Job ID = 6454818 SRX = SRX2592417 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:42:10 prefetch.2.10.7: 1) Downloading 'SRR5289694'... 2020-06-21T09:42:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:45:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:45:48 prefetch.2.10.7: 1) 'SRR5289694' was downloaded successfully Read 26445392 spots for SRR5289694/SRR5289694.sra Written 26445392 spots for SRR5289694/SRR5289694.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:31 26445392 reads; of these: 26445392 (100.00%) were unpaired; of these: 2215552 (8.38%) aligned 0 times 19627331 (74.22%) aligned exactly 1 time 4602509 (17.40%) aligned >1 times 91.62% overall alignment rate Time searching: 00:07:32 Overall time: 00:07:32 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] 7713230 / 24229840 = 0.3183 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 19:00:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.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 19:00:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:00:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:00:43: 1000000 INFO @ Sun, 21 Jun 2020 19:00:48: 2000000 INFO @ Sun, 21 Jun 2020 19:00:54: 3000000 INFO @ Sun, 21 Jun 2020 19:01:00: 4000000 INFO @ Sun, 21 Jun 2020 19:01:05: 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 19:01:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.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 19:01:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:01:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:01:11: 6000000 INFO @ Sun, 21 Jun 2020 19:01:13: 1000000 INFO @ Sun, 21 Jun 2020 19:01:17: 7000000 INFO @ Sun, 21 Jun 2020 19:01:20: 2000000 INFO @ Sun, 21 Jun 2020 19:01:24: 8000000 INFO @ Sun, 21 Jun 2020 19:01:26: 3000000 INFO @ Sun, 21 Jun 2020 19:01:30: 9000000 INFO @ Sun, 21 Jun 2020 19:01:32: 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 @ Sun, 21 Jun 2020 19:01:36: 10000000 INFO @ Sun, 21 Jun 2020 19:01:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.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 19:01:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:01:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:01:38: 5000000 INFO @ Sun, 21 Jun 2020 19:01:42: 11000000 INFO @ Sun, 21 Jun 2020 19:01:43: 1000000 INFO @ Sun, 21 Jun 2020 19:01:45: 6000000 INFO @ Sun, 21 Jun 2020 19:01:48: 12000000 INFO @ Sun, 21 Jun 2020 19:01:50: 2000000 INFO @ Sun, 21 Jun 2020 19:01:51: 7000000 INFO @ Sun, 21 Jun 2020 19:01:55: 13000000 INFO @ Sun, 21 Jun 2020 19:01:56: 3000000 INFO @ Sun, 21 Jun 2020 19:01:57: 8000000 INFO @ Sun, 21 Jun 2020 19:02:01: 14000000 INFO @ Sun, 21 Jun 2020 19:02:02: 4000000 INFO @ Sun, 21 Jun 2020 19:02:03: 9000000 INFO @ Sun, 21 Jun 2020 19:02:07: 15000000 INFO @ Sun, 21 Jun 2020 19:02:08: 5000000 INFO @ Sun, 21 Jun 2020 19:02:09: 10000000 INFO @ Sun, 21 Jun 2020 19:02:14: 16000000 INFO @ Sun, 21 Jun 2020 19:02:15: 6000000 INFO @ Sun, 21 Jun 2020 19:02:15: 11000000 INFO @ Sun, 21 Jun 2020 19:02:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:02:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:02:17: #1 total tags in treatment: 16516610 INFO @ Sun, 21 Jun 2020 19:02:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:02:17: #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 19:02:18: #1 tags after filtering in treatment: 16516495 INFO @ Sun, 21 Jun 2020 19:02:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:02:18: #1 finished! INFO @ Sun, 21 Jun 2020 19:02:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:02:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:02:19: #2 number of paired peaks: 2357 INFO @ Sun, 21 Jun 2020 19:02:19: start model_add_line... INFO @ Sun, 21 Jun 2020 19:02:19: start X-correlation... INFO @ Sun, 21 Jun 2020 19:02:19: end of X-cor INFO @ Sun, 21 Jun 2020 19:02:19: #2 finished! INFO @ Sun, 21 Jun 2020 19:02:19: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 19:02:19: #2 alternative fragment length(s) may be 3,175,185 bps INFO @ Sun, 21 Jun 2020 19:02:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.05_model.r INFO @ Sun, 21 Jun 2020 19:02:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:02:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:02:21: 7000000 INFO @ Sun, 21 Jun 2020 19:02:22: 12000000 INFO @ Sun, 21 Jun 2020 19:02:27: 8000000 INFO @ Sun, 21 Jun 2020 19:02:28: 13000000 INFO @ Sun, 21 Jun 2020 19:02:33: 9000000 INFO @ Sun, 21 Jun 2020 19:02:34: 14000000 INFO @ Sun, 21 Jun 2020 19:02:39: 10000000 INFO @ Sun, 21 Jun 2020 19:02:40: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:02:46: 11000000 INFO @ Sun, 21 Jun 2020 19:02:47: 16000000 INFO @ Sun, 21 Jun 2020 19:02:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:02:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:02:50: #1 total tags in treatment: 16516610 INFO @ Sun, 21 Jun 2020 19:02:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:02:50: #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 19:02:50: #1 tags after filtering in treatment: 16516495 INFO @ Sun, 21 Jun 2020 19:02:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:02:50: #1 finished! INFO @ Sun, 21 Jun 2020 19:02:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:02:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:02:52: 12000000 INFO @ Sun, 21 Jun 2020 19:02:52: #2 number of paired peaks: 2357 INFO @ Sun, 21 Jun 2020 19:02:52: start model_add_line... INFO @ Sun, 21 Jun 2020 19:02:52: start X-correlation... INFO @ Sun, 21 Jun 2020 19:02:52: end of X-cor INFO @ Sun, 21 Jun 2020 19:02:52: #2 finished! INFO @ Sun, 21 Jun 2020 19:02:52: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 19:02:52: #2 alternative fragment length(s) may be 3,175,185 bps INFO @ Sun, 21 Jun 2020 19:02:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.10_model.r INFO @ Sun, 21 Jun 2020 19:02:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:02:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:02:58: 13000000 INFO @ Sun, 21 Jun 2020 19:03:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:03:04: 14000000 INFO @ Sun, 21 Jun 2020 19:03:09: 15000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:03:15: 16000000 INFO @ Sun, 21 Jun 2020 19:03:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:03:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:03:18: #1 total tags in treatment: 16516610 INFO @ Sun, 21 Jun 2020 19:03:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:03:18: #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 19:03:19: #1 tags after filtering in treatment: 16516495 INFO @ Sun, 21 Jun 2020 19:03:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:03:19: #1 finished! INFO @ Sun, 21 Jun 2020 19:03:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:03:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:03:20: #2 number of paired peaks: 2357 INFO @ Sun, 21 Jun 2020 19:03:20: start model_add_line... INFO @ Sun, 21 Jun 2020 19:03:21: start X-correlation... INFO @ Sun, 21 Jun 2020 19:03:21: end of X-cor INFO @ Sun, 21 Jun 2020 19:03:21: #2 finished! INFO @ Sun, 21 Jun 2020 19:03:21: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 19:03:21: #2 alternative fragment length(s) may be 3,175,185 bps INFO @ Sun, 21 Jun 2020 19:03:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.20_model.r INFO @ Sun, 21 Jun 2020 19:03:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:03:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:03:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:03:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:03:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.05_summits.bed INFO @ Sun, 21 Jun 2020 19:03:23: Done! pass1 - making usageList (204 chroms): 3 millis pass2 - checking and writing primary data (16544 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:03:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:03:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:03:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:03:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.10_summits.bed INFO @ Sun, 21 Jun 2020 19:03:54: Done! pass1 - making usageList (156 chroms): 2 millis pass2 - checking and writing primary data (11329 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:04:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:04:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:04:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:04:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592417/SRX2592417.20_summits.bed INFO @ Sun, 21 Jun 2020 19:04:23: Done! pass1 - making usageList (118 chroms): 2 millis pass2 - checking and writing primary data (5264 records, 4 fields): 9 millis CompletedMACS2peakCalling