Job ID = 6453083 SRX = SRX1032393 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:01:53 prefetch.2.10.7: 1) Downloading 'SRR2031891'... 2020-06-21T08:01:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:04:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:04:50 prefetch.2.10.7: 1) 'SRR2031891' was downloaded successfully Read 24535827 spots for SRR2031891/SRR2031891.sra Written 24535827 spots for SRR2031891/SRR2031891.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: 00:06:05 24535827 reads; of these: 24535827 (100.00%) were unpaired; of these: 828242 (3.38%) aligned 0 times 19381539 (78.99%) aligned exactly 1 time 4326046 (17.63%) aligned >1 times 96.62% overall alignment rate Time searching: 00:06:05 Overall time: 00:06:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 5423953 / 23707585 = 0.2288 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 @ Sun, 21 Jun 2020 17:17:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.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 @ Sun, 21 Jun 2020 17:17:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:17:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:17:48: 1000000 INFO @ Sun, 21 Jun 2020 17:17:54: 2000000 INFO @ Sun, 21 Jun 2020 17:17:59: 3000000 INFO @ Sun, 21 Jun 2020 17:18:04: 4000000 INFO @ Sun, 21 Jun 2020 17:18:09: 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 @ Sun, 21 Jun 2020 17:18:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.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 @ Sun, 21 Jun 2020 17:18:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:18:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:18:15: 6000000 INFO @ Sun, 21 Jun 2020 17:18:19: 1000000 INFO @ Sun, 21 Jun 2020 17:18:21: 7000000 INFO @ Sun, 21 Jun 2020 17:18:25: 2000000 INFO @ Sun, 21 Jun 2020 17:18:26: 8000000 INFO @ Sun, 21 Jun 2020 17:18:30: 3000000 INFO @ Sun, 21 Jun 2020 17:18:32: 9000000 INFO @ Sun, 21 Jun 2020 17:18:36: 4000000 INFO @ Sun, 21 Jun 2020 17:18:37: 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 @ Sun, 21 Jun 2020 17:18:42: 5000000 INFO @ Sun, 21 Jun 2020 17:18:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.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 @ Sun, 21 Jun 2020 17:18:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:18:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:18:43: 11000000 INFO @ Sun, 21 Jun 2020 17:18:48: 6000000 INFO @ Sun, 21 Jun 2020 17:18:49: 1000000 INFO @ Sun, 21 Jun 2020 17:18:49: 12000000 INFO @ Sun, 21 Jun 2020 17:18:54: 7000000 INFO @ Sun, 21 Jun 2020 17:18:55: 13000000 INFO @ Sun, 21 Jun 2020 17:18:55: 2000000 INFO @ Sun, 21 Jun 2020 17:19:01: 14000000 INFO @ Sun, 21 Jun 2020 17:19:01: 8000000 INFO @ Sun, 21 Jun 2020 17:19:01: 3000000 INFO @ Sun, 21 Jun 2020 17:19:07: 9000000 INFO @ Sun, 21 Jun 2020 17:19:07: 15000000 INFO @ Sun, 21 Jun 2020 17:19:07: 4000000 INFO @ Sun, 21 Jun 2020 17:19:13: 10000000 INFO @ Sun, 21 Jun 2020 17:19:13: 16000000 INFO @ Sun, 21 Jun 2020 17:19:14: 5000000 INFO @ Sun, 21 Jun 2020 17:19:19: 11000000 INFO @ Sun, 21 Jun 2020 17:19:19: 17000000 INFO @ Sun, 21 Jun 2020 17:19:20: 6000000 INFO @ Sun, 21 Jun 2020 17:19:25: 12000000 INFO @ Sun, 21 Jun 2020 17:19:25: 18000000 INFO @ Sun, 21 Jun 2020 17:19:26: 7000000 INFO @ Sun, 21 Jun 2020 17:19:27: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:19:27: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:19:27: #1 total tags in treatment: 18283632 INFO @ Sun, 21 Jun 2020 17:19:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:19:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:19:28: #1 tags after filtering in treatment: 18283627 INFO @ Sun, 21 Jun 2020 17:19:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:19:28: #1 finished! INFO @ Sun, 21 Jun 2020 17:19:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:19:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:19:29: #2 number of paired peaks: 4967 INFO @ Sun, 21 Jun 2020 17:19:29: start model_add_line... INFO @ Sun, 21 Jun 2020 17:19:30: start X-correlation... INFO @ Sun, 21 Jun 2020 17:19:30: end of X-cor INFO @ Sun, 21 Jun 2020 17:19:30: #2 finished! INFO @ Sun, 21 Jun 2020 17:19:30: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 17:19:30: #2 alternative fragment length(s) may be 4,142 bps INFO @ Sun, 21 Jun 2020 17:19:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.05_model.r INFO @ Sun, 21 Jun 2020 17:19:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:19:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:19:30: 