Job ID = 6498728 SRX = SRX749053 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T23:58:34 prefetch.2.10.7: 1) Downloading 'SRR1636781'... 2020-06-25T23:58:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:01:24 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:01:24 prefetch.2.10.7: 1) 'SRR1636781' was downloaded successfully Read 10788856 spots for SRR1636781/SRR1636781.sra Written 10788856 spots for SRR1636781/SRR1636781.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: 00:46:12 10788856 reads; of these: 10788856 (100.00%) were paired; of these: 304126 (2.82%) aligned concordantly 0 times 2539946 (23.54%) aligned concordantly exactly 1 time 7944784 (73.64%) aligned concordantly >1 times ---- 304126 pairs aligned concordantly 0 times; of these: 3353 (1.10%) aligned discordantly 1 time ---- 300773 pairs aligned 0 times concordantly or discordantly; of these: 601546 mates make up the pairs; of these: 417408 (69.39%) aligned 0 times 44258 (7.36%) aligned exactly 1 time 139880 (23.25%) aligned >1 times 98.07% overall alignment rate Time searching: 00:46:12 Overall time: 00:46:12 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 854141 / 10465814 = 0.0816 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 @ Fri, 26 Jun 2020 09:54:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.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 @ Fri, 26 Jun 2020 09:54:38: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:54:38: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:54:44: 1000000 INFO @ Fri, 26 Jun 2020 09:54:50: 2000000 INFO @ Fri, 26 Jun 2020 09:54:56: 3000000 INFO @ Fri, 26 Jun 2020 09:55:02: 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 @ Fri, 26 Jun 2020 09:55:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.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 @ Fri, 26 Jun 2020 09:55:08: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:55:08: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:55:08: 5000000 INFO @ Fri, 26 Jun 2020 09:55:14: 1000000 INFO @ Fri, 26 Jun 2020 09:55:15: 6000000 INFO @ Fri, 26 Jun 2020 09:55:21: 2000000 INFO @ Fri, 26 Jun 2020 09:55:22: 7000000 INFO @ Fri, 26 Jun 2020 09:55:28: 3000000 INFO @ Fri, 26 Jun 2020 09:55:28: 8000000 INFO @ Fri, 26 Jun 2020 09:55:34: 4000000 INFO @ Fri, 26 Jun 2020 09:55:35: 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 @ Fri, 26 Jun 2020 09:55:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.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 @ Fri, 26 Jun 2020 09:55:38: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:55:38: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:55:41: 5000000 INFO @ Fri, 26 Jun 2020 09:55:42: 10000000 INFO @ Fri, 26 Jun 2020 09:55:44: 1000000 INFO @ Fri, 26 Jun 2020 09:55:48: 6000000 INFO @ Fri, 26 Jun 2020 09:55:48: 11000000 INFO @ Fri, 26 Jun 2020 09:55:51: 2000000 INFO @ Fri, 26 Jun 2020 09:55:55: 7000000 INFO @ Fri, 26 Jun 2020 09:55:55: 12000000 INFO @ Fri, 26 Jun 2020 09:55:58: 3000000 INFO @ Fri, 26 Jun 2020 09:56:01: 8000000 INFO @ Fri, 26 Jun 2020 09:56:02: 13000000 INFO @ Fri, 26 Jun 2020 09:56:05: 4000000 INFO @ Fri, 26 Jun 2020 09:56:08: 9000000 INFO @ Fri, 26 Jun 2020 09:56:09: 14000000 INFO @ Fri, 26 Jun 2020 09:56:11: 5000000 INFO @ Fri, 26 Jun 2020 09:56:15: 10000000 INFO @ Fri, 26 Jun 2020 09:56:15: 15000000 INFO @ Fri, 26 Jun 2020 09:56:18: 6000000 INFO @ Fri, 26 Jun 2020 09:56:22: 11000000 INFO @ Fri, 26 Jun 2020 09:56:22: 16000000 INFO @ Fri, 26 Jun 2020 09:56:25: 7000000 INFO @ Fri, 26 Jun 2020 09:56:28: 12000000 INFO @ Fri, 26 Jun 2020 09:56:29: 17000000 INFO @ Fri, 26 Jun 2020 09:56:31: 8000000 INFO @ Fri, 26 Jun 2020 09:56:35: 13000000 INFO @ Fri, 26 Jun 2020 09:56:36: 18000000 INFO @ Fri, 26 Jun 2020 09:56:38: 9000000 INFO @ Fri, 26 Jun 2020 09:56:42: 14000000 INFO @ Fri, 26 Jun 2020 09:56:42: 19000000 INFO @ Fri, 26 Jun 2020 09:56:45: 10000000 INFO @ Fri, 26 Jun 2020 09:56:45: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:56:45: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:56:45: #1 total tags in treatment: 9630706 INFO @ Fri, 26 Jun 2020 09:56:45: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:56:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:56:45: #1 tags after filtering in treatment: 7638899 INFO @ Fri, 26 Jun 2020 09:56:45: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 26 Jun 2020 09:56:45: #1 finished! INFO @ Fri, 26 Jun 2020 09:56:45: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:56:45: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:56:46: #2 number of paired peaks: 8242 INFO @ Fri, 26 Jun 2020 09:56:46: start model_add_line... INFO @ Fri, 26 Jun 2020 09:56:47: start X-correlation... INFO @ Fri, 26 Jun 2020 09:56:47: end of X-cor INFO @ Fri, 26 Jun 