Job ID = 6497815 SRX = SRX1728718 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:59:42 prefetch.2.10.7: 1) Downloading 'SRR3452735'... 2020-06-25T22:59:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:02:05 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:02:05 prefetch.2.10.7: 1) 'SRR3452735' was downloaded successfully 2020-06-25T23:02:05 prefetch.2.10.7: 'SRR3452735' has 0 unresolved dependencies Read 23794846 spots for SRR3452735/SRR3452735.sra Written 23794846 spots for SRR3452735/SRR3452735.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: 00:47:02 23794846 reads; of these: 23794846 (100.00%) were paired; of these: 2522339 (10.60%) aligned concordantly 0 times 15173645 (63.77%) aligned concordantly exactly 1 time 6098862 (25.63%) aligned concordantly >1 times ---- 2522339 pairs aligned concordantly 0 times; of these: 308960 (12.25%) aligned discordantly 1 time ---- 2213379 pairs aligned 0 times concordantly or discordantly; of these: 4426758 mates make up the pairs; of these: 3232476 (73.02%) aligned 0 times 702076 (15.86%) aligned exactly 1 time 492206 (11.12%) aligned >1 times 93.21% overall alignment rate Time searching: 00:47:02 Overall time: 00:47:02 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 20 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] 9446687 / 21526230 = 0.4388 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 09:00:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.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 09:00:08: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:00:08: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:00:16: 1000000 INFO @ Fri, 26 Jun 2020 09:00:23: 2000000 INFO @ Fri, 26 Jun 2020 09:00:30: 3000000 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 09:00:37: 4000000 INFO @ Fri, 26 Jun 2020 09:00:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.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 09:00:38: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:00:38: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:00:45: 5000000 INFO @ Fri, 26 Jun 2020 09:00:46: 1000000 INFO @ Fri, 26 Jun 2020 09:00:53: 6000000 INFO @ Fri, 26 Jun 2020 09:00:53: 2000000 INFO @ Fri, 26 Jun 2020 09:01:01: 3000000 INFO @ Fri, 26 Jun 2020 09:01:01: 7000000 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 09:01:08: 4000000 INFO @ Fri, 26 Jun 2020 09:01:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.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 09:01:09: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:01:09: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:01:09: 8000000 INFO @ Fri, 26 Jun 2020 09:01:16: 5000000 INFO @ Fri, 26 Jun 2020 09:01:16: 1000000 INFO @ Fri, 26 Jun 2020 09:01:17: 9000000 INFO @ Fri, 26 Jun 2020 09:01:23: 6000000 INFO @ Fri, 26 Jun 2020 09:01:24: 2000000 INFO @ Fri, 26 Jun 2020 09:01:25: 10000000 INFO @ Fri, 26 Jun 2020 09:01:31: 7000000 INFO @ Fri, 26 Jun 2020 09:01:32: 3000000 INFO @ Fri, 26 Jun 2020 09:01:33: 11000000 INFO @ Fri, 26 Jun 2020 09:01:38: 8000000 INFO @ Fri, 26 Jun 2020 09:01:39: 4000000 INFO @ Fri, 26 Jun 2020 09:01:41: 12000000 INFO @ Fri, 26 Jun 2020 09:01:46: 9000000 INFO @ Fri, 26 Jun 2020 09:01:47: 5000000 INFO @ Fri, 26 Jun 2020 09:01:49: 13000000 INFO @ Fri, 26 Jun 2020 09:01:54: 10000000 INFO @ Fri, 26 Jun 2020 09:01:54: 6000000 INFO @ Fri, 26 Jun 2020 09:01:57: 14000000 INFO @ Fri, 26 Jun 2020 09:02:01: 11000000 INFO @ Fri, 26 Jun 2020 09:02:02: 7000000 INFO @ Fri, 26 Jun 2020 09:02:05: 15000000 INFO @ Fri, 26 Jun 2020 09:02:09: 12000000 INFO @ Fri, 26 Jun 2020 09:02:10: 8000000 INFO @ Fri, 26 Jun 2020 09:02:13: 16000000 INFO @ Fri, 26 Jun 2020 09:02:16: 13000000 INFO @ Fri, 26 Jun 2020 09:02:17: 9000000 INFO @ Fri, 26 Jun 2020 09:02:21: 17000000 INFO @ Fri, 26 Jun 2020 09:02:24: 14000000 INFO @ Fri, 26 Jun 2020 09:02:25: 10000000 INFO @ Fri, 26 Jun 2020 09:02:29: 18000000 INFO @ Fri, 26 Jun 2020 09:02:31: 15000000 INFO @ Fri, 26 Jun 2020 09:02:32: 11000000 INFO @ Fri, 26 Jun 2020 09:02:38: 19000000 INFO @ Fri, 26 Jun 2020 09:02:39: 16000000 INFO @ Fri, 26 Jun 2020 09:02:40: 12000000 INFO @ Fri, 26 Jun 2020 09:02:46: 20000000 INFO @ Fri, 26 Jun 2020 09:02:47: 17000000 INFO @ Fri, 26 Jun 2020 09:02:47: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:02:54: 18000000 INFO @ Fri, 26 Jun 2020 09:02:54: 21000000 INFO @ Fri, 26 Jun 2020 09:02:55: 14000000 INFO @ Fri, 26 Jun 2020 09:03:02: 19000000 INFO @ Fri, 26 Jun 2020 09:03:03: 22000000 INFO @ Fri, 26 Jun 2020 09:03:03: 15000000 INFO @ Fri, 26 Jun 2020 09:03:10: 20000000 INFO @ Fri, 26 Jun 2020 09:03:10: 16000000 INFO @ Fri, 26 Jun 2020 09:03:11: 23000000 INFO @ Fri, 26 Jun 2020 09:03:17: 21000000 INFO @ Fri, 26 Jun 2020 09:03:18: 17000000 INFO @ Fri, 26 Jun 2020 09:03:19: 24000000 INFO @ Fri, 26 Jun 2020 09:03:25: 22000000 INFO @ Fri, 26 Jun 2020 09:03:26: 18000000 INFO @ Fri, 26 Jun 2020 09:03:27: 25000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:03:30: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:03:30: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:03:30: #1 total tags in treatment: 11881863 INFO @ Fri, 26 Jun 2020 09:03:30: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:03:30: #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 09:03:31: #1 tags after filtering in treatment: 8936754 INFO @ Fri, 26 Jun 2020 09:03:31: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 26 Jun 2020 09:03:31: #1 finished! INFO @ Fri, 26 Jun 2020 09:03:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:03:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:03:32: #2 number of paired peaks: 3238 INFO @ Fri, 26 Jun 2020 09:03:32: start model_add_line... INFO @ Fri, 26 Jun 2020 09:03:32: start X-correlation... INFO @ Fri, 26 Jun 2020 09:03:32: end of X-cor INFO @ Fri, 26 Jun 2020 09:03:32: #2 finished! INFO @ Fri, 26 Jun 2020 09:03:32: #2 predicted fragment length is 175 bps INFO @ Fri, 26 Jun 2020 09:03:32: #2 alternative fragment length(s) may be 175 bps INFO @ Fri, 26 Jun 2020 09:03:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.05_model.r INFO @ Fri, 26 Jun 2020 09:03:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:03:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:03:33: 23000000 INFO @ Fri, 26 Jun 2020 09:03:33: 19000000 INFO @ Fri, 26 Jun 2020 09:03:40: 24000000 INFO @ Fri, 26 Jun 2020 09:03:41: 20000000 INFO @ Fri, 26 Jun 2020 09:03:47: 25000000 INFO @ Fri, 26 Jun 2020 09:03:48: 21000000 INFO @ Fri, 26 Jun 2020 09:03:50: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:03:50: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:03:50: #1 total tags in treatment: 11881863 INFO @ Fri, 26 Jun 2020 09:03:50: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:03:50: #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 09:03:50: #1 tags after filtering in treatment: 8936754 INFO @ Fri, 26 Jun 2020 09:03:50: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 26 Jun 2020 09:03:50: #1 finished! INFO @ Fri, 26 Jun 2020 09:03:50: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:03:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:03:51: #2 number of paired peaks: 3238 INFO @ Fri, 26 Jun 2020 09:03:51: start model_add_line... INFO @ Fri, 26 Jun 2020 09:03:51: start X-correlation... INFO @ Fri, 26 Jun 2020 09:03:51: end of X-cor INFO @ Fri, 26 Jun 2020 09:03:51: #2 finished! INFO @ Fri, 26 Jun 2020 09:03:51: #2 predicted fragment length is 175 bps INFO @ Fri, 26 Jun 2020 09:03:51: #2 alternative fragment length(s) may be 175 bps INFO @ Fri, 26 Jun 2020 09:03:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.10_model.r INFO @ Fri, 26 Jun 2020 09:03:51: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:03:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:03:54: 22000000 INFO @ Fri, 26 Jun 2020 09:03:55: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:04:00: 23000000 INFO @ Fri, 26 Jun 2020 09:04:06: 24000000 INFO @ Fri, 26 Jun 2020 09:04:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:04:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:04:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.05_summits.bed INFO @ Fri, 26 Jun 2020 09:04:07: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8550 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:04:12: 25000000 INFO @ Fri, 26 Jun 2020 09:04:15: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:04:15: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:04:15: #1 total tags in treatment: 11881863 INFO @ Fri, 26 Jun 2020 09:04:15: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:04:15: #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 09:04:15: #1 tags after filtering in treatment: 8936754 INFO @ Fri, 26 Jun 2020 09:04:15: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 26 Jun 2020 09:04:15: #1 finished! INFO @ Fri, 26 Jun 2020 09:04:15: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:04:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:04:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:04:16: #2 number of paired peaks: 3238 INFO @ Fri, 26 Jun 2020 09:04:16: start model_add_line... INFO @ Fri, 26 Jun 2020 09:04:16: start X-correlation... INFO @ Fri, 26 Jun 2020 09:04:16: end of X-cor INFO @ Fri, 26 Jun 2020 09:04:16: #2 finished! INFO @ Fri, 26 Jun 2020 09:04:16: #2 predicted fragment length is 175 bps INFO @ Fri, 26 Jun 2020 09:04:16: #2 alternative fragment length(s) may be 175 bps INFO @ Fri, 26 Jun 2020 09:04:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.20_model.r INFO @ Fri, 26 Jun 2020 09:04:16: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:04:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:04:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:04:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:04:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.10_summits.bed INFO @ Fri, 26 Jun 2020 09:04:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6413 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:04:41: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:04:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:04:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:04:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1728718/SRX1728718.20_summits.bed INFO @ Fri, 26 Jun 2020 09:04:53: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4172 records, 4 fields): 7 millis CompletedMACS2peakCalling