Job ID = 6498729 SRX = SRX749054 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T00:02:25 prefetch.2.10.7: 1) Downloading 'SRR1636782'... 2020-06-26T00:02:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:04:25 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:04:25 prefetch.2.10.7: 1) 'SRR1636782' was downloaded successfully Read 11161888 spots for SRR1636782/SRR1636782.sra Written 11161888 spots for SRR1636782/SRR1636782.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: 00:44:58 11161888 reads; of these: 11161888 (100.00%) were paired; of these: 1197011 (10.72%) aligned concordantly 0 times 2182781 (19.56%) aligned concordantly exactly 1 time 7782096 (69.72%) aligned concordantly >1 times ---- 1197011 pairs aligned concordantly 0 times; of these: 149573 (12.50%) aligned discordantly 1 time ---- 1047438 pairs aligned 0 times concordantly or discordantly; of these: 2094876 mates make up the pairs; of these: 1256222 (59.97%) aligned 0 times 458697 (21.90%) aligned exactly 1 time 379957 (18.14%) aligned >1 times 94.37% overall alignment rate Time searching: 00:44:58 Overall time: 00:44:58 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] 930290 / 10071138 = 0.0924 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 09:56:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.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 09:56:19: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:56:19: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:56:25: 1000000 INFO @ Fri, 26 Jun 2020 09:56:30: 2000000 INFO @ Fri, 26 Jun 2020 09:56:36: 3000000 INFO @ Fri, 26 Jun 2020 09:56:41: 4000000 INFO @ Fri, 26 Jun 2020 09:56:47: 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 @ Fri, 26 Jun 2020 09:56:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.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 09:56:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:56:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:56:52: 6000000 INFO @ Fri, 26 Jun 2020 09:56:55: 1000000 INFO @ Fri, 26 Jun 2020 09:56:58: 7000000 INFO @ Fri, 26 Jun 2020 09:57:01: 2000000 INFO @ Fri, 26 Jun 2020 09:57:04: 8000000 INFO @ Fri, 26 Jun 2020 09:57:07: 3000000 INFO @ Fri, 26 Jun 2020 09:57:10: 9000000 INFO @ Fri, 26 Jun 2020 09:57:13: 4000000 INFO @ Fri, 26 Jun 2020 09:57:16: 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 @ Fri, 26 Jun 2020 09:57:18: 5000000 INFO @ Fri, 26 Jun 2020 09:57:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.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 09:57:19: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:57:19: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:57:22: 11000000 INFO @ Fri, 26 Jun 2020 09:57:24: 6000000 INFO @ Fri, 26 Jun 2020 09:57:25: 1000000 INFO @ Fri, 26 Jun 2020 09:57:28: 12000000 INFO @ Fri, 26 Jun 2020 09:57:30: 7000000 INFO @ Fri, 26 Jun 2020 09:57:31: 2000000 INFO @ Fri, 26 Jun 2020 09:57:34: 13000000 INFO @ Fri, 26 Jun 2020 09:57:36: 8000000 INFO @ Fri, 26 Jun 2020 09:57:37: 3000000 INFO @ Fri, 26 Jun 2020 09:57:40: 14000000 INFO @ Fri, 26 Jun 2020 09:57:42: 9000000 INFO @ Fri, 26 Jun 2020 09:57:43: 4000000 INFO @ Fri, 26 Jun 2020 09:57:46: 15000000 INFO @ Fri, 26 Jun 2020 09:57:48: 10000000 INFO @ Fri, 26 Jun 2020 09:57:49: 5000000 INFO @ Fri, 26 Jun 2020 09:57:52: 16000000 INFO @ Fri, 26 Jun 2020 09:57:54: 11000000 INFO @ Fri, 26 Jun 2020 09:57:55: 6000000 INFO @ Fri, 26 Jun 2020 09:57:58: 17000000 INFO @ Fri, 26 Jun 2020 09:57:59: 12000000 INFO @ Fri, 26 Jun 2020 09:58:01: 7000000 INFO @ Fri, 26 Jun 2020 09:58:04: 18000000 INFO @ Fri, 26 Jun 2020 09:58:05: 13000000 INFO @ Fri, 26 Jun 2020 09:58:06: 8000000 INFO @ Fri, 26 Jun 2020 09:58:10: 19000000 INFO @ Fri, 26 Jun 2020 09:58:11: 14000000 INFO @ Fri, 26 Jun 2020 09:58:11: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:58:11: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:58:11: #1 total tags in treatment: 9118971 INFO @ Fri, 26 Jun 2020 09:58:11: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:58:11: #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 09:58:11: #1 tags after filtering in treatment: 7056380 INFO @ Fri, 26 Jun 2020 09:58:11: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 26 Jun 2020 09:58:11: #1 finished! INFO @ Fri, 26 Jun 2020 09:58:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:58:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:58:12: 9000000 INFO @ Fri, 26 Jun 2020 09:58:12: #2 number of paired peaks: 9127 INFO @ Fri, 26 Jun 2020 09:58:12: start model_add_line... INFO @ Fri, 26 Jun 2020 09:58:13: start X-correlation... INFO @ Fri, 26 Jun 2020 09:58:13: end of X-cor INFO @ Fri, 26 Jun 2020 09:58:13: #2 finished! INFO @ Fri, 26 Jun 2020 09:58:13: #2 predicted fragment length is 