Job ID = 6456014 SRX = SRX3159471 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:24:55 prefetch.2.10.7: 1) Downloading 'SRR6004201'... 2020-06-21T10:24:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:27:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:27:00 prefetch.2.10.7: 'SRR6004201' is valid 2020-06-21T10:27:00 prefetch.2.10.7: 1) 'SRR6004201' was downloaded successfully 2020-06-21T10:27:00 prefetch.2.10.7: 'SRR6004201' has 0 unresolved dependencies Read 18572951 spots for SRR6004201/SRR6004201.sra Written 18572951 spots for SRR6004201/SRR6004201.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: 00:04:06 18572951 reads; of these: 18572951 (100.00%) were unpaired; of these: 1567107 (8.44%) aligned 0 times 14940453 (80.44%) aligned exactly 1 time 2065391 (11.12%) aligned >1 times 91.56% overall alignment rate Time searching: 00:04:06 Overall time: 00:04:06 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] 4899599 / 17005844 = 0.2881 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 19:35:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.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 19:35:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:42: 1000000 INFO @ Sun, 21 Jun 2020 19:35:48: 2000000 INFO @ Sun, 21 Jun 2020 19:35:54: 3000000 INFO @ Sun, 21 Jun 2020 19:36:00: 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 19:36:06: 5000000 INFO @ Sun, 21 Jun 2020 19:36:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.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 19:36:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:36:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:36:12: 6000000 INFO @ Sun, 21 Jun 2020 19:36:13: 1000000 INFO @ Sun, 21 Jun 2020 19:36:19: 7000000 INFO @ Sun, 21 Jun 2020 19:36:19: 2000000 INFO @ Sun, 21 Jun 2020 19:36:25: 8000000 INFO @ Sun, 21 Jun 2020 19:36:26: 3000000 INFO @ Sun, 21 Jun 2020 19:36:32: 9000000 INFO @ Sun, 21 Jun 2020 19:36:32: 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 19:36:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.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 19:36:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:36:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:36:38: 10000000 INFO @ Sun, 21 Jun 2020 19:36:39: 5000000 INFO @ Sun, 21 Jun 2020 19:36:44: 1000000 INFO @ Sun, 21 Jun 2020 19:36:46: 11000000 INFO @ Sun, 21 Jun 2020 19:36:46: 6000000 INFO @ Sun, 21 Jun 2020 19:36:52: 2000000 INFO @ Sun, 21 Jun 2020 19:36:53: 7000000 INFO @ Sun, 21 Jun 2020 19:36:53: 12000000 INFO @ Sun, 21 Jun 2020 19:36:54: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:36:54: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:36:54: #1 total tags in treatment: 12106245 INFO @ Sun, 21 Jun 2020 19:36:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:54: #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 19:36:54: #1 tags after filtering in treatment: 12106239 INFO @ Sun, 21 Jun 2020 19:36:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:54: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:56: #2 number of paired peaks: 4878 INFO @ Sun, 21 Jun 2020 19:36:56: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:56: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:56: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:56: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:56: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 19:36:56: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 21 Jun 2020 19:36:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.05_model.r INFO @ Sun, 21 Jun 2020 19:36:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:37:00: 8000000 INFO @ Sun, 21 Jun 2020 19:37:00: 3000000 INFO @ Sun, 21 Jun 2020 19:37:07: 9000000 INFO @ Sun, 21 Jun 2020 19:37:08: 4000000 INFO @ Sun, 21 Jun 2020 19:37:14: 10000000 INFO @ Sun, 21 Jun 2020 19:37:16: 5000000 INFO @ Sun, 21 Jun 2020 19:37:21: 11000000 INFO @ Sun, 21 Jun 2020 19:37:24: 6000000 INFO @ Sun, 21 Jun 2020 19:37:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:29: 12000000 INFO @ Sun, 21 Jun 2020 19:37:29: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:37:29: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:37:29: #1 total tags in treatment: 12106245 INFO @ Sun, 21 Jun 2020 19:37:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:37:29: #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 19:37:30: #1 tags after filtering in treatment: 12106239 INFO @ Sun, 21 Jun 2020 19:37:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:37:30: #1 finished! INFO @ Sun, 21 Jun 2020 19:37:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:37:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:37:31: #2 number of paired peaks: 4878 INFO @ Sun, 21 Jun 2020 19:37:31: start model_add_line... INFO @ Sun, 21 Jun 2020 19:37:31: start X-correlation... INFO @ Sun, 21 Jun 2020 19:37:31: end of X-cor INFO @ Sun, 21 Jun 2020 19:37:31: #2 finished! INFO @ Sun, 21 Jun 2020 19:37:31: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 19:37:31: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 21 Jun 2020 19:37:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.10_model.r INFO @ Sun, 21 Jun 2020 19:37:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:37:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:37:31: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:37:38: 8000000 INFO @ Sun, 21 Jun 2020 19:37:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.05_summits.bed INFO @ Sun, 21 Jun 2020 19:37:43: Done! pass1 - making usageList (353 chroms): 2 millis pass2 - checking and writing primary data (7686 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:37:45: 9000000 INFO @ Sun, 21 Jun 2020 19:37:52: 10000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:38:00: 11000000 INFO @ Sun, 21 Jun 2020 19:38:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:08: 12000000 INFO @ Sun, 21 Jun 2020 19:38:08: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:38:08: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:38:08: #1 total tags in treatment: 12106245 INFO @ Sun, 21 Jun 2020 19:38:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:38:08: #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 19:38:09: #1 tags after filtering in treatment: 12106239 INFO @ Sun, 21 Jun 2020 19:38:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:38:09: #1 finished! INFO @ Sun, 21 Jun 2020 19:38:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:38:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:38:10: #2 number of paired peaks: 4878 INFO @ Sun, 21 Jun 2020 19:38:10: start model_add_line... INFO @ Sun, 21 Jun 2020 19:38:10: start X-correlation... INFO @ Sun, 21 Jun 2020 19:38:10: end of X-cor INFO @ Sun, 21 Jun 2020 19:38:10: #2 finished! INFO @ Sun, 21 Jun 2020 19:38:10: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 19:38:10: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 21 Jun 2020 19:38:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.20_model.r INFO @ Sun, 21 Jun 2020 19:38:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:38:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:38:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.10_summits.bed INFO @ Sun, 21 Jun 2020 19:38:20: Done! pass1 - making usageList (207 chroms): 2 millis pass2 - checking and writing primary data (6326 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:38:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159471/SRX3159471.20_summits.bed INFO @ Sun, 21 Jun 2020 19:38:59: Done! pass1 - making usageList (110 chroms): 2 millis pass2 - checking and writing primary data (5111 records, 4 fields): 9 millis CompletedMACS2peakCalling