Job ID = 14521957 SRX = SRX7637536 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2225858 spots for SRR10972016/SRR10972016.sra Written 2225858 spots for SRR10972016/SRR10972016.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: 00:02:21 2225858 reads; of these: 2225858 (100.00%) were paired; of these: 91245 (4.10%) aligned concordantly 0 times 1910954 (85.85%) aligned concordantly exactly 1 time 223659 (10.05%) aligned concordantly >1 times ---- 91245 pairs aligned concordantly 0 times; of these: 2346 (2.57%) aligned discordantly 1 time ---- 88899 pairs aligned 0 times concordantly or discordantly; of these: 177798 mates make up the pairs; of these: 154825 (87.08%) aligned 0 times 18807 (10.58%) aligned exactly 1 time 4166 (2.34%) aligned >1 times 96.52% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 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] 94688 / 2135828 = 0.0443 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 21:57:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.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 21:57:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:57:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:57:57: 1000000 INFO @ Sat, 15 Jan 2022 21:58:06: 2000000 INFO @ Sat, 15 Jan 2022 21:58:14: 3000000 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 21:58:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.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 21:58:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:58:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:58:23: 4000000 INFO @ Sat, 15 Jan 2022 21:58:24: #1 tag size is determined as 74 bps INFO @ Sat, 15 Jan 2022 21:58:24: #1 tag size = 74 INFO @ Sat, 15 Jan 2022 21:58:24: #1 total tags in treatment: 2039962 INFO @ Sat, 15 Jan 2022 21:58:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:58:24: #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 21:58:24: #1 tags after filtering in treatment: 1727907 INFO @ Sat, 15 Jan 2022 21:58:24: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 15 Jan 2022 21:58:24: #1 finished! INFO @ Sat, 15 Jan 2022 21:58:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:58:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:58:24: #2 number of paired peaks: 147 WARNING @ Sat, 15 Jan 2022 21:58:24: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Sat, 15 Jan 2022 21:58:24: start model_add_line... INFO @ Sat, 15 Jan 2022 21:58:24: start X-correlation... INFO @ Sat, 15 Jan 2022 21:58:24: end of X-cor INFO @ Sat, 15 Jan 2022 21:58:24: #2 finished! INFO @ Sat, 15 Jan 2022 21:58:24: #2 predicted fragment length is 254 bps INFO @ Sat, 15 Jan 2022 21:58:24: #2 alternative fragment length(s) may be 2,254,277 bps INFO @ Sat, 15 Jan 2022 21:58:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.05_model.r INFO @ Sat, 15 Jan 2022 21:58:24: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:58:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:58:28: 1000000 INFO @ Sat, 15 Jan 2022 21:58:30: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:58:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:58:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:58:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.05_summits.bed INFO @ Sat, 15 Jan 2022 21:58:32: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:58:37: 2000000 INFO @ Sat, 15 Jan 2022 21:58:45: 3000000 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 21:58:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.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 21:58:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:58:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:58:54: 4000000 INFO @ Sat, 15 Jan 2022 21:58:55: #1 tag size is determined as 74 bps INFO @ Sat, 15 Jan 2022 21:58:55: #1 tag size = 74 INFO @ Sat, 15 Jan 2022 21:58:55: #1 total tags in treatment: 2039962 INFO @ Sat, 15 Jan 2022 21:58:55: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:58:55: #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 21:58:55: #1 tags after filtering in treatment: 1727907 INFO @ Sat, 15 Jan 2022 21:58:55: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 15 Jan 2022 21:58:55: #1 finished! INFO @ Sat, 15 Jan 2022 21:58:55: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:58:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:58:55: #2 number of paired peaks: 147 WARNING @ Sat, 15 Jan 2022 21:58:55: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Sat, 15 Jan 2022 21:58:55: start model_add_line... INFO @ Sat, 15 Jan 2022 21:58:55: start X-correlation... INFO @ Sat, 15 Jan 2022 21:58:55: end of X-cor INFO @ Sat, 15 Jan 2022 21:58:55: #2 finished! INFO @ Sat, 15 Jan 2022 21:58:55: #2 predicted fragment length is 254 bps INFO @ Sat, 15 Jan 2022 21:58:55: #2 alternative fragment length(s) may be 2,254,277 bps INFO @ Sat, 15 Jan 2022 21:58:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.10_model.r INFO @ Sat, 15 Jan 2022 21:58:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:58:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:58:58: 1000000 INFO @ Sat, 15 Jan 2022 21:59:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:59:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:59:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:59:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.10_summits.bed INFO @ Sat, 15 Jan 2022 21:59:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (28 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:59:07: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:59:16: 3000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:59:24: 4000000 INFO @ Sat, 15 Jan 2022 21:59:25: #1 tag size is determined as 74 bps INFO @ Sat, 15 Jan 2022 21:59:25: #1 tag size = 74 INFO @ Sat, 15 Jan 2022 21:59:25: #1 total tags in treatment: 2039962 INFO @ Sat, 15 Jan 2022 21:59:25: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:59:25: #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 21:59:25: #1 tags after filtering in treatment: 1727907 INFO @ Sat, 15 Jan 2022 21:59:25: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 15 Jan 2022 21:59:25: #1 finished! INFO @ Sat, 15 Jan 2022 21:59:25: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:59:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:59:26: #2 number of paired peaks: 147 WARNING @ Sat, 15 Jan 2022 21:59:26: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Sat, 15 Jan 2022 21:59:26: start model_add_line... INFO @ Sat, 15 Jan 2022 21:59:26: start X-correlation... INFO @ Sat, 15 Jan 2022 21:59:26: end of X-cor INFO @ Sat, 15 Jan 2022 21:59:26: #2 finished! INFO @ Sat, 15 Jan 2022 21:59:26: #2 predicted fragment length is 254 bps INFO @ Sat, 15 Jan 2022 21:59:26: #2 alternative fragment length(s) may be 2,254,277 bps INFO @ Sat, 15 Jan 2022 21:59:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.20_model.r INFO @ Sat, 15 Jan 2022 21:59:26: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:59:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:59:32: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:59:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:59:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:59:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7637536/SRX7637536.20_summits.bed INFO @ Sat, 15 Jan 2022 21:59:34: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 2 millis CompletedMACS2peakCalling