Job ID = 14518158 SRX = SRX9430827 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7519463 spots for SRR12978982/SRR12978982.sra Written 7519463 spots for SRR12978982/SRR12978982.sra Read 8627470 spots for SRR12978983/SRR12978983.sra Written 8627470 spots for SRR12978983/SRR12978983.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:49:32 16146933 reads; of these: 16146933 (100.00%) were unpaired; of these: 1751982 (10.85%) aligned 0 times 7786552 (48.22%) aligned exactly 1 time 6608399 (40.93%) aligned >1 times 89.15% overall alignment rate Time searching: 00:49:33 Overall time: 00:49:33 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 8 files... [bam_rmdupse_core] 2195746 / 14394951 = 0.1525 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 11:13:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.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 11:13:59: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:13:59: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:14:05: 1000000 INFO @ Sat, 15 Jan 2022 11:14:11: 2000000 INFO @ Sat, 15 Jan 2022 11:14:16: 3000000 INFO @ Sat, 15 Jan 2022 11:14:21: 4000000 INFO @ Sat, 15 Jan 2022 11:14:27: 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 11:14:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.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 11:14:29: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:14:29: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:14:32: 6000000 INFO @ Sat, 15 Jan 2022 11:14:35: 1000000 INFO @ Sat, 15 Jan 2022 11:14:38: 7000000 INFO @ Sat, 15 Jan 2022 11:14:41: 2000000 INFO @ Sat, 15 Jan 2022 11:14:44: 8000000 INFO @ Sat, 15 Jan 2022 11:14:47: 3000000 INFO @ Sat, 15 Jan 2022 11:14:50: 9000000 INFO @ Sat, 15 Jan 2022 11:14:52: 4000000 INFO @ Sat, 15 Jan 2022 11:14:55: 10000000 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 11:14:58: 5000000 INFO @ Sat, 15 Jan 2022 11:14:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.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 11:14:59: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:14:59: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:15:01: 11000000 INFO @ Sat, 15 Jan 2022 11:15:04: 6000000 INFO @ Sat, 15 Jan 2022 11:15:05: 1000000 INFO @ Sat, 15 Jan 2022 11:15:07: 12000000 INFO @ Sat, 15 Jan 2022 11:15:09: #1 tag size is determined as 55 bps INFO @ Sat, 15 Jan 2022 11:15:09: #1 tag size = 55 INFO @ Sat, 15 Jan 2022 11:15:09: #1 total tags in treatment: 12199205 INFO @ Sat, 15 Jan 2022 11:15:09: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:15:09: #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 11:15:09: #1 tags after filtering in treatment: 12199028 INFO @ Sat, 15 Jan 2022 11:15:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:15:09: #1 finished! INFO @ Sat, 15 Jan 2022 11:15:09: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:15:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:15:10: 7000000 INFO @ Sat, 15 Jan 2022 11:15:11: #2 number of paired peaks: 34277 INFO @ Sat, 15 Jan 2022 11:15:11: start model_add_line... INFO @ Sat, 15 Jan 2022 11:15:11: 2000000 INFO @ Sat, 15 Jan 2022 11:15:11: start X-correlation... INFO @ Sat, 15 Jan 2022 11:15:11: end of X-cor INFO @ Sat, 15 Jan 2022 11:15:11: #2 finished! INFO @ Sat, 15 Jan 2022 11:15:11: #2 predicted fragment length is 126 bps INFO @ Sat, 15 Jan 2022 11:15:11: #2 alternative fragment length(s) may be 126 bps INFO @ Sat, 15 Jan 2022 11:15:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.05_model.r INFO @ Sat, 15 Jan 2022 11:15:11: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:15:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 11:15:16: 8000000 INFO @ Sat, 15 Jan 2022 11:15:17: 3000000 INFO @ Sat, 15 Jan 2022 11:15:21: 9000000 INFO @ Sat, 15 Jan 2022 11:15:23: 4000000 INFO @ Sat, 15 Jan 2022 11:15:27: 10000000 INFO @ Sat, 15 Jan 2022 11:15:28: 5000000 INFO @ Sat, 15 Jan 2022 11:15:33: 11000000 INFO @ Sat, 15 Jan 2022 11:15:34: 6000000 INFO @ Sat, 15 Jan 2022 11:15:39: 12000000 INFO @ Sat, 15 Jan 2022 11:15:40: 7000000 INFO @ Sat, 15 Jan 2022 11:15:40: #1 tag size is determined