Job ID = 14519550 SRX = SRX9963481 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 33984260 spots for SRR13565197/SRR13565197.sra Written 33984260 spots for SRR13565197/SRR13565197.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:59:05 33984260 reads; of these: 33984260 (100.00%) were unpaired; of these: 5403054 (15.90%) aligned 0 times 23744711 (69.87%) aligned exactly 1 time 4836495 (14.23%) aligned >1 times 84.10% overall alignment rate Time searching: 00:59:08 Overall time: 00:59:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 5448144 / 28581206 = 0.1906 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 17:12:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 15 Jan 2022 17:12:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:12:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:12:41: 1000000 INFO @ Sat, 15 Jan 2022 17:12:49: 2000000 INFO @ Sat, 15 Jan 2022 17:12:56: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 17:13:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 15 Jan 2022 17:13:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:13:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:13:04: 4000000 INFO @ Sat, 15 Jan 2022 17:13:11: 1000000 INFO @ Sat, 15 Jan 2022 17:13:12: 5000000 INFO @ Sat, 15 Jan 2022 17:13:19: 2000000 INFO @ Sat, 15 Jan 2022 17:13:21: 6000000 INFO @ Sat, 15 Jan 2022 17:13:27: 3000000 INFO @ Sat, 15 Jan 2022 17:13:30: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 17:13:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 15 Jan 2022 17:13:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:13:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:13:36: 4000000 INFO @ Sat, 15 Jan 2022 17:13:39: 8000000 INFO @ Sat, 15 Jan 2022 17:13:41: 1000000 INFO @ Sat, 15 Jan 2022 17:13:44: 5000000 INFO @ Sat, 15 Jan 2022 17:13:48: 9000000 INFO @ Sat, 15 Jan 2022 17:13:49: 2000000 INFO @ Sat, 15 Jan 2022 17:13:53: 6000000 INFO @ Sat, 15 Jan 2022 17:13:57: 10000000 INFO @ Sat, 15 Jan 2022 17:13:58: 3000000 INFO @ Sat, 15 Jan 2022 17:14:02: 7000000 INFO @ Sat, 15 Jan 2022 17:14:06: 11000000 INFO @ Sat, 15 Jan 2022 17:14:06: 4000000 INFO @ Sat, 15 Jan 2022 17:14:10: 8000000 INFO @ Sat, 15 Jan 2022 17:14:14: 12000000 INFO @ Sat, 15 Jan 2022 17:14:14: 5000000 INFO @ Sat, 15 Jan 2022 17:14:19: 9000000 INFO @ Sat, 15 Jan 2022 17:14:23: 6000000 INFO @ Sat, 15 Jan 2022 17:14:23: 13000000 INFO @ Sat, 15 Jan 2022 17:14:28: 10000000 INFO @ Sat, 15 Jan 2022 17:14:31: 7000000 INFO @ Sat, 15 Jan 2022 17:14:32: 14000000 INFO @ Sat, 15 Jan 2022 17:14:36: 11000000 INFO @ Sat, 15 Jan 2022 17:14:40: 8000000 INFO @ Sat, 15 Jan 2022 17:14:41: 15000000 INFO @ Sat, 15 Jan 2022 17:14:45: 12000000 INFO @ Sat, 15 Jan 2022 17:14:48: 9000000 INFO @ Sat, 15 Jan 2022 17:14:50: 16000000 INFO @ Sat, 15 Jan 2022 17:14:53: 13000000 INFO @ Sat, 15 Jan 2022 17:14:56: 10000000 INFO @ Sat, 15 Jan 2022 17:14:58: 17000000 INFO @ Sat, 15 Jan 2022 17:15:02: 14000000 INFO @ Sat, 15 Jan 2022 17:15:05: 11000000 INFO @ Sat, 15 Jan 2022 17:15:07: 18000000 INFO @ Sat, 15 Jan 2022 17:15:10: 15000000 INFO @ Sat, 15 Jan 2022 17:15:13: 12000000 INFO @ Sat, 15 Jan 2022 17:15:16: 19000000 INFO @ Sat, 15 Jan 2022 17:15:19: 16000000 INFO @ Sat, 15 Jan 2022 17:15:21: 13000000 INFO @ Sat, 15 Jan 2022 17:15:24: 20000000 INFO @ Sat, 15 Jan 2022 17:15:27: 17000000 INFO @ Sat, 15 Jan 2022 17:15:30: 14000000 INFO @ Sat, 15 Jan 2022 17:15:33: 21000000 INFO @ Sat, 15 Jan 2022 17:15:36: 18000000 INFO @ Sat, 15 Jan 2022 17:15:38: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:15:42: 22000000 INFO @ Sat, 15 Jan 2022 17:15:44: 19000000 INFO @ Sat, 15 Jan 2022 17:15:47: 16000000 INFO @ Sat, 15 Jan 2022 17:15:51: 23000000 INFO @ Sat, 15 Jan 2022 17:15:52: 20000000 INFO @ Sat, 15 Jan 2022 17:15:53: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 17:15:53: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 17:15:53: #1 total tags in treatment: 23133062 INFO @ Sat, 15 Jan 2022 17:15:53: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:15:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 17:15:53: #1 tags after filtering in treatment: 23132898 INFO @ Sat, 15 Jan 2022 17:15:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:15:53: #1 finished! INFO @ Sat, 15 Jan 2022 17:15:53: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:15:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:15:55: 17000000 INFO @ Sat, 15 Jan 2022 17:15:57: #2 number of paired peaks: 72163 INFO @ Sat, 15 Jan 2022 17:15:57: start model_add_line... INFO @ Sat, 15 Jan 2022 17:15:57: start X-correlation... INFO @ Sat, 15 Jan 2022 17:15:57: end of X-cor INFO @ Sat, 15 Jan 2022 17:15:57: #2 finished! INFO @ Sat, 15 Jan 2022 17:15:57: #2 predicted fragment length is 191 bps INFO @ Sat, 15 Jan 2022 17:15:57: #2 alternative fragment length(s) may be 191 bps INFO @ Sat, 15 Jan 2022 17:15:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.05_model.r INFO @ Sat, 15 Jan 2022 17:15:57: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:15:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:16:01: 21000000 INFO @ Sat, 15 Jan 2022 17:16:03: 18000000 INFO @ Sat, 15 Jan 2022 17:16:09: 22000000 INFO @ Sat, 15 Jan 2022 17:16:12: 19000000 INFO @ Sat, 15 Jan 2022 17:16:17: 23000000 INFO @ Sat, 15 Jan 2022 17:16:19: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 17:16:19: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 17:16:19: #1 total tags in treatment: 23133062 INFO @ Sat, 15 Jan 2022 17:16:19: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:16:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 17:16:19: #1 tags after filtering in treatment: 23132898 INFO @ Sat, 15 Jan 2022 17:16:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:16:19: #1 finished! INFO @ Sat, 15 Jan 2022 17:16:19: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:16:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:16:19: 20000000 INFO @ Sat, 15 Jan 2022 17:16:23: #2 number of paired peaks: 72163 INFO @ Sat, 15 Jan 2022 17:16:23: start model_add_line... INFO @ Sat, 15 Jan 2022 17:16:23: start X-correlation... INFO @ Sat, 15 Jan 2022 17:16:23: end of X-cor INFO @ Sat, 15 Jan 2022 17:16:23: #2 finished! INFO @ Sat, 15 Jan 2022 17:16:23: #2 predicted fragment length is 191 bps INFO @ Sat, 15 Jan 2022 17:16:23: #2 alternative fragment length(s) may be 191 bps INFO @ Sat, 15 Jan 2022 17:16:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.10_model.r INFO @ Sat, 15 Jan 2022 17:16:23: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:16:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:16:27: 21000000 INFO @ Sat, 15 Jan 2022 17:16:35: 22000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:16:42: 23000000 INFO @ Sat, 15 Jan 2022 17:16:43: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 17:16:43: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 17:16:43: #1 total tags in treatment: 23133062 INFO @ Sat, 15 Jan 2022 17:16:43: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:16:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 17:16:44: #1 tags after filtering in treatment: 23132898 INFO @ Sat, 15 Jan 2022 17:16:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:16:44: #1 finished! INFO @ Sat, 15 Jan 2022 17:16:44: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:16:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:16:48: #2 number of paired peaks: 72163 INFO @ Sat, 15 Jan 2022 17:16:48: start model_add_line... INFO @ Sat, 15 Jan 2022 17:16:48: start X-correlation... INFO @ Sat, 15 Jan 2022 17:16:48: end of X-cor INFO @ Sat, 15 Jan 2022 17:16:48: #2 finished! INFO @ Sat, 15 Jan 2022 17:16:48: #2 predicted fragment length is 191 bps INFO @ Sat, 15 Jan 2022 17:16:48: #2 alternative fragment length(s) may be 191 bps INFO @ Sat, 15 Jan 2022 17:16:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.20_model.r INFO @ Sat, 15 Jan 2022 17:16:48: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:16:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:16:52: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:17:19: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:17:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:17:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:17:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.05_summits.bed INFO @ Sat, 15 Jan 2022 17:17:22: Done! pass1 - making usageList (95 chroms): 1 millis pass2 - checking and writing primary data (7686 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:17:44: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:17:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:17:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:17:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.10_summits.bed INFO @ Sat, 15 Jan 2022 17:17:48: Done! pass1 - making usageList (75 chroms): 2 millis pass2 - checking and writing primary data (3732 records, 4 fields): 324 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:18:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:18:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:18:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963481/SRX9963481.20_summits.bed INFO @ Sat, 15 Jan 2022 17:18:13: Done! pass1 - making usageList (58 chroms): 1 millis pass2 - checking and writing primary data (1369 records, 4 fields): 6 millis CompletedMACS2peakCalling