139 bps INFO @ Fri, 26 Jun 2020 09:58:13: #2 alternative fragment length(s) may be 139 bps INFO @ Fri, 26 Jun 2020 09:58:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.05_model.r INFO @ Fri, 26 Jun 2020 09:58:13: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:58:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:58:17: 15000000 INFO @ Fri, 26 Jun 2020 09:58:18: 10000000 INFO @ Fri, 26 Jun 2020 09:58:23: 16000000 INFO @ Fri, 26 Jun 2020 09:58:24: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:58:29: 17000000 INFO @ Fri, 26 Jun 2020 09:58:30: 12000000 INFO @ Fri, 26 Jun 2020 09:58:31: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:58:34: 18000000 INFO @ Fri, 26 Jun 2020 09:58:36: 13000000 INFO @ Fri, 26 Jun 2020 09:58:40: 19000000 INFO @ Fri, 26 Jun 2020 09:58:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:58:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:58:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.05_summits.bed INFO @ Fri, 26 Jun 2020 09:58:41: Done! INFO @ Fri, 26 Jun 2020 09:58:41: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:58:41: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:58:41: #1 total tags in treatment: 9118971 INFO @ Fri, 26 Jun 2020 09:58:41: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:58:41: #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 (17817 records, 4 fields): 17 millis INFO @ Fri, 26 Jun 2020 09:58:42: #1 tags after filtering in treatment: 7056380 INFO @ Fri, 26 Jun 2020 09:58:42: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 26 Jun 2020 09:58:42: #1 finished! INFO @ Fri, 26 Jun 2020 09:58:42: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:58:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:58:42: 14000000 CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:58:43: #2 number of paired peaks: 9127 INFO @ Fri, 26 Jun 2020 09:58:43: start model_add_line... INFO @ Fri, 26 Jun 2020 09:58:43: start X-correlation... INFO @ Fri, 26 Jun 2020 09:58:43: end of X-cor INFO @ Fri, 26 Jun 2020 09:58:43: #2 finished! INFO @ Fri, 26 Jun 2020 09:58:43: #2 predicted fragment length is 139 bps INFO @ Fri, 26 Jun 2020 09:58:43: #2 alternative fragment length(s) may be 139 bps INFO @ Fri, 26 Jun 2020 09:58:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.10_model.r INFO @ Fri, 26 Jun 2020 09:58:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:58:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:58:47: 15000000 INFO @ Fri, 26 Jun 2020 09:58:53: 16000000 INFO @ Fri, 26 Jun 2020 09:58:58: 17000000 INFO @ Fri, 26 Jun 2020 09:59:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:59:04: 18000000 INFO @ Fri, 26 Jun 2020 09:59:10: 19000000 INFO @ Fri, 26 Jun 2020 09:59:11: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:59:11: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:59:11: #1 total tags in treatment: 9118971 INFO @ Fri, 26 Jun 2020 09:59:11: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:59:11: #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 09:59:11: #1 tags after filtering in treatment: 7056380 INFO @ Fri, 26 Jun 2020 09:59:11: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 26 Jun 2020 09:59:11: #1 finished! INFO @ Fri, 26 Jun 2020 09:59:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:59:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:59:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:59:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:59:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.10_summits.bed INFO @ Fri, 26 Jun 2020 09:59:12: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (12159 records, 4 fields): 12 millis INFO @ Fri, 26 Jun 2020 09:59:12: #2 number of paired peaks: 9127 INFO @ Fri, 26 Jun 2020 09:59:12: start model_add_line... CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:59:12: start X-correlation... INFO @ Fri, 26 Jun 2020 09:59:12: end of X-cor INFO @ Fri, 26 Jun 2020 09:59:12: #2 finished! INFO @ Fri, 26 Jun 2020 09:59:12: #2 predicted fragment length is 139 bps INFO @ Fri, 26 Jun 2020 09:59:12: #2 alternative fragment length(s) may be 139 bps INFO @ Fri, 26 Jun 2020 09:59:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.20_model.r INFO @ Fri, 26 Jun 2020 09:59:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:59:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:59:31: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:59:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:59:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:59:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749054/SRX749054.20_summits.bed INFO @ Fri, 26 Jun 2020 09:59:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6731 records, 4 fields): 8 millis CompletedMACS2peakCalling