Job ID = 6456437 SRX = SRX3404032 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:58:01 prefetch.2.10.7: 1) Downloading 'SRR6303509'... 2020-06-21T10:58:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:00:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:00:18 prefetch.2.10.7: 1) 'SRR6303509' was downloaded successfully 2020-06-21T11:00:18 prefetch.2.10.7: 'SRR6303509' has 0 unresolved dependencies Read 29461218 spots for SRR6303509/SRR6303509.sra Written 29461218 spots for SRR6303509/SRR6303509.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: 00:06:48 29461218 reads; of these: 29461218 (100.00%) were unpaired; of these: 952072 (3.23%) aligned 0 times 23382705 (79.37%) aligned exactly 1 time 5126441 (17.40%) aligned >1 times 96.77% overall alignment rate Time searching: 00:06:48 Overall time: 00:06:48 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] 4220850 / 28509146 = 0.1481 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 20:14:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.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 20:14:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:14:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:14:23: 1000000 INFO @ Sun, 21 Jun 2020 20:14:28: 2000000 INFO @ Sun, 21 Jun 2020 20:14:34: 3000000 INFO @ Sun, 21 Jun 2020 20:14:39: 4000000 INFO @ Sun, 21 Jun 2020 20:14:44: 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 20:14:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.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 20:14:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:14:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:14:49: 6000000 INFO @ Sun, 21 Jun 2020 20:14:54: 1000000 INFO @ Sun, 21 Jun 2020 20:14:55: 7000000 INFO @ Sun, 21 Jun 2020 20:15:00: 2000000 INFO @ Sun, 21 Jun 2020 20:15:00: 8000000 INFO @ Sun, 21 Jun 2020 20:15:05: 3000000 INFO @ Sun, 21 Jun 2020 20:15:06: 9000000 INFO @ Sun, 21 Jun 2020 20:15:11: 4000000 INFO @ Sun, 21 Jun 2020 20:15:12: 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 @ Sun, 21 Jun 2020 20:15:17: 5000000 INFO @ Sun, 21 Jun 2020 20:15:17: 11000000 INFO @ Sun, 21 Jun 2020 20:15:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.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 20:15:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:15:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:15:23: 6000000 INFO @ Sun, 21 Jun 2020 20:15:23: 12000000 INFO @ Sun, 21 Jun 2020 20:15:24: 1000000 INFO @ Sun, 21 Jun 2020 20:15:28: 7000000 INFO @ Sun, 21 Jun 2020 20:15:29: 13000000 INFO @ Sun, 21 Jun 2020 20:15:30: 2000000 INFO @ Sun, 21 Jun 2020 20:15:34: 8000000 INFO @ Sun, 21 Jun 2020 20:15:34: 14000000 INFO @ Sun, 21 Jun 2020 20:15:36: 3000000 INFO @ Sun, 21 Jun 2020 20:15:40: 9000000 INFO @ Sun, 21 Jun 2020 20:15:40: 15000000 INFO @ Sun, 21 Jun 2020 20:15:41: 4000000 INFO @ Sun, 21 Jun 2020 20:15:46: 10000000 INFO @ Sun, 21 Jun 2020 20:15:46: 16000000 INFO @ Sun, 21 Jun 2020 20:15:47: 5000000 INFO @ Sun, 21 Jun 2020 20:15:51: 11000000 INFO @ Sun, 21 Jun 2020 20:15:52: 17000000 INFO @ Sun, 21 Jun 2020 20:15:53: 6000000 INFO @ Sun, 21 Jun 2020 20:15:57: 12000000 INFO @ Sun, 21 Jun 2020 20:15:57: 18000000 INFO @ Sun, 21 Jun 2020 20:15:59: 7000000 INFO @ Sun, 21 Jun 2020 20:16:03: 13000000 INFO @ Sun, 21 Jun 2020 20:16:03: 19000000 INFO @ Sun, 21 Jun 2020 20:16:04: 8000000 INFO @ Sun, 21 Jun 2020 20:16:09: 14000000 INFO @ Sun, 21 Jun 2020 20:16:09: 20000000 INFO @ Sun, 21 Jun 2020 20:16:10: 9000000 INFO @ Sun, 21 Jun 2020 20:16:14: 15000000 INFO @ Sun, 21 Jun 2020 20:16:15: 21000000 INFO @ Sun, 21 Jun 2020 20:16:16: 10000000 INFO @ Sun, 21 Jun 2020 20:16:20: 16000000 INFO @ Sun, 21 Jun 2020 20:16:21: 22000000 INFO @ Sun, 21 Jun 2020 20:16:21: 11000000 INFO @ Sun, 21 Jun 2020 20:16:26: 17000000 INFO @ Sun, 21 Jun 2020 20:16:26: 23000000 INFO @ Sun, 21 Jun 2020 20:16:27: 12000000 INFO @ Sun, 21 Jun 2020 20:16:32: 18000000 INFO @ Sun, 21 Jun 2020 20:16:32: 24000000 INFO @ Sun, 21 Jun 2020 20:16:33: 13000000 INFO @ Sun, 21 Jun 2020 20:16:34: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:16:34: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:16:34: #1 total tags in treatment: 24288296 INFO @ Sun, 21 Jun 2020 20:16:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:16:34: #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 20:16:35: #1 tags after filtering in treatment: 24288176 INFO @ Sun, 21 Jun 2020 20:16:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:16:35: #1 finished! INFO @ Sun, 21 Jun 2020 20:16:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:16:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:16:36: #2 number of paired peaks: 443 WARNING @ Sun, 21 Jun 2020 20:16:36: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Sun, 21 Jun 2020 20:16:36: start model_add_line... INFO @ Sun, 21 Jun 2020 20:16:36: start X-correlation... INFO @ Sun, 21 Jun 2020 20:16:36: end of X-cor INFO @ Sun, 21 Jun 2020 20:16:36: #2 finished! INFO @ Sun, 21 Jun 2020 20:16:36: #2 predicted fragment length is 