Job ID = 6498743 SRX = SRX749079 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T00:03:11 prefetch.2.10.7: 1) Downloading 'SRR1636807'... 2020-06-26T00:03:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:06:24 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:06:24 prefetch.2.10.7: 1) 'SRR1636807' was downloaded successfully Read 19395330 spots for SRR1636807/SRR1636807.sra Written 19395330 spots for SRR1636807/SRR1636807.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: 00:37:15 19395330 reads; of these: 19395330 (100.00%) were paired; of these: 1214946 (6.26%) aligned concordantly 0 times 14654467 (75.56%) aligned concordantly exactly 1 time 3525917 (18.18%) aligned concordantly >1 times ---- 1214946 pairs aligned concordantly 0 times; of these: 12036 (0.99%) aligned discordantly 1 time ---- 1202910 pairs aligned 0 times concordantly or discordantly; of these: 2405820 mates make up the pairs; of these: 1859304 (77.28%) aligned 0 times 421350 (17.51%) aligned exactly 1 time 125166 (5.20%) aligned >1 times 95.21% overall alignment rate Time searching: 00:37:15 Overall time: 00:37:15 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 16 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] 5987446 / 18178536 = 0.3294 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 09:56:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.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 09:56:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:56:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:57:02: 1000000 INFO @ Fri, 26 Jun 2020 09:57:08: 2000000 INFO @ Fri, 26 Jun 2020 09:57:14: 3000000 INFO @ Fri, 26 Jun 2020 09:57:20: 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 09:57:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.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 09:57:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:57:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:57:26: 5000000 INFO @ Fri, 26 Jun 2020 09:57:31: 1000000 INFO @ Fri, 26 Jun 2020 09:57:32: 6000000 INFO @ Fri, 26 Jun 2020 09:57:36: 2000000 INFO @ Fri, 26 Jun 2020 09:57:37: 7000000 INFO @ Fri, 26 Jun 2020 09:57:41: 3000000 INFO @ Fri, 26 Jun 2020 09:57:43: 8000000 INFO @ Fri, 26 Jun 2020 09:57:47: 4000000 INFO @ Fri, 26 Jun 2020 09:57:49: 9000000 INFO @ Fri, 26 Jun 2020 09:57:52: 5000000 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 09:57:55: 10000000 INFO @ Fri, 26 Jun 2020 09:57:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.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 09:57:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:57:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:57:57: 6000000 INFO @ Fri, 26 Jun 2020 09:58:01: 11000000 INFO @ Fri, 26 Jun 2020 09:58:01: 1000000 INFO @ Fri, 26 Jun 2020 09:58:03: 7000000 INFO @ Fri, 26 Jun 2020 09:58:07: 12000000 INFO @ Fri, 26 Jun 2020 09:58:07: 2000000 INFO @ Fri, 26 Jun 2020 09:58:09: 8000000 INFO @ Fri, 26 Jun 2020 09:58:13: 3000000 INFO @ Fri, 26 Jun 2020 09:58:13: 13000000 INFO @ Fri, 26 Jun 2020 09:58:15: 9000000 INFO @ Fri, 26 Jun 2020 09:58:18: 4000000 INFO @ Fri, 26 Jun 2020 09:58:19: 14000000 INFO @ Fri, 26 Jun 2020 09:58:20: 10000000 INFO @ Fri, 26 Jun 2020 09:58:24: 5000000 INFO @ Fri, 26 Jun 2020 09:58:24: 15000000 INFO @ Fri, 26 Jun 2020 09:58:26: 11000000 INFO @ Fri, 26 Jun 2020 09:58:29: 6000000 INFO @ Fri, 26 Jun 2020 09:58:30: 16000000 INFO @ Fri, 26 Jun 2020 09:58:32: 12000000 INFO @ Fri, 26 Jun 2020 09:58:35: 7000000 INFO @ Fri, 26 Jun 2020 09:58:37: 17000000 INFO @ Fri, 26 Jun 2020 09:58:38: 13000000 INFO @ Fri, 26 Jun 2020 09:58:41: 8000000 INFO @ Fri, 26 Jun 2020 09:58:43: 18000000 INFO @ Fri, 26 Jun 2020 09:58:44: 14000000 INFO @ Fri, 26 Jun 2020 09:58:48: 9000000 INFO @ Fri, 26 Jun 2020 09:58:49: 19000000 INFO @ Fri, 26 Jun 2020 09:58:50: 15000000 INFO @ Fri, 26 Jun 2020 09:58:54: 10000000 INFO @ Fri, 26 Jun 2020 09:58:55: 20000000 INFO @ Fri, 26 Jun 2020 09:58:57: 16000000 INFO @ Fri, 26 Jun 2020 09:59:00: 11000000 INFO @ Fri, 26 Jun 2020 09:59:01: 21000000 INFO @ Fri, 26 Jun 2020 09:59:03: 17000000 INFO @ Fri, 26 Jun 2020 09:59:06: 12000000 INFO @ Fri, 26 Jun 2020 09:59:08: 22000000 INFO @ Fri, 26 Jun 2020 09:59:09: 18000000 INFO @ Fri, 26 Jun 2020 09:59:13: 13000000 INFO @ Fri, 26 Jun 2020 09:59:14: 23000000 INFO @ Fri, 26 Jun 2020 09:59:16: 19000000 INFO @ Fri, 26 Jun 2020 09:59:19: 14000000 INFO @ Fri, 26 Jun 2020 09:59:20: 24000000 INFO @ Fri, 26 Jun 2020 09:59:23: 20000000 INFO @ Fri, 26 Jun 2020 09:59:25: 15000000 INFO @ Fri, 26 Jun 2020 09:59:27: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:59:27: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:59:27: #1 total tags in treatment: 12195196 INFO @ Fri, 26 Jun 2020 09:59:27: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:59:27: #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 09:59:27: #1 tags after filtering in treatment: 9696063 INFO @ Fri, 26 Jun 2020 09:59:27: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 26 Jun 2020 09:59:27: #1 finished! INFO @ Fri, 26 Jun 2020 