Job ID = 6497817 SRX = SRX1728720 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:49:12 prefetch.2.10.7: 1) Downloading 'SRR3452737'... 2020-06-25T22:49:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:54:28 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:54:28 prefetch.2.10.7: 1) 'SRR3452737' was downloaded successfully 2020-06-25T22:54:28 prefetch.2.10.7: 'SRR3452737' has 0 unresolved dependencies Read 30146221 spots for SRR3452737/SRR3452737.sra Written 30146221 spots for SRR3452737/SRR3452737.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: 00:45:38 30146221 reads; of these: 30146221 (100.00%) were paired; of these: 7927822 (26.30%) aligned concordantly 0 times 16582857 (55.01%) aligned concordantly exactly 1 time 5635542 (18.69%) aligned concordantly >1 times ---- 7927822 pairs aligned concordantly 0 times; of these: 204243 (2.58%) aligned discordantly 1 time ---- 7723579 pairs aligned 0 times concordantly or discordantly; of these: 15447158 mates make up the pairs; of these: 14445479 (93.52%) aligned 0 times 560047 (3.63%) aligned exactly 1 time 441632 (2.86%) aligned >1 times 76.04% overall alignment rate Time searching: 00:45:38 Overall time: 00:45:38 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] 9478069 / 22364829 = 0.4238 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 08:54:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.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 08:54:58: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:54:58: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:55:05: 1000000 INFO @ Fri, 26 Jun 2020 08:55:11: 2000000 INFO @ Fri, 26 Jun 2020 08:55:17: 3000000 INFO @ Fri, 26 Jun 2020 08:55:23: 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 08:55:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.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 08:55:28: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:55:28: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:55:30: 5000000 INFO @ Fri, 26 Jun 2020 08:55:35: 1000000 INFO @ Fri, 26 Jun 2020 08:55:37: 6000000 INFO @ Fri, 26 Jun 2020 08:55:42: 2000000 INFO @ Fri, 26 Jun 2020 08:55:44: 7000000 INFO @ Fri, 26 Jun 2020 08:55:49: 3000000 INFO @ Fri, 26 Jun 2020 08:55:51: 8000000 INFO @ Fri, 26 Jun 2020 08:55:56: 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 @ Fri, 26 Jun 2020 08:55:58: 9000000 INFO @ Fri, 26 Jun 2020 08:55:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.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 08:55:58: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:55:58: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:56:03: 5000000 INFO @ Fri, 26 Jun 2020 08:56:05: 10000000 INFO @ Fri, 26 Jun 2020 08:56:06: 1000000 INFO @ Fri, 26 Jun 2020 08:56:10: 6000000 INFO @ Fri, 26 Jun 2020 08:56:12: 11000000 INFO @ Fri, 26 Jun 2020 08:56:13: 2000000 INFO @ Fri, 26 Jun 2020 08:56:17: 7000000 INFO @ Fri, 26 Jun 2020 08:56:19: 12000000 INFO @ Fri, 26 Jun 2020 08:56:20: 3000000 INFO @ Fri, 26 Jun 2020 08:56:24: 8000000 INFO @ Fri, 26 Jun 2020 08:56:26: 13000000 INFO @ Fri, 26 Jun 2020 08:56:27: 4000000 INFO @ Fri, 26 Jun 2020 08:56:31: 9000000 INFO @ Fri, 26 Jun 2020 08:56:33: 14000000 INFO @ Fri, 26 Jun 2020 08:56:34: 5000000 INFO @ Fri, 26 Jun 2020 08:56:38: 10000000 INFO @ Fri, 26 Jun 2020 08:56:40: 15000000 INFO @ Fri, 26 Jun 2020 08:56:42: 6000000 INFO @ Fri, 26 Jun 2020 08:56:46: 11000000 INFO @ Fri, 26 Jun 2020 08:56:47: 16000000 INFO @ Fri, 26 Jun 2020 08:56:49: 7000000 INFO @ Fri, 26 Jun 2020 08:56:53: 12000000 INFO @ Fri, 26 Jun 2020 08:56:53: 17000000 INFO @ Fri, 26 Jun 2020 08:56:56: 8000000 INFO @ Fri, 26 Jun 2020 08:56:59: 13000000 INFO @ Fri, 26 Jun 2020 08:57:00: 18000000 INFO @ Fri, 26 Jun 2020 08:57:03: 9000000 INFO @ Fri, 26 Jun 2020 08:57:06: 14000000 INFO @ Fri, 26 Jun 2020 08:57:07: 19000000 INFO @ Fri, 26 Jun 2020 08:57:10: 10000000 INFO @ Fri, 26 Jun 2020 08:57:13: 15000000 INFO @ Fri, 26 Jun 2020 08:57:14: 20000000 INFO @ Fri, 26 Jun 2020 08:57:17: 11000000 INFO @ Fri, 26 Jun 2020 08:57:20: 16000000 INFO @ Fri, 26 Jun 2020 08:57:21: 21000000 INFO @ Fri, 26 Jun 2020 08:57:25: 12000000 INFO @ Fri, 26 Jun 2020 08:57:27: 17000000 INFO @ Fri, 26 Jun 2020 08:57:28: 22000000 INFO @ Fri, 26 Jun 2020 08:57:31: 13000000 INFO @ Fri, 26 Jun 2020 08:57:34: 18000000 INFO @ Fri, 26 Jun 2020 08:57:35: 23000000 INFO @ Fri, 26 Jun 2020 08:57:38: 14000000 INFO @ Fri, 26 Jun 2020 08:57:41: 19000000 INFO @ Fri, 26 Jun 2020 08:57:42: 24000000 INFO @ Fri, 26 Jun 2020 08:57:46: 15000000 INFO @ Fri, 26 Jun 2020 08:57:48: 20000000 INFO @ Fri, 26 Jun 2020 08:57:49: 25000000 INFO @ Fri, 26 Jun 2020 08:57:53: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:57:55: 21000000 INFO @ Fri, 26 Jun 2020 08:57:56: 26000000 INFO @ Fri, 26 Jun 2020 08:58:00: 17000000 INFO @ Fri, 26 Jun 2020 08:58:02: 22000000 INFO @ Fri, 26 Jun 2020 08:58:02: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:58:02: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:58:02: #1 total tags in treatment: 12817064 INFO @ Fri, 26 Jun 2020 08:58:02: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:58:02: #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 08:58:03: #1 tags after