163 bps INFO @ Sun, 21 Jun 2020 20:16:36: #2 alternative fragment length(s) may be 163 bps INFO @ Sun, 21 Jun 2020 20:16:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.05_model.r INFO @ Sun, 21 Jun 2020 20:16:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:16:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:16:37: 19000000 INFO @ Sun, 21 Jun 2020 20:16:38: 14000000 INFO @ Sun, 21 Jun 2020 20:16:43: 20000000 INFO @ Sun, 21 Jun 2020 20:16:44: 15000000 INFO @ Sun, 21 Jun 2020 20:16:49: 21000000 INFO @ Sun, 21 Jun 2020 20:16:50: 16000000 INFO @ Sun, 21 Jun 2020 20:16:55: 22000000 INFO @ Sun, 21 Jun 2020 20:16:55: 17000000 INFO @ Sun, 21 Jun 2020 20:17:01: 18000000 INFO @ Sun, 21 Jun 2020 20:17:01: 23000000 INFO @ Sun, 21 Jun 2020 20:17:06: 19000000 INFO @ Sun, 21 Jun 2020 20:17:07: 24000000 INFO @ Sun, 21 Jun 2020 20:17:09: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:17:09: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:17:09: #1 total tags in treatment: 24288296 INFO @ Sun, 21 Jun 2020 20:17:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:17:09: #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 20:17:09: #1 tags after filtering in treatment: 24288176 INFO @ Sun, 21 Jun 2020 20:17:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:17:09: #1 finished! INFO @ Sun, 21 Jun 2020 20:17:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:17:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:17:11: #2 number of paired peaks: 443 WARNING @ Sun, 21 Jun 2020 20:17:11: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Sun, 21 Jun 2020 20:17:11: start model_add_line... INFO @ Sun, 21 Jun 2020 20:17:11: start X-correlation... INFO @ Sun, 21 Jun 2020 20:17:11: end of X-cor INFO @ Sun, 21 Jun 2020 20:17:11: #2 finished! INFO @ Sun, 21 Jun 2020 20:17:11: #2 predicted fragment length is 163 bps INFO @ Sun, 21 Jun 2020 20:17:11: #2 alternative fragment length(s) may be 163 bps INFO @ Sun, 21 Jun 2020 20:17:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.10_model.r INFO @ Sun, 21 Jun 2020 20:17:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:17:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:17:12: 20000000 INFO @ Sun, 21 Jun 2020 20:17:18: 21000000 INFO @ Sun, 21 Jun 2020 20:17:23: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:17:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:17:29: 23000000 INFO @ Sun, 21 Jun 2020 20:17:34: 24000000 INFO @ Sun, 21 Jun 2020 20:17:36: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:17:36: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:17:36: #1 total tags in treatment: 24288296 INFO @ Sun, 21 Jun 2020 20:17:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:17:36: #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 20:17:37: #1 tags after filtering in treatment: 24288176 INFO @ Sun, 21 Jun 2020 20:17:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:17:37: #1 finished! INFO @ Sun, 21 Jun 2020 20:17:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:17:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:17:38: #2 number of paired peaks: 443 WARNING @ Sun, 21 Jun 2020 20:17:38: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Sun, 21 Jun 2020 20:17:38: start model_add_line... INFO @ Sun, 21 Jun 2020 20:17:38: start X-correlation... INFO @ Sun, 21 Jun 2020 20:17:38: end of X-cor INFO @ Sun, 21 Jun 2020 20:17:38: #2 finished! INFO @ Sun, 21 Jun 2020 20:17:38: #2 predicted fragment length is 163 bps INFO @ Sun, 21 Jun 2020 20:17:38: #2 alternative fragment length(s) may be 163 bps INFO @ Sun, 21 Jun 2020 20:17:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.20_model.r INFO @ Sun, 21 Jun 2020 20:17:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:17:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:17:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:17:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:17:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.05_summits.bed INFO @ Sun, 21 Jun 2020 20:17:53: Done! pass1 - making usageList (395 chroms): 2 millis pass2 - checking and writing primary data (13673 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:17:59: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:18:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:18:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:18:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.10_summits.bed INFO @ Sun, 21 Jun 2020 20:18:24: Done! pass1 - making usageList (301 chroms): 1 millis pass2 - checking and writing primary data (3225 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:18:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:18:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:18:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:18:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404032/SRX3404032.20_summits.bed INFO @ Sun, 21 Jun 2020 20:18:51: Done! pass1 - making usageList (191 chroms): 1 millis pass2 - checking and writing primary data (1042 records, 4 fields): 6 millis CompletedMACS2peakCalling