as 55 bps INFO @ Sat, 15 Jan 2022 11:15:40: #1 tag size = 55 INFO @ Sat, 15 Jan 2022 11:15:40: #1 total tags in treatment: 12199205 INFO @ Sat, 15 Jan 2022 11:15:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:15:40: #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 11:15:40: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 11:15:40: #1 tags after filtering in treatment: 12199028 INFO @ Sat, 15 Jan 2022 11:15:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:15:40: #1 finished! INFO @ Sat, 15 Jan 2022 11:15:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:15:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:15:42: #2 number of paired peaks: 34277 INFO @ Sat, 15 Jan 2022 11:15:42: start model_add_line... INFO @ Sat, 15 Jan 2022 11:15:43: start X-correlation... INFO @ Sat, 15 Jan 2022 11:15:43: end of X-cor INFO @ Sat, 15 Jan 2022 11:15:43: #2 finished! INFO @ Sat, 15 Jan 2022 11:15:43: #2 predicted fragment length is 126 bps INFO @ Sat, 15 Jan 2022 11:15:43: #2 alternative fragment length(s) may be 126 bps INFO @ Sat, 15 Jan 2022 11:15:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.10_model.r INFO @ Sat, 15 Jan 2022 11:15:43: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:15:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 11:15:45: 8000000 INFO @ Sat, 15 Jan 2022 11:15:50: 9000000 INFO @ Sat, 15 Jan 2022 11:15:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.05_peaks.xls INFO @ Sat, 15 Jan 2022 11:15:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:15:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.05_summits.bed INFO @ Sat, 15 Jan 2022 11:15:55: Done! pass1 - making usageList (110 chroms): 3 millis pass2 - checking and writing primary data (15590 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 11:15:57: 10000000 INFO @ Sat, 15 Jan 2022 11:16:03: 11000000 INFO @ Sat, 15 Jan 2022 11:16:09: 12000000 INFO @ Sat, 15 Jan 2022 11:16:10: #1 tag size is determined as 55 bps INFO @ Sat, 15 Jan 2022 11:16:10: #1 tag size = 55 INFO @ Sat, 15 Jan 2022 11:16:10: #1 total tags in treatment: 12199205 INFO @ Sat, 15 Jan 2022 11:16:10: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:16:10: #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 11:16:10: #1 tags after filtering in treatment: 12199028 INFO @ Sat, 15 Jan 2022 11:16:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:16:10: #1 finished! INFO @ Sat, 15 Jan 2022 11:16:10: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:16:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:16:10: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 11:16:12: #2 number of paired peaks: 34277 INFO @ Sat, 15 Jan 2022 11:16:12: start model_add_line... INFO @ Sat, 15 Jan 2022 11:16:12: start X-correlation... INFO @ Sat, 15 Jan 2022 11:16:12: end of X-cor INFO @ Sat, 15 Jan 2022 11:16:12: #2 finished! INFO @ Sat, 15 Jan 2022 11:16:12: #2 predicted fragment length is 126 bps INFO @ Sat, 15 Jan 2022 11:16:12: #2 alternative fragment length(s) may be 126 bps INFO @ Sat, 15 Jan 2022 11:16:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.20_model.r INFO @ Sat, 15 Jan 2022 11:16:12: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:16:12: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 11:16:25: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.10_peaks.xls INFO @ Sat, 15 Jan 2022 11:16:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:16:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.10_summits.bed INFO @ Sat, 15 Jan 2022 11:16:25: Done! pass1 - making usageList (61 chroms): 1 millis pass2 - checking and writing primary data (4264 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 11:16:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 11:16:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.20_peaks.xls INFO @ Sat, 15 Jan 2022 11:16:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:16:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430827/SRX9430827.20_summits.bed INFO @ Sat, 15 Jan 2022 11:16:55: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (1161 records, 4 fields): 3 millis CompletedMACS2peakCalling