2020 09:56:47: #2 finished! INFO @ Fri, 26 Jun 2020 09:56:47: #2 predicted fragment length is 149 bps INFO @ Fri, 26 Jun 2020 09:56:47: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 26 Jun 2020 09:56:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.05_model.r INFO @ Fri, 26 Jun 2020 09:56:47: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:56:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:56:48: 15000000 INFO @ Fri, 26 Jun 2020 09:56:51: 11000000 INFO @ Fri, 26 Jun 2020 09:56:55: 16000000 INFO @ Fri, 26 Jun 2020 09:56:58: 12000000 INFO @ Fri, 26 Jun 2020 09:57:02: 17000000 INFO @ Fri, 26 Jun 2020 09:57:04: 13000000 INFO @ Fri, 26 Jun 2020 09:57:07: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:57:09: 18000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:57:11: 14000000 INFO @ Fri, 26 Jun 2020 09:57:16: 19000000 INFO @ Fri, 26 Jun 2020 09:57:17: 15000000 INFO @ Fri, 26 Jun 2020 09:57:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:57:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:57:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.05_summits.bed INFO @ Fri, 26 Jun 2020 09:57:18: Done! INFO @ Fri, 26 Jun 2020 09:57:19: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:57:19: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:57:19: #1 total tags in treatment: 9630706 INFO @ Fri, 26 Jun 2020 09:57:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:57:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (17682 records, 4 fields): 16 millis INFO @ Fri, 26 Jun 2020 09:57:19: #1 tags after filtering in treatment: 7638899 INFO @ Fri, 26 Jun 2020 09:57:19: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 26 Jun 2020 09:57:19: #1 finished! INFO @ Fri, 26 Jun 2020 09:57:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:57:19: #2 looking for paired plus/minus strand peaks... CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:57:20: #2 number of paired peaks: 8242 INFO @ Fri, 26 Jun 2020 09:57:20: start model_add_line... INFO @ Fri, 26 Jun 2020 09:57:20: start X-correlation... INFO @ Fri, 26 Jun 2020 09:57:20: end of X-cor INFO @ Fri, 26 Jun 2020 09:57:20: #2 finished! INFO @ Fri, 26 Jun 2020 09:57:20: #2 predicted fragment length is 149 bps INFO @ Fri, 26 Jun 2020 09:57:20: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 26 Jun 2020 09:57:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.10_model.r INFO @ Fri, 26 Jun 2020 09:57:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:57:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:57:24: 16000000 INFO @ Fri, 26 Jun 2020 09:57:30: 17000000 INFO @ Fri, 26 Jun 2020 09:57:37: 18000000 INFO @ Fri, 26 Jun 2020 09:57:41: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:57:43: 19000000 INFO @ Fri, 26 Jun 2020 09:57:46: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:57:46: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:57:46: #1 total tags in treatment: 9630706 INFO @ Fri, 26 Jun 2020 09:57:46: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:57:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:57:46: #1 tags after filtering in treatment: 7638899 INFO @ Fri, 26 Jun 2020 09:57:46: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 26 Jun 2020 09:57:46: #1 finished! INFO @ Fri, 26 Jun 2020 09:57:46: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:57:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:57:47: #2 number of paired peaks: 8242 INFO @ Fri, 26 Jun 2020 09:57:47: start model_add_line... INFO @ Fri, 26 Jun 2020 09:57:48: start X-correlation... INFO @ Fri, 26 Jun 2020 09:57:48: end of X-cor INFO @ Fri, 26 Jun 2020 09:57:48: #2 finished! INFO @ Fri, 26 Jun 2020 09:57:48: #2 predicted fragment length is 149 bps INFO @ Fri, 26 Jun 2020 09:57:48: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 26 Jun 2020 09:57:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.20_model.r INFO @ Fri, 26 Jun 2020 09:57:48: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:57:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:57:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:57:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:57:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.10_summits.bed INFO @ Fri, 26 Jun 2020 09:57:52: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11707 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:58:06: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:58:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:58:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:58:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749053/SRX749053.20_summits.bed INFO @ Fri, 26 Jun 2020 09:58:16: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6345 records, 4 fields): 7 millis CompletedMACS2peakCalling