09:59:27: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:59:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:59:28: #2 number of paired peaks: 4472 INFO @ Fri, 26 Jun 2020 09:59:28: start model_add_line... INFO @ Fri, 26 Jun 2020 09:59:28: start X-correlation... INFO @ Fri, 26 Jun 2020 09:59:28: end of X-cor INFO @ Fri, 26 Jun 2020 09:59:28: #2 finished! INFO @ Fri, 26 Jun 2020 09:59:28: #2 predicted fragment length is 156 bps INFO @ Fri, 26 Jun 2020 09:59:28: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 26 Jun 2020 09:59:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.05_model.r INFO @ Fri, 26 Jun 2020 09:59:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:59:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:59:29: 21000000 INFO @ Fri, 26 Jun 2020 09:59:32: 16000000 INFO @ Fri, 26 Jun 2020 09:59:35: 22000000 INFO @ Fri, 26 Jun 2020 09:59:38: 17000000 INFO @ Fri, 26 Jun 2020 09:59:42: 23000000 INFO @ Fri, 26 Jun 2020 09:59:44: 18000000 INFO @ Fri, 26 Jun 2020 09:59:48: 24000000 INFO @ Fri, 26 Jun 2020 09:59:51: 19000000 INFO @ Fri, 26 Jun 2020 09:59:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:59:54: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:59:54: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:59:54: #1 total tags in treatment: 12195196 INFO @ Fri, 26 Jun 2020 09:59:54: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:59:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:59:54: #1 tags after filtering in treatment: 9696063 INFO @ Fri, 26 Jun 2020 09:59:54: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 26 Jun 2020 09:59:54: #1 finished! INFO @ Fri, 26 Jun 2020 09:59:54: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:59:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:59:55: #2 number of paired peaks: 4472 INFO @ Fri, 26 Jun 2020 09:59:55: start model_add_line... INFO @ Fri, 26 Jun 2020 09:59:55: start X-correlation... INFO @ Fri, 26 Jun 2020 09:59:56: end of X-cor INFO @ Fri, 26 Jun 2020 09:59:56: #2 finished! INFO @ Fri, 26 Jun 2020 09:59:56: #2 predicted fragment length is 156 bps INFO @ Fri, 26 Jun 2020 09:59:56: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 26 Jun 2020 09:59:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.10_model.r INFO @ Fri, 26 Jun 2020 09:59:56: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:59:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:59:57: 20000000 INFO @ Fri, 26 Jun 2020 10:00:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.05_peaks.xls INFO @ Fri, 26 Jun 2020 10:00:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:00:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.05_summits.bed INFO @ Fri, 26 Jun 2020 10:00:03: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8137 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:00:03: 21000000 INFO @ Fri, 26 Jun 2020 10:00:09: 22000000 INFO @ Fri, 26 Jun 2020 10:00:15: 23000000 INFO @ Fri, 26 Jun 2020 10:00:18: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:00:21: 24000000 INFO @ Fri, 26 Jun 2020 10:00:27: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 10:00:27: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 10:00:27: #1 total tags in treatment: 12195196 INFO @ Fri, 26 Jun 2020 10:00:27: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:00:27: #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 10:00:27: #1 tags after filtering in treatment: 9696063 INFO @ Fri, 26 Jun 2020 10:00:27: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 26 Jun 2020 10:00:27: #1 finished! INFO @ Fri, 26 Jun 2020 10:00:27: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:00:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:00:28: #2 number of paired peaks: 4472 INFO @ Fri, 26 Jun 2020 10:00:28: start model_add_line... INFO @ Fri, 26 Jun 2020 10:00:28: start X-correlation... INFO @ Fri, 26 Jun 2020 10:00:28: end of X-cor INFO @ Fri, 26 Jun 2020 10:00:28: #2 finished! INFO @ Fri, 26 Jun 2020 10:00:28: #2 predicted fragment length is 156 bps INFO @ Fri, 26 Jun 2020 10:00:28: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 26 Jun 2020 10:00:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.20_model.r INFO @ Fri, 26 Jun 2020 10:00:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:00:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:00:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.10_peaks.xls INFO @ Fri, 26 Jun 2020 10:00:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:00:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.10_summits.bed INFO @ Fri, 26 Jun 2020 10:00:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6796 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 10:00:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:01:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.20_peaks.xls INFO @ Fri, 26 Jun 2020 10:01:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:01:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749079/SRX749079.20_summits.bed INFO @ Fri, 26 Jun 2020 10:01:03: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5710 records, 4 fields): 9 millis CompletedMACS2peakCalling