Job ID = 14522044 SRX = SRX9773811 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1545280 spots for SRR13347752/SRR13347752.sra Written 1545280 spots for SRR13347752/SRR13347752.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: 00:00:43 1545280 reads; of these: 1545280 (100.00%) were paired; of these: 868679 (56.21%) aligned concordantly 0 times 462417 (29.92%) aligned concordantly exactly 1 time 214184 (13.86%) aligned concordantly >1 times ---- 868679 pairs aligned concordantly 0 times; of these: 119311 (13.73%) aligned discordantly 1 time ---- 749368 pairs aligned 0 times concordantly or discordantly; of these: 1498736 mates make up the pairs; of these: 743981 (49.64%) aligned 0 times 483696 (32.27%) aligned exactly 1 time 271059 (18.09%) aligned >1 times 75.93% overall alignment rate Time searching: 00:00:43 Overall time: 00:00:43 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] 77312 / 708135 = 0.1092 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 22:04:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.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 22:04:31: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:04:31: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:04:35: 1000000 INFO @ Sat, 15 Jan 2022 22:04:40: 2000000 INFO @ Sat, 15 Jan 2022 22:04:40: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 22:04:40: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 22:04:40: #1 total tags in treatment: 600897 INFO @ Sat, 15 Jan 2022 22:04:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:04:40: #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 22:04:40: #1 tags after filtering in treatment: 443494 INFO @ Sat, 15 Jan 2022 22:04:40: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 22:04:40: #1 finished! INFO @ Sat, 15 Jan 2022 22:04:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:04:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:04:40: #2 number of paired peaks: 135 WARNING @ Sat, 15 Jan 2022 22:04:40: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Sat, 15 Jan 2022 22:04:40: start model_add_line... INFO @ Sat, 15 Jan 2022 22:04:40: start X-correlation... INFO @ Sat, 15 Jan 2022 22:04:40: end of X-cor INFO @ Sat, 15 Jan 2022 22:04:40: #2 finished! INFO @ Sat, 15 Jan 2022 22:04:40: #2 predicted fragment length is 261 bps INFO @ Sat, 15 Jan 2022 22:04:40: #2 alternative fragment length(s) may be 0,42,117,170,202,261,297,355,469 bps INFO @ Sat, 15 Jan 2022 22:04:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.05_model.r INFO @ Sat, 15 Jan 2022 22:04:40: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:04:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:04:42: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:04:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.05_peaks.xls INFO @ Sat, 15 Jan 2022 22:04:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:04:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.05_summits.bed INFO @ Sat, 15 Jan 2022 22:04:42: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (20 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 22:05:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.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 22:05:01: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:05:01: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:05:05: 1000000 INFO @ Sat, 15 Jan 2022 22:05:09: 2000000 INFO @ Sat, 15 Jan 2022 22:05:10: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 22:05:10: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 22:05:10: #1 total tags in treatment: 600897 INFO @ Sat, 15 Jan 2022 22:05:10: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:05:10: #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 22:05:10: #1 tags after filtering in treatment: 443494 INFO @ Sat, 15 Jan 2022 22:05:10: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 22:05:10: #1 finished! INFO @ Sat, 15 Jan 2022 22:05:10: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:05:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:05:10: #2 number of paired peaks: 135 WARNING @ Sat, 15 Jan 2022 22:05:10: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Sat, 15 Jan 2022 22:05:10: start model_add_line... INFO @ Sat, 15 Jan 2022 22:05:10: start X-correlation... INFO @ Sat, 15 Jan 2022 22:05:10: end of X-cor INFO @ Sat, 15 Jan 2022 22:05:10: #2 finished! INFO @ Sat, 15 Jan 2022 22:05:10: #2 predicted fragment length is 261 bps INFO @ Sat, 15 Jan 2022 22:05:10: #2 alternative fragment length(s) may be 0,42,117,170,202,261,297,355,469 bps INFO @ Sat, 15 Jan 2022 22:05:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.10_model.r INFO @ Sat, 15 Jan 2022 22:05:10: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:05:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:05:12: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:05:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.10_peaks.xls INFO @ Sat, 15 Jan 2022 22:05:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:05:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.10_summits.bed INFO @ Sat, 15 Jan 2022 22:05:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (10 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 22:05:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.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 22:05:31: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:05:31: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:05:35: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:05:40: 2000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 22:05:40: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 22:05:40: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 22:05:40: #1 total tags in treatment: 600897 INFO @ Sat, 15 Jan 2022 22:05:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:05:40: #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 22:05:40: #1 tags after filtering in treatment: 443494 INFO @ Sat, 15 Jan 2022 22:05:40: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 22:05:40: #1 finished! INFO @ Sat, 15 Jan 2022 22:05:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:05:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:05:40: #2 number of paired peaks: 135 WARNING @ Sat, 15 Jan 2022 22:05:40: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Sat, 15 Jan 2022 22:05:40: start model_add_line... INFO @ Sat, 15 Jan 2022 22:05:40: start X-correlation... INFO @ Sat, 15 Jan 2022 22:05:40: end of X-cor INFO @ Sat, 15 Jan 2022 22:05:40: #2 finished! INFO @ Sat, 15 Jan 2022 22:05:40: #2 predicted fragment length is 261 bps INFO @ Sat, 15 Jan 2022 22:05:40: #2 alternative fragment length(s) may be 0,42,117,170,202,261,297,355,469 bps INFO @ Sat, 15 Jan 2022 22:05:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.20_model.r INFO @ Sat, 15 Jan 2022 22:05:40: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:05:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:05:42: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:05:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.20_peaks.xls INFO @ Sat, 15 Jan 2022 22:05:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:05:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9773811/SRX9773811.20_summits.bed INFO @ Sat, 15 Jan 2022 22:05:42: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 1 millis CompletedMACS2peakCalling