Job ID = 6454794 SRX = SRX2592397 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:41:55 prefetch.2.10.7: 1) Downloading 'SRR5289674'... 2020-06-21T09:41:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:46:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:46:30 prefetch.2.10.7: 1) 'SRR5289674' was downloaded successfully Read 26290525 spots for SRR5289674/SRR5289674.sra Written 26290525 spots for SRR5289674/SRR5289674.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: 00:07:24 26290525 reads; of these: 26290525 (100.00%) were unpaired; of these: 2026855 (7.71%) aligned 0 times 19924416 (75.79%) aligned exactly 1 time 4339254 (16.51%) aligned >1 times 92.29% overall alignment rate Time searching: 00:07:24 Overall time: 00:07:24 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] 7025876 / 24263670 = 0.2896 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 19:01:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.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 19:01:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:01:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:01:33: 1000000 INFO @ Sun, 21 Jun 2020 19:01:41: 2000000 INFO @ Sun, 21 Jun 2020 19:01:48: 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 @ Sun, 21 Jun 2020 19:01:55: 4000000 INFO @ Sun, 21 Jun 2020 19:01:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.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 19:01:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:01:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:02:03: 5000000 INFO @ Sun, 21 Jun 2020 19:02:04: 1000000 INFO @ Sun, 21 Jun 2020 19:02:11: 6000000 INFO @ Sun, 21 Jun 2020 19:02:12: 2000000 INFO @ Sun, 21 Jun 2020 19:02:19: 7000000 INFO @ Sun, 21 Jun 2020 19:02:20: 3000000 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 19:02:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.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 19:02:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:02:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:02:27: 4000000 INFO @ Sun, 21 Jun 2020 19:02:28: 8000000 INFO @ Sun, 21 Jun 2020 19:02:33: 1000000 INFO @ Sun, 21 Jun 2020 19:02:35: 5000000 INFO @ Sun, 21 Jun 2020 19:02:36: 9000000 INFO @ Sun, 21 Jun 2020 19:02:41: 2000000 INFO @ Sun, 21 Jun 2020 19:02:43: 6000000 INFO @ Sun, 21 Jun 2020 19:02:44: 10000000 INFO @ Sun, 21 Jun 2020 19:02:49: 3000000 INFO @ Sun, 21 Jun 2020 19:02:52: 7000000 INFO @ Sun, 21 Jun 2020 19:02:52: 11000000 INFO @ Sun, 21 Jun 2020 19:02:56: 4000000 INFO @ Sun, 21 Jun 2020 19:03:00: 8000000 INFO @ Sun, 21 Jun 2020 19:03:01: 12000000 INFO @ Sun, 21 Jun 2020 19:03:04: 5000000 INFO @ Sun, 21 Jun 2020 19:03:08: 9000000 INFO @ Sun, 21 Jun 2020 19:03:09: 13000000 INFO @ Sun, 21 Jun 2020 19:03:11: 6000000 INFO @ Sun, 21 Jun 2020 19:03:16: 10000000 INFO @ Sun, 21 Jun 2020 19:03:18: 14000000 INFO @ Sun, 21 Jun 2020 19:03:19: 7000000 INFO @ Sun, 21 Jun 2020 19:03:24: 11000000 INFO @ Sun, 21 Jun 2020 19:03:26: 15000000 INFO @ Sun, 21 Jun 2020 19:03:26: 8000000 INFO @ Sun, 21 Jun 2020 19:03:32: 12000000 INFO @ Sun, 21 Jun 2020 19:03:34: 9000000 INFO @ Sun, 21 Jun 2020 19:03:35: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:03:40: 13000000 INFO @ Sun, 21 Jun 2020 19:03:42: 10000000 INFO @ Sun, 21 Jun 2020 19:03:43: 17000000 INFO @ Sun, 21 Jun 2020 19:03:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:03:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:03:45: #1 total tags in treatment: 17237794 INFO @ Sun, 21 Jun 2020 19:03:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:03:45: #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 19:03:46: #1 tags after filtering in treatment: 17237706 INFO @ Sun, 21 Jun 2020 19:03:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:03:46: #1 finished! INFO @ Sun, 21 Jun 2020 19:03:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:03:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:03:47: #2 number of paired peaks: 4911 INFO @ Sun, 21 Jun 2020 19:03:47: start model_add_line... INFO @ Sun, 21 Jun 2020 19:03:48: start X-correlation... INFO @ Sun, 21 Jun 2020 19:03:48: end of X-cor INFO @ Sun, 21 Jun 2020 19:03:48: #2 finished! INFO @ Sun, 21 Jun 2020 19:03:48: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 19:03:48: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 19:03:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.05_model.r INFO @ Sun, 21 Jun 2020 19:03:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:03:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:03:48: 14000000 INFO @ Sun, 21 Jun 2020 19:03:49: 11000000 INFO @ Sun, 21 Jun 2020 19:03:56: 15000000 INFO @ Sun, 21 Jun 2020 19:03:56: 12000000 INFO @ Sun, 21 Jun 2020 19:04:04: 13000000 INFO @ Sun, 21 Jun 2020 19:04:04: 16000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:04:11: 14000000 INFO @ Sun, 21 Jun 2020 19:04:12: 17000000 INFO @ Sun, 21 Jun 2020 19:04:14: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:04:14: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:04:14: #1 total tags in treatment: 17237794 INFO @ Sun, 21 Jun 2020 19:04:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:14: #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 19:04:15: #1 tags after filtering in treatment: 17237706 INFO @ Sun, 21 Jun 2020 19:04:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:15: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:16: #2 number of paired peaks: 4911 INFO @ Sun, 21 Jun 2020 19:04:16: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:16: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:16: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:16: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:16: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 19:04:16: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 19:04:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.10_model.r INFO @ Sun, 21 Jun 2020 19:04:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:04:18: 15000000 INFO @ Sun, 21 Jun 2020 19:04:24: 16000000 INFO @ Sun, 21 Jun 2020 19:04:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:04:31: 17000000 INFO @ Sun, 21 Jun 2020 19:04:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:04:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:04:32: #1 total tags in treatment: 17237794 INFO @ Sun, 21 Jun 2020 19:04:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:32: #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 19:04:33: #1 tags after filtering in treatment: 17237706 INFO @ Sun, 21 Jun 2020 19:04:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:33: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:34: #2 number of paired peaks: 4911 INFO @ Sun, 21 Jun 2020 19:04:34: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:35: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:35: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:35: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:35: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 19:04:35: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 19:04:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.20_model.r INFO @ Sun, 21 Jun 2020 19:04:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:04:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:04:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:04:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.05_summits.bed INFO @ Sun, 21 Jun 2020 19:04:48: Done! pass1 - making usageList (374 chroms): 3 millis pass2 - checking and writing primary data (17293 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:04:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:05:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:05:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.10_summits.bed INFO @ Sun, 21 Jun 2020 19:05:18: Done! pass1 - making usageList (252 chroms): 2 millis pass2 - checking and writing primary data (13497 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:05:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592397/SRX2592397.20_summits.bed INFO @ Sun, 21 Jun 2020 19:05:34: Done! pass1 - making usageList (150 chroms): 2 millis pass2 - checking and writing primary data (8700 records, 4 fields): 14 millis CompletedMACS2peakCalling