13000000 INFO @ Sun, 21 Jun 2020 17:19:31: 8000000 INFO @ Sun, 21 Jun 2020 17:19:36: 14000000 INFO @ Sun, 21 Jun 2020 17:19:37: 9000000 INFO @ Sun, 21 Jun 2020 17:19:42: 15000000 INFO @ Sun, 21 Jun 2020 17:19:43: 10000000 INFO @ Sun, 21 Jun 2020 17:19:48: 16000000 INFO @ Sun, 21 Jun 2020 17:19:48: 11000000 INFO @ Sun, 21 Jun 2020 17:19:53: 17000000 INFO @ Sun, 21 Jun 2020 17:19:54: 12000000 INFO @ Sun, 21 Jun 2020 17:19:59: 18000000 INFO @ Sun, 21 Jun 2020 17:20:00: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:20:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:20:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:20:01: #1 total tags in treatment: 18283632 INFO @ Sun, 21 Jun 2020 17:20:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:20:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:20:02: #1 tags after filtering in treatment: 18283627 INFO @ Sun, 21 Jun 2020 17:20:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:20:02: #1 finished! INFO @ Sun, 21 Jun 2020 17:20:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:20:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:20:03: #2 number of paired peaks: 4967 INFO @ Sun, 21 Jun 2020 17:20:03: start model_add_line... INFO @ Sun, 21 Jun 2020 17:20:03: start X-correlation... INFO @ Sun, 21 Jun 2020 17:20:03: end of X-cor INFO @ Sun, 21 Jun 2020 17:20:03: #2 finished! INFO @ Sun, 21 Jun 2020 17:20:03: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 17:20:03: #2 alternative fragment length(s) may be 4,142 bps INFO @ Sun, 21 Jun 2020 17:20:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.10_model.r INFO @ Sun, 21 Jun 2020 17:20:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:20:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:20:05: 14000000 INFO @ Sun, 21 Jun 2020 17:20:11: 15000000 INFO @ Sun, 21 Jun 2020 17:20:16: 16000000 INFO @ Sun, 21 Jun 2020 17:20:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:20:22: 17000000 INFO @ Sun, 21 Jun 2020 17:20:27: 18000000 INFO @ Sun, 21 Jun 2020 17:20:29: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:20:29: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:20:29: #1 total tags in treatment: 18283632 INFO @ Sun, 21 Jun 2020 17:20:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:20:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:20:30: #1 tags after filtering in treatment: 18283627 INFO @ Sun, 21 Jun 2020 17:20:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:20:30: #1 finished! INFO @ Sun, 21 Jun 2020 17:20:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:20:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:20:31: #2 number of paired peaks: 4967 INFO @ Sun, 21 Jun 2020 17:20:31: start model_add_line... INFO @ Sun, 21 Jun 2020 17:20:32: start X-correlation... INFO @ Sun, 21 Jun 2020 17:20:32: end of X-cor INFO @ Sun, 21 Jun 2020 17:20:32: #2 finished! INFO @ Sun, 21 Jun 2020 17:20:32: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 17:20:32: #2 alternative fragment length(s) may be 4,142 bps INFO @ Sun, 21 Jun 2020 17:20:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.20_model.r INFO @ Sun, 21 Jun 2020 17:20:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:20:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:20:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:20:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:20:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.05_summits.bed INFO @ Sun, 21 Jun 2020 17:20:37: Done! pass1 - making usageList (499 chroms): 2 millis pass2 - checking and writing primary data (5053 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:20:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:21:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:21:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:21:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.10_summits.bed INFO @ Sun, 21 Jun 2020 17:21:10: Done! pass1 - making usageList (326 chroms): 1 millis pass2 - checking and writing primary data (2018 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:21:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:21:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:21:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:21:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032393/SRX1032393.20_summits.bed INFO @ Sun, 21 Jun 2020 17:21:40: Done! pass1 - making usageList (225 chroms): 1 millis pass2 - checking and writing primary data (696 records, 4 fields): 8 millis CompletedMACS2peakCalling