Job ID = 14518154 SRX = SRX9430823 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 4272914 spots for SRR12978974/SRR12978974.sra Written 4272914 spots for SRR12978974/SRR12978974.sra Read 5073970 spots for SRR12978975/SRR12978975.sra Written 5073970 spots for SRR12978975/SRR12978975.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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:27:37 9346884 reads; of these: 9346884 (100.00%) were unpaired; of these: 933962 (9.99%) aligned 0 times 5075292 (54.30%) aligned exactly 1 time 3337630 (35.71%) aligned >1 times 90.01% overall alignment rate Time searching: 00:27:39 Overall time: 00:27:39 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_rmdupse_core] 1780169 / 8412922 = 0.2116 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 10:47:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.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 10:47:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 10:47:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 10:47:43: 1000000 INFO @ Sat, 15 Jan 2022 10:47:48: 2000000 INFO @ Sat, 15 Jan 2022 10:47:53: 3000000 INFO @ Sat, 15 Jan 2022 10:47:58: 4000000 INFO @ Sat, 15 Jan 2022 10:48:03: 5000000 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 10:48:08: 6000000 INFO @ Sat, 15 Jan 2022 10:48:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.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 10:48:08: #1 read tag files... INFO @ Sat, 15 Jan 2022 10:48:08: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 10:48:12: #1 tag size is determined as 47 bps INFO @ Sat, 15 Jan 2022 10:48:12: #1 tag size = 47 INFO @ Sat, 15 Jan 2022 10:48:12: #1 total tags in treatment: 6632753 INFO @ Sat, 15 Jan 2022 10:48:12: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 10:48:12: #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 10:48:12: #1 tags after filtering in treatment: 6632550 INFO @ Sat, 15 Jan 2022 10:48:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 10:48:12: #1 finished! INFO @ Sat, 15 Jan 2022 10:48:12: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 10:48:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 10:48:13: 1000000 INFO @ Sat, 15 Jan 2022 10:48:13: #2 number of paired peaks: 30048 INFO @ Sat, 15 Jan 2022 10:48:13: start model_add_line... INFO @ Sat, 15 Jan 2022 10:48:14: start X-correlation... INFO @ Sat, 15 Jan 2022 10:48:14: end of X-cor INFO @ Sat, 15 Jan 2022 10:48:14: #2 finished! INFO @ Sat, 15 Jan 2022 10:48:14: #2 predicted fragment length is 118 bps INFO @ Sat, 15 Jan 2022 10:48:14: #2 alternative fragment length(s) may be 118 bps INFO @ Sat, 15 Jan 2022 10:48:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.05_model.r INFO @ Sat, 15 Jan 2022 10:48:14: #3 Call peaks... INFO @ Sat, 15 Jan 2022 10:48:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 10:48:18: 2000000 INFO @ Sat, 15 Jan 2022 10:48:23: 3000000 INFO @ Sat, 15 Jan 2022 10:48:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 10:48:28: 4000000 INFO @ Sat, 15 Jan 2022 10:48:33: 5000000 INFO @ Sat, 15 Jan 2022 10:48:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.05_peaks.xls INFO @ Sat, 15 Jan 2022 10:48:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 10:48:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.05_summits.bed INFO @ Sat, 15 Jan 2022 10:48:36: Done! pass1 - making usageList (84 chroms): 2 millis pass2 - checking and writing primary data (7096 records, 4 fields): 55 millis CompletedMACS2peakCalling 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 10:48:38: 6000000 INFO @ Sat, 15 Jan 2022 10:48:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.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 10:48:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 10:48:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 10:48:42: #1 tag size is determined as 47 bps INFO @ Sat, 15 Jan 2022 10:48:42: #1 tag size = 47 INFO @ Sat, 15 Jan 2022 10:48:42: #1 total tags in treatment: 6632753 INFO @ Sat, 15 Jan 2022 10:48:42: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 10:48:42: #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 10:48:42: #1 tags after filtering in treatment: 6632550 INFO @ Sat, 15 Jan 2022 10:48:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 10:48:42: #1 finished! INFO @ Sat, 15 Jan 2022 10:48:42: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 10:48:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 10:48:43: 1000000 INFO @ Sat, 15 Jan 2022 10:48:44: #2 number of paired peaks: 30048 INFO @ Sat, 15 Jan 2022 10:48:44: start model_add_line... INFO @ Sat, 15 Jan 2022 10:48:44: start X-correlation... INFO @ Sat, 15 Jan 2022 10:48:44: end of X-cor INFO @ Sat, 15 Jan 2022 10:48:44: #2 finished! INFO @ Sat, 15 Jan 2022 10:48:44: #2 predicted fragment length is 118 bps INFO @ Sat, 15 Jan 2022 10:48:44: #2 alternative fragment length(s) may be 118 bps INFO @ Sat, 15 Jan 2022 10:48:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.10_model.r INFO @ Sat, 15 Jan 2022 10:48:44: #3 Call peaks... INFO @ Sat, 15 Jan 2022 10:48:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 10:48:49: 2000000 INFO @ Sat, 15 Jan 2022 10:48:54: 3000000 INFO @ Sat, 15 Jan 2022 10:48:59: 4000000 INFO @ Sat, 15 Jan 2022 10:48:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 10:49:04: 5000000 INFO @ Sat, 15 Jan 2022 10:49:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.10_peaks.xls INFO @ Sat, 15 Jan 2022 10:49:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 10:49:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.10_summits.bed INFO @ Sat, 15 Jan 2022 10:49:07: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (1690 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 10:49:09: 6000000 INFO @ Sat, 15 Jan 2022 10:49:13: #1 tag size is determined as 47 bps INFO @ Sat, 15 Jan 2022 10:49:13: #1 tag size = 47 INFO @ Sat, 15 Jan 2022 10:49:13: #1 total tags in treatment: 6632753 INFO @ Sat, 15 Jan 2022 10:49:13: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 10:49:13: #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 10:49:13: #1 tags after filtering in treatment: 6632550 INFO @ Sat, 15 Jan 2022 10:49:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 10:49:13: #1 finished! INFO @ Sat, 15 Jan 2022 10:49:13: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 10:49:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 10:49:14: #2 number of paired peaks: 30048 INFO @ Sat, 15 Jan 2022 10:49:14: start model_add_line... INFO @ Sat, 15 Jan 2022 10:49:14: start X-correlation... INFO @ Sat, 15 Jan 2022 10:49:15: end of X-cor INFO @ Sat, 15 Jan 2022 10:49:15: #2 finished! INFO @ Sat, 15 Jan 2022 10:49:15: #2 predicted fragment length is 118 bps INFO @ Sat, 15 Jan 2022 10:49:15: #2 alternative fragment length(s) may be 118 bps INFO @ Sat, 15 Jan 2022 10:49:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.20_model.r INFO @ Sat, 15 Jan 2022 10:49:15: #3 Call peaks... INFO @ Sat, 15 Jan 2022 10:49:15: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 10:49:30: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 10:49:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.20_peaks.xls INFO @ Sat, 15 Jan 2022 10:49:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 10:49:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430823/SRX9430823.20_summits.bed INFO @ Sat, 15 Jan 2022 10:49:37: Done! BigWig に変換しました。 pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (483 records, 4 fields): 34 millis CompletedMACS2peakCalling