Job ID = 14521487 SRX = SRX10468487 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1966696 spots for SRR14094798/SRR14094798.sra Written 1966696 spots for SRR14094798/SRR14094798.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: 00:00:54 1966696 reads; of these: 1966696 (100.00%) were paired; of these: 628831 (31.97%) aligned concordantly 0 times 955836 (48.60%) aligned concordantly exactly 1 time 382029 (19.42%) aligned concordantly >1 times ---- 628831 pairs aligned concordantly 0 times; of these: 37042 (5.89%) aligned discordantly 1 time ---- 591789 pairs aligned 0 times concordantly or discordantly; of these: 1183578 mates make up the pairs; of these: 1119927 (94.62%) aligned 0 times 24337 (2.06%) aligned exactly 1 time 39314 (3.32%) aligned >1 times 71.53% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 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] 48144 / 1371382 = 0.0351 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 21:05:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.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 21:05:53: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:05:53: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:05:57: 1000000 INFO @ Sat, 15 Jan 2022 21:06:02: 2000000 INFO @ Sat, 15 Jan 2022 21:06:05: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 21:06:05: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 21:06:05: #1 total tags in treatment: 1290314 INFO @ Sat, 15 Jan 2022 21:06:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:06:05: #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 21:06:05: #1 tags after filtering in treatment: 987354 INFO @ Sat, 15 Jan 2022 21:06:05: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 21:06:05: #1 finished! INFO @ Sat, 15 Jan 2022 21:06:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:06:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:06:05: #2 number of paired peaks: 158 WARNING @ Sat, 15 Jan 2022 21:06:05: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 15 Jan 2022 21:06:05: start model_add_line... INFO @ Sat, 15 Jan 2022 21:06:05: start X-correlation... INFO @ Sat, 15 Jan 2022 21:06:05: end of X-cor INFO @ Sat, 15 Jan 2022 21:06:05: #2 finished! INFO @ Sat, 15 Jan 2022 21:06:05: #2 predicted fragment length is 117 bps INFO @ Sat, 15 Jan 2022 21:06:05: #2 alternative fragment length(s) may be 4,117 bps INFO @ Sat, 15 Jan 2022 21:06:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.05_model.r INFO @ Sat, 15 Jan 2022 21:06:05: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:06:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:06:07: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:06:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:06:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:06:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.05_summits.bed INFO @ Sat, 15 Jan 2022 21:06:08: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (618 records, 4 fields): 3 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 21:06:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.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 21:06:23: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:06:23: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:06:27: 1000000 INFO @ Sat, 15 Jan 2022 21:06:31: 2000000 INFO @ Sat, 15 Jan 2022 21:06:35: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 21:06:35: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 21:06:35: #1 total tags in treatment: 1290314 INFO @ Sat, 15 Jan 2022 21:06:35: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:06:35: #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 21:06:35: #1 tags after filtering in treatment: 987354 INFO @ Sat, 15 Jan 2022 21:06:35: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 21:06:35: #1 finished! INFO @ Sat, 15 Jan 2022 21:06:35: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:06:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:06:35: #2 number of paired peaks: 158 WARNING @ Sat, 15 Jan 2022 21:06:35: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 15 Jan 2022 21:06:35: start model_add_line... INFO @ Sat, 15 Jan 2022 21:06:35: start X-correlation... INFO @ Sat, 15 Jan 2022 21:06:35: end of X-cor INFO @ Sat, 15 Jan 2022 21:06:35: #2 finished! INFO @ Sat, 15 Jan 2022 21:06:35: #2 predicted fragment length is 117 bps INFO @ Sat, 15 Jan 2022 21:06:35: #2 alternative fragment length(s) may be 4,117 bps INFO @ Sat, 15 Jan 2022 21:06:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.10_model.r INFO @ Sat, 15 Jan 2022 21:06:35: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:06:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:06:37: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:06:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:06:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:06:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.10_summits.bed INFO @ Sat, 15 Jan 2022 21:06:38: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (360 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 21:06:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.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 21:06:53: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:06:53: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:06:57: 1000000 INFO @ Sat, 15 Jan 2022 21:07:02: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:07:05: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 21:07:05: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 21:07:05: #1 total tags in treatment: 1290314 INFO @ Sat, 15 Jan 2022 21:07:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:07:05: #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 21:07:05: #1 tags after filtering in treatment: 987354 INFO @ Sat, 15 Jan 2022 21:07:05: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 21:07:05: #1 finished! INFO @ Sat, 15 Jan 2022 21:07:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:07:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:07:05: #2 number of paired peaks: 158 WARNING @ Sat, 15 Jan 2022 21:07:05: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 15 Jan 2022 21:07:05: start model_add_line... INFO @ Sat, 15 Jan 2022 21:07:05: start X-correlation... INFO @ Sat, 15 Jan 2022 21:07:05: end of X-cor INFO @ Sat, 15 Jan 2022 21:07:05: #2 finished! INFO @ Sat, 15 Jan 2022 21:07:05: #2 predicted fragment length is 117 bps INFO @ Sat, 15 Jan 2022 21:07:05: #2 alternative fragment length(s) may be 4,117 bps INFO @ Sat, 15 Jan 2022 21:07:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.20_model.r INFO @ Sat, 15 Jan 2022 21:07:05: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:07:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:07:07: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:07:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.20_peaks.xls BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:07:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:07:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468487/SRX10468487.20_summits.bed INFO @ Sat, 15 Jan 2022 21:07:09: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (121 records, 4 fields): 505 millis CompletedMACS2peakCalling