filtering in treatment: 11620956 INFO @ Fri, 26 Jun 2020 08:58:03: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 08:58:03: #1 finished! INFO @ Fri, 26 Jun 2020 08:58:03: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:58:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:58:03: #2 number of paired peaks: 1075 INFO @ Fri, 26 Jun 2020 08:58:03: start model_add_line... INFO @ Fri, 26 Jun 2020 08:58:04: start X-correlation... INFO @ Fri, 26 Jun 2020 08:58:04: end of X-cor INFO @ Fri, 26 Jun 2020 08:58:04: #2 finished! INFO @ Fri, 26 Jun 2020 08:58:04: #2 predicted fragment length is 123 bps INFO @ Fri, 26 Jun 2020 08:58:04: #2 alternative fragment length(s) may be 123 bps INFO @ Fri, 26 Jun 2020 08:58:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.05_model.r INFO @ Fri, 26 Jun 2020 08:58:04: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:58:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:58:07: 18000000 INFO @ Fri, 26 Jun 2020 08:58:09: 23000000 INFO @ Fri, 26 Jun 2020 08:58:14: 19000000 INFO @ Fri, 26 Jun 2020 08:58:16: 24000000 INFO @ Fri, 26 Jun 2020 08:58:21: 20000000 INFO @ Fri, 26 Jun 2020 08:58:23: 25000000 INFO @ Fri, 26 Jun 2020 08:58:28: 21000000 INFO @ Fri, 26 Jun 2020 08:58:29: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:58:30: 26000000 INFO @ Fri, 26 Jun 2020 08:58:35: 22000000 INFO @ Fri, 26 Jun 2020 08:58:36: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:58:36: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:58:36: #1 total tags in treatment: 12817064 INFO @ Fri, 26 Jun 2020 08:58:36: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:58:36: #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 08:58:37: #1 tags after filtering in treatment: 11620956 INFO @ Fri, 26 Jun 2020 08:58:37: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 08:58:37: #1 finished! INFO @ Fri, 26 Jun 2020 08:58:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:58:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:58:38: #2 number of paired peaks: 1075 INFO @ Fri, 26 Jun 2020 08:58:38: start model_add_line... INFO @ Fri, 26 Jun 2020 08:58:38: start X-correlation... INFO @ Fri, 26 Jun 2020 08:58:38: end of X-cor INFO @ Fri, 26 Jun 2020 08:58:38: #2 finished! INFO @ Fri, 26 Jun 2020 08:58:38: #2 predicted fragment length is 123 bps INFO @ Fri, 26 Jun 2020 08:58:38: #2 alternative fragment length(s) may be 123 bps INFO @ Fri, 26 Jun 2020 08:58:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.10_model.r INFO @ Fri, 26 Jun 2020 08:58:38: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:58:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:58:42: 23000000 INFO @ Fri, 26 Jun 2020 08:58:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:58:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:58:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.05_summits.bed INFO @ Fri, 26 Jun 2020 08:58:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10417 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:58:48: 24000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:58:54: 25000000 INFO @ Fri, 26 Jun 2020 08:59:00: 26000000 INFO @ Fri, 26 Jun 2020 08:59:03: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:59:06: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:59:06: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:59:06: #1 total tags in treatment: 12817064 INFO @ Fri, 26 Jun 2020 08:59:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:59:06: #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 08:59:06: #1 tags after filtering in treatment: 11620956 INFO @ Fri, 26 Jun 2020 08:59:06: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 08:59:06: #1 finished! INFO @ Fri, 26 Jun 2020 08:59:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:59:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:59:07: #2 number of paired peaks: 1075 INFO @ Fri, 26 Jun 2020 08:59:07: start model_add_line... INFO @ Fri, 26 Jun 2020 08:59:07: start X-correlation... INFO @ Fri, 26 Jun 2020 08:59:07: end of X-cor INFO @ Fri, 26 Jun 2020 08:59:07: #2 finished! INFO @ Fri, 26 Jun 2020 08:59:07: #2 predicted fragment length is 123 bps INFO @ Fri, 26 Jun 2020 08:59:07: #2 alternative fragment length(s) may be 123 bps INFO @ Fri, 26 Jun 2020 08:59:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.20_model.r INFO @ Fri, 26 Jun 2020 08:59:07: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:59:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:59:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:59:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:59:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.10_summits.bed INFO @ Fri, 26 Jun 2020 08:59:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6574 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:59:32: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:59:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:59:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:59:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1728720/SRX1728720.20_summits.bed INFO @ Fri, 26 Jun 2020 08:59:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3532 records, 4 fields): 5 millis CompletedMACS2peakCalling