Job ID = 6456452 SRX = SRX3404049 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:55:46 prefetch.2.10.7: 1) Downloading 'SRR6303526'... 2020-06-21T10:55:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:57:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:57:58 prefetch.2.10.7: 'SRR6303526' is valid 2020-06-21T10:57:58 prefetch.2.10.7: 1) 'SRR6303526' was downloaded successfully 2020-06-21T10:57:58 prefetch.2.10.7: 'SRR6303526' has 0 unresolved dependencies Read 17892526 spots for SRR6303526/SRR6303526.sra Written 17892526 spots for SRR6303526/SRR6303526.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: 00:05:05 17892526 reads; of these: 17892526 (100.00%) were unpaired; of these: 634695 (3.55%) aligned 0 times 12735222 (71.18%) aligned exactly 1 time 4522609 (25.28%) aligned >1 times 96.45% overall alignment rate Time searching: 00:05:05 Overall time: 00:05:05 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] 2052752 / 17257831 = 0.1189 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 20:08:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.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 20:08:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:08:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:08:29: 1000000 INFO @ Sun, 21 Jun 2020 20:08:36: 2000000 INFO @ Sun, 21 Jun 2020 20:08:42: 3000000 INFO @ Sun, 21 Jun 2020 20:08:49: 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 20:08:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.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 20:08:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:08:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:08:55: 5000000 INFO @ Sun, 21 Jun 2020 20:08:59: 1000000 INFO @ Sun, 21 Jun 2020 20:09:02: 6000000 INFO @ Sun, 21 Jun 2020 20:09:06: 2000000 INFO @ Sun, 21 Jun 2020 20:09:09: 7000000 INFO @ Sun, 21 Jun 2020 20:09:12: 3000000 INFO @ Sun, 21 Jun 2020 20:09:16: 8000000 INFO @ Sun, 21 Jun 2020 20:09:18: 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 20:09:23: 9000000 INFO @ Sun, 21 Jun 2020 20:09:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.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 20:09:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:09:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:09:24: 5000000 INFO @ Sun, 21 Jun 2020 20:09:30: 10000000 INFO @ Sun, 21 Jun 2020 20:09:30: 1000000 INFO @ Sun, 21 Jun 2020 20:09:31: 6000000 INFO @ Sun, 21 Jun 2020 20:09:37: 11000000 INFO @ Sun, 21 Jun 2020 20:09:37: 7000000 INFO @ Sun, 21 Jun 2020 20:09:37: 2000000 INFO @ Sun, 21 Jun 2020 20:09:43: 8000000 INFO @ Sun, 21 Jun 2020 20:09:44: 12000000 INFO @ Sun, 21 Jun 2020 20:09:44: 3000000 INFO @ Sun, 21 Jun 2020 20:09:50: 9000000 INFO @ Sun, 21 Jun 2020 20:09:51: 13000000 INFO @ Sun, 21 Jun 2020 20:09:51: 4000000 INFO @ Sun, 21 Jun 2020 20:09:56: 10000000 INFO @ Sun, 21 Jun 2020 20:09:58: 14000000 INFO @ Sun, 21 Jun 2020 20:09:58: 5000000 INFO @ Sun, 21 Jun 2020 20:10:02: 11000000 INFO @ Sun, 21 Jun 2020 20:10:05: 15000000 INFO @ Sun, 21 Jun 2020 20:10:05: 6000000 INFO @ Sun, 21 Jun 2020 20:10:06: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:10:06: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:10:06: #1 total tags in treatment: 15205079 INFO @ Sun, 21 Jun 2020 20:10:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:10:06: #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 20:10:07: #1 tags after filtering in treatment: 15204986 INFO @ Sun, 21 Jun 2020 20:10:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:10:07: #1 finished! INFO @ Sun, 21 Jun 2020 20:10:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:10:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:10:08: #2 number of paired peaks: 729 WARNING @ Sun, 21 Jun 2020 20:10:08: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Sun, 21 Jun 2020 20:10:08: start model_add_line... INFO @ Sun, 21 Jun 2020 20:10:08: start X-correlation... INFO @ Sun, 21 Jun 2020 20:10:08: end of X-cor INFO @ Sun, 21 Jun 2020 20:10:08: #2 finished! INFO @ Sun, 21 Jun 2020 20:10:08: #2 predicted fragment length is 105 bps INFO @ Sun, 21 Jun 2020 20:10:08: #2 alternative fragment length(s) may be 4,105 bps INFO @ Sun, 21 Jun 2020 20:10:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.05_model.r INFO @ Sun, 21 Jun 2020 20:10:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:10:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:10:09: 12000000 INFO @ Sun, 21 Jun 2020 20:10:12: 