Job ID = 14520738 SRX = SRX8245500 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12663921 spots for SRR11684711/SRR11684711.sra Written 12663921 spots for SRR11684711/SRR11684711.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: 00:07:13 12663921 reads; of these: 12663921 (100.00%) were paired; of these: 8964420 (70.79%) aligned concordantly 0 times 2989709 (23.61%) aligned concordantly exactly 1 time 709792 (5.60%) aligned concordantly >1 times ---- 8964420 pairs aligned concordantly 0 times; of these: 40729 (0.45%) aligned discordantly 1 time ---- 8923691 pairs aligned 0 times concordantly or discordantly; of these: 17847382 mates make up the pairs; of these: 14279669 (80.01%) aligned 0 times 2866616 (16.06%) aligned exactly 1 time 701097 (3.93%) aligned >1 times 43.62% overall alignment rate Time searching: 00:07:13 Overall time: 00:07:13 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] 530943 / 3738080 = 0.1420 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 19:55:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.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 19:55:58: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:55:58: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:56:09: 1000000 INFO @ Sat, 15 Jan 2022 19:56:18: 2000000 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 19:56:28: 3000000 INFO @ Sat, 15 Jan 2022 19:56:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.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 19:56:28: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:56:28: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:56:37: 1000000 INFO @ Sat, 15 Jan 2022 19:56:38: 4000000 INFO @ Sat, 15 Jan 2022 19:56:44: 2000000 INFO @ Sat, 15 Jan 2022 19:56:47: 5000000 INFO @ Sat, 15 Jan 2022 19:56:52: 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 19:56:57: 6000000 INFO @ Sat, 15 Jan 2022 19:56:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.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 19:56:58: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:56:58: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:57:00: 4000000 INFO @ Sat, 15 Jan 2022 19:57:07: 7000000 INFO @ Sat, 15 Jan 2022 19:57:08: 1000000 INFO @ Sat, 15 Jan 2022 19:57:08: 5000000 INFO @ Sat, 15 Jan 2022 19:57:16: 6000000 INFO @ Sat, 15 Jan 2022 19:57:17: 8000000 INFO @ Sat, 15 Jan 2022 19:57:18: 2000000 INFO @ Sat, 15 Jan 2022 19:57:24: 7000000 INFO @ Sat, 15 Jan 2022 19:57:27: 9000000 INFO @ Sat, 15 Jan 2022 19:57:28: 3000000 INFO @ Sat, 15 Jan 2022 19:57:32: 8000000 INFO @ Sat, 15 Jan 2022 19:57:36: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:57:36: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:57:36: #1 total tags in treatment: 3171626 INFO @ Sat, 15 Jan 2022 19:57:36: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:57:36: #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 19:57:36: #1 tags after filtering in treatment: 2131649 INFO @ Sat, 15 Jan 2022 19:57:36: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 15 Jan 2022 19:57:36: #1 finished! INFO @ Sat, 15 Jan 2022 19:57:36: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:57:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:57:36: #2 number of paired peaks: 150 WARNING @ Sat, 15 Jan 2022 19:57:36: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Sat, 15 Jan 2022 19:57:36: start model_add_line... INFO @ Sat, 15 Jan 2022 19:57:36: start X-correlation... INFO @ Sat, 15 Jan 2022 19:57:36: end of X-cor INFO @ Sat, 15 Jan 2022 19:57:36: #2 finished! INFO @ Sat, 15 Jan 2022 19:57:36: #2 predicted fragment length is 233 bps INFO @ Sat, 15 Jan 2022 19:57:36: #2 alternative fragment length(s) may be 0,188,204,233,262 bps INFO @ Sat, 15 Jan 2022 19:57:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.05_model.r INFO @ Sat, 15 Jan 2022 19:57:36: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:57:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:57:37: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:57:40: 9000000 INFO @ Sat, 15 Jan 2022 19:57:42: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:57:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:57:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:57:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.05_summits.bed INFO @ Sat, 15 Jan 2022 19:57:44: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (45 records, 4 fields): 75 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:57:47: 5000000 INFO @ Sat, 15 Jan 2022 19:57:48: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:57:48: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:57:48: #1 total tags in treatment: 3171626 INFO @ Sat, 15 Jan 2022 19:57:48: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:57:48: #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 19:57:48: #1 tags after filtering in treatment: 2131649 INFO @ Sat, 15 Jan 2022 19:57:48: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 15 Jan 2022 19:57:48: #1 finished! INFO @ Sat, 15 Jan 2022 19:57:48: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:57:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:57:48: #2 number of paired peaks: 150 WARNING @ Sat, 15 Jan 2022 19:57:48: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Sat, 15 Jan 2022 19:57:48: start model_add_line... INFO @ Sat, 15 Jan 2022 19:57:48: start X-correlation... INFO @ Sat, 15 Jan 2022 19:57:48: end of X-cor INFO @ Sat, 15 Jan 2022 19:57:48: #2 finished! INFO @ Sat, 15 Jan 2022 19:57:48: #2 predicted fragment length is 233 bps INFO @ Sat, 15 Jan 2022 19:57:48: #2 alternative fragment length(s) may be 0,188,204,233,262 bps INFO @ Sat, 15 Jan 2022 19:57:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.10_model.r INFO @ Sat, 15 Jan 2022 19:57:48: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:57:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:57:54: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:57:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:57:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:57:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.10_summits.bed INFO @ Sat, 15 Jan 2022 19:57:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (18 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:57:57: 6000000 INFO @ Sat, 15 Jan 2022 19:58:07: 7000000 INFO @ Sat, 15 Jan 2022 19:58:16: 8000000 INFO @ Sat, 15 Jan 2022 19:58:26: 9000000 INFO @ Sat, 15 Jan 2022 19:58:36: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:58:36: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:58:36: #1 total tags in treatment: 3171626 INFO @ Sat, 15 Jan 2022 19:58:36: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:58:36: #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 19:58:36: #1 tags after filtering in treatment: 2131649 INFO @ Sat, 15 Jan 2022 19:58:36: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 15 Jan 2022 19:58:36: #1 finished! INFO @ Sat, 15 Jan 2022 19:58:36: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:58:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:58:36: #2 number of paired peaks: 150 WARNING @ Sat, 15 Jan 2022 19:58:36: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Sat, 15 Jan 2022 19:58:36: start model_add_line... INFO @ Sat, 15 Jan 2022 19:58:36: start X-correlation... INFO @ Sat, 15 Jan 2022 19:58:36: end of X-cor INFO @ Sat, 15 Jan 2022 19:58:36: #2 finished! INFO @ Sat, 15 Jan 2022 19:58:36: #2 predicted fragment length is 233 bps INFO @ Sat, 15 Jan 2022 19:58:36: #2 alternative fragment length(s) may be 0,188,204,233,262 bps INFO @ Sat, 15 Jan 2022 19:58:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.20_model.r INFO @ Sat, 15 Jan 2022 19:58:36: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:58:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:58:42: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:58:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:58:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:58:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245500/SRX8245500.20_summits.bed INFO @ Sat, 15 Jan 2022 19:58:44: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (10 records, 4 fields): 1 millis CompletedMACS2peakCalling