Job ID = 6456439 SRX = SRX3404036 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:06:54 prefetch.2.10.7: 1) Downloading 'SRR6303513'... 2020-06-21T11:06:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:08:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:08:08 prefetch.2.10.7: 'SRR6303513' is valid 2020-06-21T11:08:08 prefetch.2.10.7: 1) 'SRR6303513' was downloaded successfully 2020-06-21T11:08:08 prefetch.2.10.7: 'SRR6303513' has 0 unresolved dependencies Read 24357846 spots for SRR6303513/SRR6303513.sra Written 24357846 spots for SRR6303513/SRR6303513.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: 00:06:17 24357846 reads; of these: 24357846 (100.00%) were unpaired; of these: 868043 (3.56%) aligned 0 times 17519777 (71.93%) aligned exactly 1 time 5970026 (24.51%) aligned >1 times 96.44% overall alignment rate Time searching: 00:06:17 Overall time: 00:06:17 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 12 files... [bam_rmdupse_core] 3828472 / 23489803 = 0.1630 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 20:20:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.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 20:20:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:20:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:20:36: 1000000 INFO @ Sun, 21 Jun 2020 20:20:41: 2000000 INFO @ Sun, 21 Jun 2020 20:20:47: 3000000 INFO @ Sun, 21 Jun 2020 20:20:53: 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 20:20:58: 5000000 INFO @ Sun, 21 Jun 2020 20:21:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.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 20:21:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:21:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:21:05: 6000000 INFO @ Sun, 21 Jun 2020 20:21:07: 1000000 INFO @ Sun, 21 Jun 2020 20:21:12: 7000000 INFO @ Sun, 21 Jun 2020 20:21:14: 2000000 INFO @ Sun, 21 Jun 2020 20:21:19: 8000000 INFO @ Sun, 21 Jun 2020 20:21:22: 3000000 INFO @ Sun, 21 Jun 2020 20:21:25: 9000000 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 20:21:29: 4000000 INFO @ Sun, 21 Jun 2020 20:21:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.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 20:21:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:21:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:21:32: 10000000 INFO @ Sun, 21 Jun 2020 20:21:37: 5000000 INFO @ Sun, 21 Jun 2020 20:21:37: 1000000 INFO @ Sun, 21 Jun 2020 20:21:39: 11000000 INFO @ Sun, 21 Jun 2020 20:21:44: 2000000 INFO @ Sun, 21 Jun 2020 20:21:44: 6000000 INFO @ Sun, 21 Jun 2020 20:21:46: 12000000 INFO @ Sun, 21 Jun 2020 20:21:51: 3000000 INFO @ Sun, 21 Jun 2020 20:21:51: 7000000 INFO @ Sun, 21 Jun 2020 20:21:53: 13000000 INFO @ Sun, 21 Jun 2020 20:21:58: 4000000 INFO @ Sun, 21 Jun 2020 20:21:59: 8000000 INFO @ Sun, 21 Jun 2020 20:22:00: 14000000 INFO @ Sun, 21 Jun 2020 20:22:05: 5000000 INFO @ Sun, 21 Jun 2020 20:22:06: 9000000 INFO @ Sun, 21 Jun 2020 20:22:07: 15000000 INFO @ Sun, 21 Jun 2020 20:22:11: 6000000 INFO @ Sun, 21 Jun 2020 20:22:13: 10000000 INFO @ Sun, 21 Jun 2020 20:22:13: 16000000 INFO @ Sun, 21 Jun 2020 20:22:18: 7000000 INFO @ Sun, 21 Jun 2020 20:22:21: 17000000 INFO @ Sun, 21 Jun 2020 20:22:21: 11000000 INFO @ Sun, 21 Jun 2020 20:22:25: 8000000 INFO @ Sun, 21 Jun 2020 20:22:27: 18000000 INFO @ Sun, 21 Jun 2020 20:22:28: 12000000 INFO @ Sun, 21 Jun 2020 20:22:32: 9000000 INFO @ Sun, 21 Jun 2020 20:22:34: 19000000 INFO @ Sun, 21 Jun 2020 20:22:35: 13000000 INFO @ Sun, 21 Jun 2020 20:22:39: 10000000 INFO @ Sun, 21 Jun 2020 20:22:39: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:22:39: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:22:39: #1 total tags in treatment: 19661331 INFO @ Sun, 21 Jun 2020 20:22:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:22:39: #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 20:22:40: #1 tags after filtering in treatment: 19661213 INFO @ Sun, 21 Jun 2020 20:22:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:22:40: #1 finished! INFO @ Sun, 21 Jun 2020 20:22:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:22:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:22:41: #2 number of paired peaks: 660 WARNING @ Sun, 21 Jun 2020 20:22:41: Fewer paired peaks (660) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 660 pairs to build model! INFO @ Sun, 21 Jun 2020 20:22:41: start model_add_line... INFO @ Sun, 21 Jun 2020 20:22:41: start X-correlation... INFO @ Sun, 21 Jun 2020 20:22:41: end of X-cor INFO @ Sun, 21 Jun 2020 20:22:41: #2 finished! INFO @ Sun, 21 Jun 2020 20:22:41: #2 predicted fragment length is 138 bps INFO @ Sun, 21 Jun 2020 20:22:41: #2 alternative fragment length(s) may be 4,138 bps INFO @ Sun, 21 Jun 2020 20:22:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.05_model.r INFO @ Sun, 21 Jun 2020 