Job ID = 5720472 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,542,339 reads read : 28,542,339 reads written : 28,542,339 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289692.sra.cache’: No such file or directory 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: 00:08:07 28542339 reads; of these: 28542339 (100.00%) were unpaired; of these: 2280303 (7.99%) aligned 0 times 21200720 (74.28%) aligned exactly 1 time 5061316 (17.73%) aligned >1 times 92.01% overall alignment rate Time searching: 00:08:07 Overall time: 00:08:07 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 12 files... [bam_rmdupse_core] 6814782 / 26262036 = 0.2595 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 @ Thu, 16 Apr 2020 00:43:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.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 @ Thu, 16 Apr 2020 00:43:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:43:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:43:48: 1000000 INFO @ Thu, 16 Apr 2020 00:43:53: 2000000 INFO @ Thu, 16 Apr 2020 00:43:57: 3000000 INFO @ Thu, 16 Apr 2020 00:44:02: 4000000 INFO @ Thu, 16 Apr 2020 00:44:07: 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 @ Thu, 16 Apr 2020 00:44:12: 6000000 INFO @ Thu, 16 Apr 2020 00:44:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.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 @ Thu, 16 Apr 2020 00:44:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:44:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:44:16: 7000000 INFO @ Thu, 16 Apr 2020 00:44:19: 1000000 INFO @ Thu, 16 Apr 2020 00:44:21: 8000000 INFO @ Thu, 16 Apr 2020 00:44:25: 2000000 INFO @ Thu, 16 Apr 2020 00:44:26: 9000000 INFO @ Thu, 16 Apr 2020 00:44:30: 3000000 INFO @ Thu, 16 Apr 2020 00:44:31: 10000000 INFO @ Thu, 16 Apr 2020 00:44:36: 11000000 INFO @ Thu, 16 Apr 2020 00:44:36: 4000000 INFO @ Thu, 16 Apr 2020 00:44:41: 12000000 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 @ Thu, 16 Apr 2020 00:44:42: 5000000 INFO @ Thu, 16 Apr 2020 00:44:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.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 @ Thu, 16 Apr 2020 00:44:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:44:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:44:46: 13000000 INFO @ Thu, 16 Apr 2020 00:44:48: 6000000 INFO @ Thu, 16 Apr 2020 00:44:49: 1000000 INFO @ Thu, 16 Apr 2020 00:44:51: 14000000 INFO @ Thu, 16 Apr 2020 00:44:53: 7000000 INFO @ Thu, 16 Apr 2020 00:44:55: 2000000 INFO @ Thu, 16 Apr 2020 00:44:56: 15000000 INFO @ Thu, 16 Apr 2020 00:44:59: 8000000 INFO @ Thu, 16 Apr 2020 00:45:00: 3000000 INFO @ Thu, 16 Apr 2020 00:45:01: 16000000 INFO @ Thu, 16 Apr 2020 00:45:04: 9000000 INFO @ Thu, 16 Apr 2020 00:45:05: 17000000 INFO @ Thu, 16 Apr 2020 00:45:06: 4000000 INFO @ Thu, 16 Apr 2020 00:45:10: 10000000 INFO @ Thu, 16 Apr 2020 00:45:10: 18000000 INFO @ Thu, 16 Apr 2020 00:45:12: 5000000 INFO @ Thu, 16 Apr 2020 00:45:15: 19000000 INFO @ Thu, 16 Apr 2020 00:45:15: 11000000 INFO @ Thu, 16 Apr 2020 00:45:18: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:45:18: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:45:18: #1 total tags in treatment: 19447254 INFO @ Thu, 16 Apr 2020 00:45:18: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:45:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:45:18: 6000000 INFO @ Thu, 16 Apr 2020 00:45:18: #1 tags after filtering in treatment: 19447254 INFO @ Thu, 16 Apr 2020 00:45:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:45:18: #1 finished! INFO @ Thu, 16 Apr 2020 00:45:18: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:45:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:45:19: #2 number of paired peaks: 2209 INFO @ Thu, 16 Apr 2020 00:45:19: start model_add_line... INFO @ Thu, 16 Apr 2020 00:45:20: start X-correlation... INFO @ Thu, 16 Apr 2020 00:45:20: end of X-cor INFO @ Thu, 16 Apr 2020 00:45:20: #2 finished! INFO @ Thu, 16 Apr 2020 00:45:20: #2 predicted fragment length is 174 bps INFO @ Thu, 16 Apr 2020 00:45:20: #2 alternative fragment length(s) may be 3,174 bps INFO @ Thu, 16 Apr 2020 00:45:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.05_model.r INFO @ Thu, 16 Apr 2020 00:45:20: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:45:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:45:21: 12000000 INFO @ Thu, 16 Apr 2020 00:45:23: 7000000 INFO @ Thu, 16 Apr 2020 00:45:26: 13000000 INFO @ Thu, 16 Apr 2020 