun 2020 19:15:25: #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 19:15:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:15:28: 1000000 INFO @ Sun, 21 Jun 2020 19:15:30: 7000000 INFO @ Sun, 21 Jun 2020 19:15:34: 2000000 INFO @ Sun, 21 Jun 2020 19:15:36: 8000000 INFO @ Sun, 21 Jun 2020 19:15:39: 3000000 INFO @ Sun, 21 Jun 2020 19:15:42: 9000000 INFO @ Sun, 21 Jun 2020 19:15:44: 4000000 INFO @ Sun, 21 Jun 2020 19:15:47: 10000000 INFO @ Sun, 21 Jun 2020 19:15:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:50: 5000000 INFO @ Sun, 21 Jun 2020 19:15:53: 11000000 INFO @ Sun, 21 Jun 2020 19:15:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:55: #1 total tags in treatment: 11374859 INFO @ Sun, 21 Jun 2020 19:15:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:55: #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 19:15:55: 6000000 INFO @ Sun, 21 Jun 2020 19:15:55: #1 tags after filtering in treatment: 11374859 INFO @ Sun, 21 Jun 2020 19:15:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:55: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:56: #2 number of paired peaks: 873 WARNING @ Sun, 21 Jun 2020 19:15:56: Fewer paired peaks (873) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 873 pairs to build model! INFO @ Sun, 21 Jun 2020 19:15:56: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:56: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:56: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:56: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:56: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 19:15:56: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sun, 21 Jun 2020 19:15:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.10_model.r WARNING @ Sun, 21 Jun 2020 19:15:56: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:15:56: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sun, 21 Jun 2020 19:15:56: #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 19:15:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:15:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.05_summits.bed INFO @ Sun, 21 Jun 2020 19:16:00: Done! pass1 - making usageList (620 chroms): 1 millis pass2 - checking and writing primary data (2328 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:16:00: 7000000 INFO @ Sun, 21 Jun 2020 19:16:05: 8000000 INFO @ Sun, 21 Jun 2020 19:16:11: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:16:16: 10000000 INFO @ Sun, 21 Jun 2020 19:16:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:16:21: 11000000 INFO @ Sun, 21 Jun 2020 19:16:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:16:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:16:24: #1 total tags in treatment: 11374859 INFO @ Sun, 21 Jun 2020 19:16:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:16:24: #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 19:16:24: #1 tags after filtering in treatment: 11374859 INFO @ Sun, 21 Jun 2020 19:16:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:16:24: #1 finished! INFO @ Sun, 21 Jun 2020 19:16:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:16:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:16:25: #2 number of paired peaks: 873 WARNING @ Sun, 21 Jun 2020 19:16:25: Fewer paired peaks (873) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 873 pairs to build model! INFO @ Sun, 21 Jun 2020 19:16:25: start model_add_line... INFO @ Sun, 21 Jun 2020 19:16:25: start X-correlation... INFO @ Sun, 21 Jun 2020 19:16:25: end of X-cor INFO @ Sun, 21 Jun 2020 19:16:25: #2 finished! INFO @ Sun, 21 Jun 2020 19:16:25: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 19:16:25: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sun, 21 Jun 2020 19:16:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.20_model.r WARNING @ Sun, 21 Jun 2020 19:16:25: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:16:25: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sun, 21 Jun 2020 19:16:25: #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 19:16:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:16:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:16:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.10_summits.bed INFO @ Sun, 21 Jun 2020 19:16:30: Done! pass1 - making usageList (509 chroms): 1 millis pass2 - checking and writing primary data (1927 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:16:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:17:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:17:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:17:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287750/SRX287750.20_summits.bed INFO @ Sun, 21 Jun 2020 19:17:00: Done! pass1 - making usageList (380 chroms): 1 millis pass2 - checking and writing primary data (915 records, 4 fields): 11 millis CompletedMACS2peakCalling