7000000 INFO @ Sun, 21 Jun 2020 20:10:15: 13000000 INFO @ Sun, 21 Jun 2020 20:10:19: 8000000 INFO @ Sun, 21 Jun 2020 20:10:21: 14000000 INFO @ Sun, 21 Jun 2020 20:10:26: 9000000 INFO @ Sun, 21 Jun 2020 20:10:28: 15000000 INFO @ Sun, 21 Jun 2020 20:10:29: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:10:29: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:10:29: #1 total tags in treatment: 15205079 INFO @ Sun, 21 Jun 2020 20:10:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:10:29: #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 20:10:30: #1 tags after filtering in treatment: 15204986 INFO @ Sun, 21 Jun 2020 20:10:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:10:30: #1 finished! INFO @ Sun, 21 Jun 2020 20:10:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:10:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:10:31: #2 number of paired peaks: 729 WARNING @ Sun, 21 Jun 2020 20:10:31: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Sun, 21 Jun 2020 20:10:31: start model_add_line... INFO @ Sun, 21 Jun 2020 20:10:31: start X-correlation... INFO @ Sun, 21 Jun 2020 20:10:31: end of X-cor INFO @ Sun, 21 Jun 2020 20:10:31: #2 finished! INFO @ Sun, 21 Jun 2020 20:10:31: #2 predicted fragment length is 105 bps INFO @ Sun, 21 Jun 2020 20:10:31: #2 alternative fragment length(s) may be 4,105 bps INFO @ Sun, 21 Jun 2020 20:10:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.10_model.r INFO @ Sun, 21 Jun 2020 20:10:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:10:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:10:33: 10000000 INFO @ Sun, 21 Jun 2020 20:10:39: 11000000 INFO @ Sun, 21 Jun 2020 20:10:42: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:10:45: 12000000 INFO @ Sun, 21 Jun 2020 20:10:52: 13000000 INFO @ Sun, 21 Jun 2020 20:10:59: 14000000 INFO @ Sun, 21 Jun 2020 20:10:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:10:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:10:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.05_summits.bed INFO @ Sun, 21 Jun 2020 20:10:59: Done! pass1 - making usageList (510 chroms): 1 millis pass2 - checking and writing primary data (2360 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:11:05: 15000000 INFO @ Sun, 21 Jun 2020 20:11:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:11:06: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:11:06: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:11:06: #1 total tags in treatment: 15205079 INFO @ Sun, 21 Jun 2020 20:11:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:11:06: #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 20:11:07: #1 tags after filtering in treatment: 15204986 INFO @ Sun, 21 Jun 2020 20:11:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:11:07: #1 finished! INFO @ Sun, 21 Jun 2020 20:11:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:11:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:11:08: #2 number of paired peaks: 729 WARNING @ Sun, 21 Jun 2020 20:11:08: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Sun, 21 Jun 2020 20:11:08: start model_add_line... INFO @ Sun, 21 Jun 2020 20:11:08: start X-correlation... INFO @ Sun, 21 Jun 2020 20:11:08: end of X-cor INFO @ Sun, 21 Jun 2020 20:11:08: #2 finished! INFO @ Sun, 21 Jun 2020 20:11:08: #2 predicted fragment length is 105 bps INFO @ Sun, 21 Jun 2020 20:11:08: #2 alternative fragment length(s) may be 4,105 bps INFO @ Sun, 21 Jun 2020 20:11:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.20_model.r INFO @ Sun, 21 Jun 2020 20:11:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:11:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:11:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:11:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:11:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.10_summits.bed INFO @ Sun, 21 Jun 2020 20:11:22: Done! pass1 - making usageList (318 chroms): 1 millis pass2 - checking and writing primary data (1176 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:11:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:11:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:11:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:11:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404049/SRX3404049.20_summits.bed INFO @ Sun, 21 Jun 2020 20:11:59: Done! pass1 - making usageList (177 chroms): 1 millis pass2 - checking and writing primary data (466 records, 4 fields): 7 millis CompletedMACS2peakCalling