00:45:29: 8000000 INFO @ Thu, 16 Apr 2020 00:45:32: 14000000 INFO @ Thu, 16 Apr 2020 00:45:34: 9000000 INFO @ Thu, 16 Apr 2020 00:45:37: 15000000 INFO @ Thu, 16 Apr 2020 00:45:40: 10000000 INFO @ Thu, 16 Apr 2020 00:45:43: 16000000 INFO @ Thu, 16 Apr 2020 00:45:45: 11000000 INFO @ Thu, 16 Apr 2020 00:45:48: 17000000 INFO @ Thu, 16 Apr 2020 00:45:51: 12000000 INFO @ Thu, 16 Apr 2020 00:45:54: 18000000 INFO @ Thu, 16 Apr 2020 00:45:56: 13000000 INFO @ Thu, 16 Apr 2020 00:46:00: 19000000 INFO @ Thu, 16 Apr 2020 00:46:02: 14000000 INFO @ Thu, 16 Apr 2020 00:46:02: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:46:02: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:46:02: #1 total tags in treatment: 19447254 INFO @ Thu, 16 Apr 2020 00:46:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:46:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:46:03: #1 tags after filtering in treatment: 19447254 INFO @ Thu, 16 Apr 2020 00:46:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:46:03: #1 finished! INFO @ Thu, 16 Apr 2020 00:46:03: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:46:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:46:04: #2 number of paired peaks: 2209 INFO @ Thu, 16 Apr 2020 00:46:04: start model_add_line... INFO @ Thu, 16 Apr 2020 00:46:04: start X-correlation... INFO @ Thu, 16 Apr 2020 00:46:04: end of X-cor INFO @ Thu, 16 Apr 2020 00:46:04: #2 finished! INFO @ Thu, 16 Apr 2020 00:46:04: #2 predicted fragment length is 174 bps INFO @ Thu, 16 Apr 2020 00:46:04: #2 alternative fragment length(s) may be 3,174 bps INFO @ Thu, 16 Apr 2020 00:46:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.10_model.r INFO @ Thu, 16 Apr 2020 00:46:04: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:46:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:46:06: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:46:08: 15000000 INFO @ Thu, 16 Apr 2020 00:46:14: 16000000 INFO @ Thu, 16 Apr 2020 00:46:20: 17000000 INFO @ Thu, 16 Apr 2020 00:46:25: 18000000 INFO @ Thu, 16 Apr 2020 00:46:32: 19000000 INFO @ Thu, 16 Apr 2020 00:46:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:46:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:46:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.05_summits.bed INFO @ Thu, 16 Apr 2020 00:46:33: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (14272 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:46:34: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:46:34: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:46:34: #1 total tags in treatment: 19447254 INFO @ Thu, 16 Apr 2020 00:46:34: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:46:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:46:35: #1 tags after filtering in treatment: 19447254 INFO @ Thu, 16 Apr 2020 00:46:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:46:35: #1 finished! INFO @ Thu, 16 Apr 2020 00:46:35: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:46:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:46:37: #2 number of paired peaks: 2209 INFO @ Thu, 16 Apr 2020 00:46:37: start model_add_line... INFO @ Thu, 16 Apr 2020 00:46:37: start X-correlation... INFO @ Thu, 16 Apr 2020 00:46:37: end of X-cor INFO @ Thu, 16 Apr 2020 00:46:37: #2 finished! INFO @ Thu, 16 Apr 2020 00:46:37: #2 predicted fragment length is 174 bps INFO @ Thu, 16 Apr 2020 00:46:37: #2 alternative fragment length(s) may be 3,174 bps INFO @ Thu, 16 Apr 2020 00:46:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.20_model.r INFO @ Thu, 16 Apr 2020 00:46:37: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:46:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:46:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:47:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:47:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:47:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.10_summits.bed INFO @ Thu, 16 Apr 2020 00:47:24: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9808 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:47:31: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:47:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:47:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:47:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592415/SRX2592415.20_summits.bed INFO @ Thu, 16 Apr 2020 00:47:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4786 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。