Job ID = 14521976 SRX = SRX7637545 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7566516 spots for SRR10972025/SRR10972025.sra Written 7566516 spots for SRR10972025/SRR10972025.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: 00:07:11 7566516 reads; of these: 7566516 (100.00%) were paired; of these: 1052930 (13.92%) aligned concordantly 0 times 4408232 (58.26%) aligned concordantly exactly 1 time 2105354 (27.82%) aligned concordantly >1 times ---- 1052930 pairs aligned concordantly 0 times; of these: 2349 (0.22%) aligned discordantly 1 time ---- 1050581 pairs aligned 0 times concordantly or discordantly; of these: 2101162 mates make up the pairs; of these: 2045779 (97.36%) aligned 0 times 34328 (1.63%) aligned exactly 1 time 21055 (1.00%) aligned >1 times 86.48% overall alignment rate Time searching: 00:07:11 Overall time: 00:07:11 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_sort_core] merging from 8 files... [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] 1660027 / 6515141 = 0.2548 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 22:06:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.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 22:06:59: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:06:59: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:07:05: 1000000 INFO @ Sat, 15 Jan 2022 22:07:11: 2000000 INFO @ Sat, 15 Jan 2022 22:07:18: 3000000 INFO @ Sat, 15 Jan 2022 22:07:24: 4000000 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 22:07:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.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 22:07:29: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:07:29: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:07:30: 5000000 INFO @ Sat, 15 Jan 2022 22:07:37: 6000000 INFO @ Sat, 15 Jan 2022 22:07:37: 1000000 INFO @ Sat, 15 Jan 2022 22:07:43: 7000000 INFO @ Sat, 15 Jan 2022 22:07:44: 2000000 INFO @ Sat, 15 Jan 2022 22:07:49: 8000000 INFO @ Sat, 15 Jan 2022 22:07:52: 3000000 INFO @ Sat, 15 Jan 2022 22:07:56: 9000000 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 22:07:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.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 22:07:59: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:07:59: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:08:00: 4000000 INFO @ Sat, 15 Jan 2022 22:08:01: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 22:08:01: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 22:08:01: #1 total tags in treatment: 4853753 INFO @ Sat, 15 Jan 2022 22:08:01: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:08:01: #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 22:08:01: #1 tags after filtering in treatment: 2770649 INFO @ Sat, 15 Jan 2022 22:08:01: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 22:08:01: #1 finished! INFO @ Sat, 15 Jan 2022 22:08:01: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:08:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:08:01: #2 number of paired peaks: 352 WARNING @ Sat, 15 Jan 2022 22:08:01: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Sat, 15 Jan 2022 22:08:01: start model_add_line... INFO @ Sat, 15 Jan 2022 22:08:01: start X-correlation... INFO @ Sat, 15 Jan 2022 22:08:01: end of X-cor INFO @ Sat, 15 Jan 2022 22:08:01: #2 finished! INFO @ Sat, 15 Jan 2022 22:08:01: #2 predicted fragment length is 317 bps INFO @ Sat, 15 Jan 2022 22:08:01: #2 alternative fragment length(s) may be 102,131,168,204,233,258,274,317,330,400,432,459,468,578 bps INFO @ Sat, 15 Jan 2022 22:08:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.05_model.r INFO @ Sat, 15 Jan 2022 22:08:02: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:08:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:08:06: 1000000 INFO @ Sat, 15 Jan 2022 22:08:08: 5000000 INFO @ Sat, 15 Jan 2022 22:08:12: 2000000 INFO @ Sat, 15 Jan 2022 22:08:16: 6000000 INFO @ Sat, 15 Jan 2022 22:08:19: 3000000 INFO @ Sat, 15 Jan 2022 22:08:23: 7000000 INFO @ Sat, 15 Jan 2022 22:08:25: 4000000 INFO @ Sat, 15 Jan 2022 22:08:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:08:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.05_peaks.xls BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:08:31: 8000000 INFO @ Sat, 15 Jan 2022 22:08:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:08:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.05_summits.bed INFO @ Sat, 15 Jan 2022 22:08:32: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (586 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:08:33: 5000000 INFO @ Sat, 15 Jan 2022 22:08:40: 9000000 INFO @ Sat, 15 Jan 2022 22:08:40: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 22:08:46: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 22:08:46: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 22:08:46: #1 total tags in treatment: 4853753 INFO @ Sat, 15 Jan 2022 22:08:46: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:08:46: #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 22:08:46: #1 tags after filtering in treatment: 2770649 INFO @ Sat, 15 Jan 2022 22:08:46: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 22:08:46: #1 finished! INFO @ Sat, 15 Jan 2022 22:08:46: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:08:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:08:46: #2 number of paired peaks: 352 WARNING @ Sat, 15 Jan 2022 22:08:46: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Sat, 15 Jan 2022 22:08:46: start model_add_line... INFO @ Sat, 15 Jan 2022 22:08:46: start X-correlation... INFO @ Sat, 15 Jan 2022 22:08:46: end of X-cor INFO @ Sat, 15 Jan 2022 22:08:46: #2 finished! INFO @ Sat, 15 Jan 2022 22:08:46: #2 predicted fragment length is 317 bps INFO @ Sat, 15 Jan 2022 22:08:46: #2 alternative fragment length(s) may be 102,131,168,204,233,258,274,317,330,400,432,459,468,578 bps INFO @ Sat, 15 Jan 2022 22:08:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.10_model.r INFO @ Sat, 15 Jan 2022 22:08:46: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:08:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:08:47: 7000000 INFO @ Sat, 15 Jan 2022 22:08:53: 8000000 INFO @ Sat, 15 Jan 2022 22:09:00: 9000000 INFO @ Sat, 15 Jan 2022 22:09:05: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 22:09:05: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 22:09:05: #1 total tags in treatment: 4853753 INFO @ Sat, 15 Jan 2022 22:09:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:09:05: #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 22:09:05: #1 tags after filtering in treatment: 2770649 INFO @ Sat, 15 Jan 2022 22:09:05: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 22:09:05: #1 finished! INFO @ Sat, 15 Jan 2022 22:09:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:09:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:09:05: #2 number of paired peaks: 352 WARNING @ Sat, 15 Jan 2022 22:09:05: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Sat, 15 Jan 2022 22:09:05: start model_add_line... INFO @ Sat, 15 Jan 2022 22:09:05: start X-correlation... INFO @ Sat, 15 Jan 2022 22:09:05: end of X-cor INFO @ Sat, 15 Jan 2022 22:09:05: #2 finished! INFO @ Sat, 15 Jan 2022 22:09:05: #2 predicted fragment length is 317 bps INFO @ Sat, 15 Jan 2022 22:09:05: #2 alternative fragment length(s) may be 102,131,168,204,233,258,274,317,330,400,432,459,468,578 bps INFO @ Sat, 15 Jan 2022 22:09:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.20_model.r INFO @ Sat, 15 Jan 2022 22:09:05: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:09:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:09:13: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:09:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.10_peaks.xls INFO @ Sat, 15 Jan 2022 22:09:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:09:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.10_summits.bed INFO @ Sat, 15 Jan 2022 22:09:16: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (517 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:09:32: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:09:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.20_peaks.xls INFO @ Sat, 15 Jan 2022 22:09:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:09:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7637545/SRX7637545.20_summits.bed INFO @ Sat, 15 Jan 2022 22:09:35: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (345 records, 4 fields): 109 millis CompletedMACS2peakCalling