Job ID = 14520402 SRX = SRX11781130 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7401824 spots for SRR15481073/SRR15481073.sra Written 7401824 spots for SRR15481073/SRR15481073.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: 00:05:09 7401824 reads; of these: 7401824 (100.00%) were paired; of these: 5030065 (67.96%) aligned concordantly 0 times 1706035 (23.05%) aligned concordantly exactly 1 time 665724 (8.99%) aligned concordantly >1 times ---- 5030065 pairs aligned concordantly 0 times; of these: 55155 (1.10%) aligned discordantly 1 time ---- 4974910 pairs aligned 0 times concordantly or discordantly; of these: 9949820 mates make up the pairs; of these: 6357939 (63.90%) aligned 0 times 2604278 (26.17%) aligned exactly 1 time 987603 (9.93%) aligned >1 times 57.05% overall alignment rate Time searching: 00:05:09 Overall time: 00:05:09 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 238214 / 2425501 = 0.0982 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 19:10:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.bam'] # control file = None # effective genome size = 1.21e+07 # 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 19:10:27: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:10:27: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:10:31: 1000000 INFO @ Sat, 15 Jan 2022 19:10:36: 2000000 INFO @ Sat, 15 Jan 2022 19:10:40: 3000000 INFO @ Sat, 15 Jan 2022 19:10:44: 4000000 INFO @ Sat, 15 Jan 2022 19:10:49: 5000000 INFO @ Sat, 15 Jan 2022 19:10:53: 6000000 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 19:10:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.bam'] # control file = None # effective genome size = 1.21e+07 # 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 19:10:57: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:10:57: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:10:57: 7000000 INFO @ Sat, 15 Jan 2022 19:11:02: 1000000 INFO @ Sat, 15 Jan 2022 19:11:02: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:11:02: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:11:02: #1 total tags in treatment: 2137128 INFO @ Sat, 15 Jan 2022 19:11:02: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:11:02: #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 19:11:02: #1 tags after filtering in treatment: 1591292 INFO @ Sat, 15 Jan 2022 19:11:02: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 19:11:02: #1 finished! INFO @ Sat, 15 Jan 2022 19:11:02: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:11:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:11:02: #2 number of paired peaks: 191 WARNING @ Sat, 15 Jan 2022 19:11:02: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Sat, 15 Jan 2022 19:11:02: start model_add_line... INFO @ Sat, 15 Jan 2022 19:11:02: start X-correlation... INFO @ Sat, 15 Jan 2022 19:11:02: end of X-cor INFO @ Sat, 15 Jan 2022 19:11:02: #2 finished! INFO @ Sat, 15 Jan 2022 19:11:02: #2 predicted fragment length is 263 bps INFO @ Sat, 15 Jan 2022 19:11:02: #2 alternative fragment length(s) may be 2,220,235,250,263 bps INFO @ Sat, 15 Jan 2022 19:11:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.05_model.r INFO @ Sat, 15 Jan 2022 19:11:02: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:11:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:11:07: 2000000 INFO @ Sat, 15 Jan 2022 19:11:08: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:11:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:11:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:11:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.05_summits.bed INFO @ Sat, 15 Jan 2022 19:11:10: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (542 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:11:12: 3000000 INFO @ Sat, 15 Jan 2022 19:11:17: 4000000 INFO @ Sat, 15 Jan 2022 19:11:22: 5000000 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 19:11:26: 6000000 INFO @ Sat, 15 Jan 2022 19:11:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.bam'] # control file = None # effective genome size = 1.21e+07 # 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 19:11:27: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:11:27: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:11:31: 7000000 INFO @ Sat, 15 Jan 2022 19:11:32: 1000000 INFO @ Sat, 15 Jan 2022 19:11:36: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:11:36: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:11:36: #1 total tags in treatment: 2137128 INFO @ Sat, 15 Jan 2022 19:11:36: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:11:36: #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 19:11:36: #1 tags after filtering in treatment: 1591292 INFO @ Sat, 15 Jan 2022 19:11:36: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 19:11:36: #1 finished! INFO @ Sat, 15 Jan 2022 19:11:36: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:11:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:11:36: #2 number of paired peaks: 191 WARNING @ Sat, 15 Jan 2022 19:11:36: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Sat, 15 Jan 2022 19:11:36: start model_add_line... INFO @ Sat, 15 Jan 2022 19:11:36: start X-correlation... INFO @ Sat, 15 Jan 2022 19:11:36: end of X-cor INFO @ Sat, 15 Jan 2022 19:11:36: #2 finished! INFO @ Sat, 15 Jan 2022 19:11:36: #2 predicted fragment length is 263 bps INFO @ Sat, 15 Jan 2022 19:11:36: #2 alternative fragment length(s) may be 2,220,235,250,263 bps INFO @ Sat, 15 Jan 2022 19:11:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.10_model.r INFO @ Sat, 15 Jan 2022 19:11:36: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:11:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:11:37: 2000000 INFO @ Sat, 15 Jan 2022 19:11:41: 3000000 INFO @ Sat, 15 Jan 2022 19:11:42: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:11:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:11:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:11:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.10_summits.bed INFO @ Sat, 15 Jan 2022 19:11:43: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (295 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:11:46: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:11:51: 5000000 INFO @ Sat, 15 Jan 2022 19:11:55: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:12:00: 7000000 INFO @ Sat, 15 Jan 2022 19:12:04: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:12:04: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:12:04: #1 total tags in treatment: 2137128 INFO @ Sat, 15 Jan 2022 19:12:04: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:12:04: #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 19:12:04: #1 tags after filtering in treatment: 1591292 INFO @ Sat, 15 Jan 2022 19:12:04: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 19:12:04: #1 finished! INFO @ Sat, 15 Jan 2022 19:12:04: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:12:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:12:04: #2 number of paired peaks: 191 WARNING @ Sat, 15 Jan 2022 19:12:04: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Sat, 15 Jan 2022 19:12:04: start model_add_line... INFO @ Sat, 15 Jan 2022 19:12:04: start X-correlation... INFO @ Sat, 15 Jan 2022 19:12:04: end of X-cor INFO @ Sat, 15 Jan 2022 19:12:04: #2 finished! INFO @ Sat, 15 Jan 2022 19:12:04: #2 predicted fragment length is 263 bps INFO @ Sat, 15 Jan 2022 19:12:04: #2 alternative fragment length(s) may be 2,220,235,250,263 bps INFO @ Sat, 15 Jan 2022 19:12:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.20_model.r INFO @ Sat, 15 Jan 2022 19:12:04: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:12:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:12:10: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:12:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:12:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:12:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781130/SRX11781130.20_summits.bed INFO @ Sat, 15 Jan 2022 19:12:11: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (106 records, 4 fields): 2 millis CompletedMACS2peakCalling