Job ID = 14521980 SRX = SRX7637549 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10369031 spots for SRR10972029/SRR10972029.sra Written 10369031 spots for SRR10972029/SRR10972029.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: 00:08:14 10369031 reads; of these: 10369031 (100.00%) were paired; of these: 1526440 (14.72%) aligned concordantly 0 times 4786547 (46.16%) aligned concordantly exactly 1 time 4056044 (39.12%) aligned concordantly >1 times ---- 1526440 pairs aligned concordantly 0 times; of these: 2227 (0.15%) aligned discordantly 1 time ---- 1524213 pairs aligned 0 times concordantly or discordantly; of these: 3048426 mates make up the pairs; of these: 2991239 (98.12%) aligned 0 times 27528 (0.90%) aligned exactly 1 time 29659 (0.97%) aligned >1 times 85.58% overall alignment rate Time searching: 00:08:14 Overall time: 00:08:14 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] 3570634 / 8844222 = 0.4037 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 22:08:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.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 22:08:26: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:08:26: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:08:30: 1000000 INFO @ Sat, 15 Jan 2022 22:08:34: 2000000 INFO @ Sat, 15 Jan 2022 22:08:39: 3000000 INFO @ Sat, 15 Jan 2022 22:08:43: 4000000 INFO @ Sat, 15 Jan 2022 22:08:47: 5000000 INFO @ Sat, 15 Jan 2022 22:08:52: 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 22:08:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.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 22:08:56: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:08:56: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:08:56: 7000000 INFO @ Sat, 15 Jan 2022 22:09:00: 1000000 INFO @ Sat, 15 Jan 2022 22:09:01: 8000000 INFO @ Sat, 15 Jan 2022 22:09:05: 2000000 INFO @ Sat, 15 Jan 2022 22:09:05: 9000000 INFO @ Sat, 15 Jan 2022 22:09:10: 3000000 INFO @ Sat, 15 Jan 2022 22:09:10: 10000000 INFO @ Sat, 15 Jan 2022 22:09:13: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 22:09:13: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 22:09:13: #1 total tags in treatment: 5272225 INFO @ Sat, 15 Jan 2022 22:09:13: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:09:13: #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 22:09:13: #1 tags after filtering in treatment: 2505343 INFO @ Sat, 15 Jan 2022 22:09:13: #1 Redundant rate of treatment: 0.52 INFO @ Sat, 15 Jan 2022 22:09:13: #1 finished! INFO @ Sat, 15 Jan 2022 22:09:13: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:09:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:09:13: #2 number of paired peaks: 481 WARNING @ Sat, 15 Jan 2022 22:09:13: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Sat, 15 Jan 2022 22:09:13: start model_add_line... INFO @ Sat, 15 Jan 2022 22:09:13: start X-correlation... INFO @ Sat, 15 Jan 2022 22:09:13: end of X-cor INFO @ Sat, 15 Jan 2022 22:09:13: #2 finished! INFO @ Sat, 15 Jan 2022 22:09:13: #2 predicted fragment length is 284 bps INFO @ Sat, 15 Jan 2022 22:09:13: #2 alternative fragment length(s) may be 50,89,115,157,192,284,399 bps INFO @ Sat, 15 Jan 2022 22:09:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.05_model.r INFO @ Sat, 15 Jan 2022 22:09:13: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:09:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:09:15: 4000000 INFO @ Sat, 15 Jan 2022 22:09:19: 5000000 INFO @ Sat, 15 Jan 2022 22:09:24: 6000000 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 22:09:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.