20:22:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:22:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:22:43: 14000000 INFO @ Sun, 21 Jun 2020 20:22:46: 11000000 INFO @ Sun, 21 Jun 2020 20:22:50: 15000000 INFO @ Sun, 21 Jun 2020 20:22:53: 12000000 INFO @ Sun, 21 Jun 2020 20:22:58: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:23:00: 13000000 INFO @ Sun, 21 Jun 2020 20:23:05: 17000000 INFO @ Sun, 21 Jun 2020 20:23:07: 14000000 INFO @ Sun, 21 Jun 2020 20:23:13: 18000000 INFO @ Sun, 21 Jun 2020 20:23:14: 15000000 INFO @ Sun, 21 Jun 2020 20:23:20: 19000000 INFO @ Sun, 21 Jun 2020 20:23:21: 16000000 INFO @ Sun, 21 Jun 2020 20:23:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:23:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:23:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:23:25: #1 total tags in treatment: 19661331 INFO @ Sun, 21 Jun 2020 20:23:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:23:25: #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 20:23:26: #1 tags after filtering in treatment: 19661213 INFO @ Sun, 21 Jun 2020 20:23:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:23:26: #1 finished! INFO @ Sun, 21 Jun 2020 20:23:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:23:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:23:27: #2 number of paired peaks: 660 WARNING @ Sun, 21 Jun 2020 20:23:27: Fewer paired peaks (660) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 660 pairs to build model! INFO @ Sun, 21 Jun 2020 20:23:27: start model_add_line... INFO @ Sun, 21 Jun 2020 20:23:27: start X-correlation... INFO @ Sun, 21 Jun 2020 20:23:27: end of X-cor INFO @ Sun, 21 Jun 2020 20:23:27: #2 finished! INFO @ Sun, 21 Jun 2020 20:23:27: #2 predicted fragment length is 138 bps INFO @ Sun, 21 Jun 2020 20:23:27: #2 alternative fragment length(s) may be 4,138 bps INFO @ Sun, 21 Jun 2020 20:23:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.10_model.r INFO @ Sun, 21 Jun 2020 20:23:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:23:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:23:28: 17000000 INFO @ Sun, 21 Jun 2020 20:23:34: 18000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:23:40: 19000000 INFO @ Sun, 21 Jun 2020 20:23:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:23:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:23:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.05_summits.bed INFO @ Sun, 21 Jun 2020 20:23:41: Done! pass1 - making usageList (751 chroms): 3 millis pass2 - checking and writing primary data (18904 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:23:44: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:23:44: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:23:44: #1 total tags in treatment: 19661331 INFO @ Sun, 21 Jun 2020 20:23:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:23:44: #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 20:23:45: #1 tags after filtering in treatment: 19661213 INFO @ Sun, 21 Jun 2020 20:23:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:23:45: #1 finished! INFO @ Sun, 21 Jun 2020 20:23:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:23:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:23:46: #2 number of paired peaks: 660 WARNING @ Sun, 21 Jun 2020 20:23:46: Fewer paired peaks (660) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 660 pairs to build model! INFO @ Sun, 21 Jun 2020 20:23:46: start model_add_line... INFO @ Sun, 21 Jun 2020 20:23:46: start X-correlation... INFO @ Sun, 21 Jun 2020 20:23:46: end of X-cor INFO @ Sun, 21 Jun 2020 20:23:46: #2 finished! INFO @ Sun, 21 Jun 2020 20:23:46: #2 predicted fragment length is 138 bps INFO @ Sun, 21 Jun 2020 20:23:46: #2 alternative fragment length(s) may be 4,138 bps INFO @ Sun, 21 Jun 2020 20:23:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.20_model.r INFO @ Sun, 21 Jun 2020 20:23:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:23:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:24:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:24:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:24:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:24:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:24:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.10_summits.bed INFO @ Sun, 21 Jun 2020 20:24:27: Done! pass1 - making usageList (623 chroms): 2 millis pass2 - checking and writing primary data (4807 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:24:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:24:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:24:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404036/SRX3404036.20_summits.bed INFO @ Sun, 21 Jun 2020 20:24:45: Done! pass1 - making usageList (363 chroms): 1 millis pass2 - checking and writing primary data (1215 records, 4 fields): 12 millis CompletedMACS2peakCalling