Job ID = 6459237 SRX = SRX6468483 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:14:20 prefetch.2.10.7: 1) Downloading 'SRR9710569'... 2020-06-21T13:14:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:20:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:20:13 prefetch.2.10.7: 1) 'SRR9710569' was downloaded successfully Read 34900307 spots for SRR9710569/SRR9710569.sra Written 34900307 spots for SRR9710569/SRR9710569.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: 00:08:19 34900307 reads; of these: 34900307 (100.00%) were unpaired; of these: 2083284 (5.97%) aligned 0 times 29073476 (83.30%) aligned exactly 1 time 3743547 (10.73%) aligned >1 times 94.03% overall alignment rate Time searching: 00:08:19 Overall time: 00:08:19 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 16 files... [bam_rmdupse_core] 20477862 / 32817023 = 0.6240 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 22:36:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.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 22:36:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:36:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:36:55: 1000000 INFO @ Sun, 21 Jun 2020 22:37:01: 2000000 INFO @ Sun, 21 Jun 2020 22:37:08: 3000000 INFO @ Sun, 21 Jun 2020 22:37:14: 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 @ Sun, 21 Jun 2020 22:37:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.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 22:37:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:37:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:37:21: 5000000 INFO @ Sun, 21 Jun 2020 22:37:26: 1000000 INFO @ Sun, 21 Jun 2020 22:37:28: 6000000 INFO @ Sun, 21 Jun 2020 22:37:33: 2000000 INFO @ Sun, 21 Jun 2020 22:37:35: 7000000 INFO @ Sun, 21 Jun 2020 22:37:40: 3000000 INFO @ Sun, 21 Jun 2020 22:37:42: 8000000 INFO @ Sun, 21 Jun 2020 22:37:47: 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 22:37:49: 9000000 INFO @ Sun, 21 Jun 2020 22:37:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.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 22:37:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:37:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:37:53: 5000000 INFO @ Sun, 21 Jun 2020 22:37:56: 1000000 INFO @ Sun, 21 Jun 2020 22:37:56: 10000000 INFO @ Sun, 21 Jun 2020 22:38:00: 6000000 INFO @ Sun, 21 Jun 2020 22:38:02: 2000000 INFO @ Sun, 21 Jun 2020 22:38:04: 11000000 INFO @ Sun, 21 Jun 2020 22:38:07: 7000000 INFO @ Sun, 21 Jun 2020 22:38:09: 3000000 INFO @ Sun, 21 Jun 2020 22:38:11: 12000000 INFO @ Sun, 21 Jun 2020 22:38:13: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:38:13: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:38:13: #1 total tags in treatment: 12339161 INFO @ Sun, 21 Jun 2020 22:38:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:38:13: #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 22:38:14: #1 tags after filtering in treatment: 12339145 INFO @ Sun, 21 Jun 2020 22:38:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:38:14: #1 finished! INFO @ Sun, 21 Jun 2020 22:38:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:38:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:38:14: 8000000 INFO @ Sun, 21 Jun 2020 22:38:15: #2 number of paired peaks: 2119 INFO @ Sun, 21 Jun 2020 22:38:15: start model_add_line... INFO @ Sun, 21 Jun 2020 22:38:15: start X-correlation... INFO @ Sun, 21 Jun 2020 22:38:15: end of X-cor INFO @ Sun, 21 Jun 2020 22:38:15: #2 finished! INFO @ Sun, 21 Jun 2020 22:38:15: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 22:38:15: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 21 Jun 2020 22:38:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.05_model.r INFO @ Sun, 21 Jun 2020 22:38:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:38:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:38:16: 4000000 INFO @ Sun, 21 Jun 2020 22:38:21: 9000000 INFO @ Sun, 21 Jun 2020 22:38:22: 5000000 INFO @ Sun, 21 Jun 2020 22:38:27: 10000000 INFO @ Sun, 21 Jun 2020 22:38:28: 6000000 INFO @ Sun, 21 Jun 2020 22:38:34: 11000000 INFO @ Sun, 21 Jun 2020 22:38:35: 7000000 INFO @ Sun, 21 Jun 2020 22:38:41: 8000000 INFO @ Sun, 21 Jun 2020 22:38:41: 12000000 INFO @ Sun, 21 Jun 2020 22:38:42: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:38:44: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:38:44: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:38:44: #1 total tags in treatment: 12339161 INFO @ Sun, 21 Jun 2020 22:38:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:38:44: #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 22:38:44: #1 tags after filtering in treatment: 12339145 INFO @ Sun, 21 Jun 2020 22:38:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:38:44: #1 finished! INFO @ Sun, 21 Jun 2020 22:38:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:38:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:38:45: #2 number of paired peaks: 2119 INFO @ Sun, 21 Jun 2020 22:38:45: start model_add_line... INFO @ Sun, 21 Jun 2020 22:38:45: start X-correlation... INFO @ Sun, 21 Jun 2020 22:38:45: end of X-cor INFO @ Sun, 21 Jun 2020 22:38:45: #2 finished! INFO @ Sun, 21 Jun 2020 22:38:45: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 22:38:45: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 21 Jun 2020 22:38:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.10_model.r INFO @ Sun, 21 Jun 2020 22:38:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:38:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:38:47: 9000000 INFO @ Sun, 21 Jun 2020 22:38:53: 10000000 INFO @ Sun, 21 Jun 2020 22:38:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:38:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:38:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.05_summits.bed INFO @ Sun, 21 Jun 2020 22:38:55: Done! pass1 - making usageList (208 chroms): 2 millis pass2 - checking and writing primary data (7933 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:39:00: 11000000 INFO @ Sun, 21 Jun 2020 22:39:05: 12000000 INFO @ Sun, 21 Jun 2020 22:39:08: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:39:08: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:39:08: #1 total tags in treatment: 12339161 INFO @ Sun, 21 Jun 2020 22:39:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:39:08: #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 22:39:08: #1 tags after filtering in treatment: 12339145 INFO @ Sun, 21 Jun 2020 22:39:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:39:08: #1 finished! INFO @ Sun, 21 Jun 2020 22:39:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:39:08: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:39:09: #2 number of paired peaks: 2119 INFO @ Sun, 21 Jun 2020 22:39:09: start model_add_line... INFO @ Sun, 21 Jun 2020 22:39:09: start X-correlation... INFO @ Sun, 21 Jun 2020 22:39:09: end of X-cor INFO @ Sun, 21 Jun 2020 22:39:09: #2 finished! INFO @ Sun, 21 Jun 2020 22:39:09: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 22:39:09: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 21 Jun 2020 22:39:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.20_model.r INFO @ Sun, 21 Jun 2020 22:39:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:39:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:39:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:39:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:39:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:39:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.10_summits.bed INFO @ Sun, 21 Jun 2020 22:39:30: Done! pass1 - making usageList (123 chroms): 2 millis pass2 - checking and writing primary data (5532 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:39:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:39:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:39:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:39:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468483/SRX6468483.20_summits.bed INFO @ Sun, 21 Jun 2020 22:39:54: Done! pass1 - making usageList (71 chroms): 1 millis pass2 - checking and writing primary data (2013 records, 4 fields): 7 millis CompletedMACS2peakCalling