Job ID = 14521257 SRX = SRX10468526 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2554582 spots for SRR14094837/SRR14094837.sra Written 2554582 spots for SRR14094837/SRR14094837.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: 00:01:15 2554582 reads; of these: 2554582 (100.00%) were paired; of these: 605594 (23.71%) aligned concordantly 0 times 1752619 (68.61%) aligned concordantly exactly 1 time 196369 (7.69%) aligned concordantly >1 times ---- 605594 pairs aligned concordantly 0 times; of these: 12381 (2.04%) aligned discordantly 1 time ---- 593213 pairs aligned 0 times concordantly or discordantly; of these: 1186426 mates make up the pairs; of these: 1139929 (96.08%) aligned 0 times 37530 (3.16%) aligned exactly 1 time 8967 (0.76%) aligned >1 times 77.69% overall alignment rate Time searching: 00:01:15 Overall time: 00:01:15 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] 37817 / 1950215 = 0.0194 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 20:45:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.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 20:45:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:45:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:45:30: 1000000 INFO @ Sat, 15 Jan 2022 20:45:35: 2000000 INFO @ Sat, 15 Jan 2022 20:45:41: 3000000 INFO @ Sat, 15 Jan 2022 20:45:46: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:45:46: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:45:46: #1 total tags in treatment: 1911185 INFO @ Sat, 15 Jan 2022 20:45:46: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:45:46: #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 20:45:46: #1 tags after filtering in treatment: 1696226 INFO @ Sat, 15 Jan 2022 20:45:46: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 15 Jan 2022 20:45:46: #1 finished! INFO @ Sat, 15 Jan 2022 20:45:46: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:45:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:45:46: #2 number of paired peaks: 252 WARNING @ Sat, 15 Jan 2022 20:45:46: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Sat, 15 Jan 2022 20:45:46: start model_add_line... INFO @ Sat, 15 Jan 2022 20:45:46: start X-correlation... INFO @ Sat, 15 Jan 2022 20:45:46: end of X-cor INFO @ Sat, 15 Jan 2022 20:45:46: #2 finished! INFO @ Sat, 15 Jan 2022 20:45:46: #2 predicted fragment length is 52 bps INFO @ Sat, 15 Jan 2022 20:45:46: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sat, 15 Jan 2022 20:45:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.05_model.r INFO @ Sat, 15 Jan 2022 20:45:46: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:45:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:45:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:45:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:45:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:45:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.05_summits.bed INFO @ Sat, 15 Jan 2022 20:45:51: Done! 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 pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (731 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:45:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.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 20:45:54: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:45:54: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:46:00: 1000000 INFO @ Sat, 15 Jan 2022 20:46:05: 2000000 INFO @ Sat, 15 Jan 2022 20:46:11: 3000000 INFO @ Sat, 15 Jan 2022 20:46:16: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:46:16: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:46:16: #1 total tags in treatment: 1911185 INFO @ Sat, 15 Jan 2022 20:46:16: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:46:16: #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 20:46:16: #1 tags after filtering in treatment: 1696226 INFO @ Sat, 15 Jan 2022 20:46:16: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 15 Jan 2022 20:46:16: #1 finished! INFO @ Sat, 15 Jan 2022 20:46:16: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:46:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:46:16: #2 number of paired peaks: 252 WARNING @ Sat, 15 Jan 2022 20:46:16: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Sat, 15 Jan 2022 20:46:16: start model_add_line... INFO @ Sat, 15 Jan 2022 20:46:16: start X-correlation... INFO @ Sat, 15 Jan 2022 20:46:16: end of X-cor INFO @ Sat, 15 Jan 2022 20:46:16: #2 finished! INFO @ Sat, 15 Jan 2022 20:46:16: #2 predicted fragment length is 52 bps INFO @ Sat, 15 Jan 2022 20:46:16: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sat, 15 Jan 2022 20:46:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.10_model.r INFO @ Sat, 15 Jan 2022 20:46:16: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:46:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:46:20: #3 Call peaks for each chromosome... 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 20:46:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:46:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:46:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.10_summits.bed INFO @ Sat, 15 Jan 2022 20:46:22: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (411 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:46:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.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 20:46:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:46:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:46:30: 1000000 INFO @ Sat, 15 Jan 2022 20:46:37: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:46:43: 3000000 INFO @ Sat, 15 Jan 2022 20:46:48: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:46:48: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:46:48: #1 total tags in treatment: 1911185 INFO @ Sat, 15 Jan 2022 20:46:48: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:46:48: #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 20:46:48: #1 tags after filtering in treatment: 1696226 INFO @ Sat, 15 Jan 2022 20:46:48: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 15 Jan 2022 20:46:48: #1 finished! INFO @ Sat, 15 Jan 2022 20:46:48: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:46:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:46:48: #2 number of paired peaks: 252 WARNING @ Sat, 15 Jan 2022 20:46:48: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Sat, 15 Jan 2022 20:46:48: start model_add_line... INFO @ Sat, 15 Jan 2022 20:46:48: start X-correlation... INFO @ Sat, 15 Jan 2022 20:46:48: end of X-cor INFO @ Sat, 15 Jan 2022 20:46:48: #2 finished! INFO @ Sat, 15 Jan 2022 20:46:48: #2 predicted fragment length is 52 bps INFO @ Sat, 15 Jan 2022 20:46:48: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sat, 15 Jan 2022 20:46:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.20_model.r INFO @ Sat, 15 Jan 2022 20:46:48: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:46:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:46:51: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:46:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:46:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:46:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468526/SRX10468526.20_summits.bed INFO @ Sat, 15 Jan 2022 20:46:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (132 records, 4 fields): 2 millis CompletedMACS2peakCalling