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 22:09:26: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:09:26: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:09:28: 7000000 INFO @ Sat, 15 Jan 2022 22:09:30: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:09:30: 1000000 INFO @ Sat, 15 Jan 2022 22:09:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.05_peaks.xls INFO @ Sat, 15 Jan 2022 22:09:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:09:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.05_summits.bed INFO @ Sat, 15 Jan 2022 22:09:32: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (668 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:09:33: 8000000 INFO @ Sat, 15 Jan 2022 22:09:36: 2000000 INFO @ Sat, 15 Jan 2022 22:09:38: 9000000 INFO @ Sat, 15 Jan 2022 22:09:41: 3000000 INFO @ Sat, 15 Jan 2022 22:09:43: 10000000 INFO @ Sat, 15 Jan 2022 22:09:46: 4000000 INFO @ Sat, 15 Jan 2022 22:09:46: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 22:09:46: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 22:09:46: #1 total tags in treatment: 5272225 INFO @ Sat, 15 Jan 2022 22:09:46: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:09:46: #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 22:09:46: #1 tags after filtering in treatment: 2505343 INFO @ Sat, 15 Jan 2022 22:09:46: #1 Redundant rate of treatment: 0.52 INFO @ Sat, 15 Jan 2022 22:09:46: #1 finished! INFO @ Sat, 15 Jan 2022 22:09:46: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:09:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:09:46: #2 number of paired peaks: 481 WARNING @ Sat, 15 Jan 2022 22:09:46: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Sat, 15 Jan 2022 22:09:46: start model_add_line... INFO @ Sat, 15 Jan 2022 22:09:46: start X-correlation... INFO @ Sat, 15 Jan 2022 22:09:46: end of X-cor INFO @ Sat, 15 Jan 2022 22:09:46: #2 finished! INFO @ Sat, 15 Jan 2022 22:09:46: #2 predicted fragment length is 284 bps INFO @ Sat, 15 Jan 2022 22:09:46: #2 alternative fragment length(s) may be 50,89,115,157,192,284,399 bps INFO @ Sat, 15 Jan 2022 22:09:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.10_model.r INFO @ Sat, 15 Jan 2022 22:09:46: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:09:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:09:50: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:09:55: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 22:09:59: 7000000 INFO @ Sat, 15 Jan 2022 22:10:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:10:03: 8000000 INFO @ Sat, 15 Jan 2022 22:10:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.10_peaks.xls INFO @ Sat, 15 Jan 2022 22:10:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:10:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.10_summits.bed INFO @ Sat, 15 Jan 2022 22:10:05: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (541 records, 4 fields): 527 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:10:08: 9000000 INFO @ Sat, 15 Jan 2022 22:10:12: 10000000 INFO @ Sat, 15 Jan 2022 22:10:15: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 22:10:15: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 22:10:15: #1 total tags in treatment: 5272225 INFO @ Sat, 15 Jan 2022 22:10:15: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:10:15: #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 22:10:15: #1 tags after filtering in treatment: 2505343 INFO @ Sat, 15 Jan 2022 22:10:15: #1 Redundant rate of treatment: 0.52 INFO @ Sat, 15 Jan 2022 22:10:15: #1 finished! INFO @ Sat, 15 Jan 2022 22:10:15: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:10:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:10:15: #2 number of paired peaks: 481 WARNING @ Sat, 15 Jan 2022 22:10:15: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Sat, 15 Jan 2022 22:10:15: start model_add_line... INFO @ Sat, 15 Jan 2022 22:10:15: start X-correlation... INFO @ Sat, 15 Jan 2022 22:10:15: end of X-cor INFO @ Sat, 15 Jan 2022 22:10:15: #2 finished! INFO @ Sat, 15 Jan 2022 22:10:15: #2 predicted fragment length is 284 bps INFO @ Sat, 15 Jan 2022 22:10:15: #2 alternative fragment length(s) may be 50,89,115,157,192,284,399 bps INFO @ Sat, 15 Jan 2022 22:10:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.20_model.r INFO @ Sat, 15 Jan 2022 22:10:15: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:10:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:10:32: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:10:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.20_peaks.xls INFO @ Sat, 15 Jan 2022 22:10:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:10:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7637549/SRX7637549.20_summits.bed INFO @ Sat, 15 Jan 2022 22:10:34: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (312 records, 4 fields): 2 millis CompletedMACS2peakCalling