Job ID = 14520386 SRX = SRX11781121 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:01:21 prefetch.2.10.7: 1) Downloading 'SRR15481064'... 2022-01-15T10:01:21 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:01:34 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:01:34 prefetch.2.10.7: 'SRR15481064' is valid 2022-01-15T10:01:34 prefetch.2.10.7: 1) 'SRR15481064' was downloaded successfully 2022-01-15T10:01:34 prefetch.2.10.7: 'SRR15481064' has 0 unresolved dependencies Read 5765977 spots for SRR15481064/SRR15481064.sra Written 5765977 spots for SRR15481064/SRR15481064.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: 00:02:27 5765977 reads; of these: 5765977 (100.00%) were paired; of these: 3922147 (68.02%) aligned concordantly 0 times 1725341 (29.92%) aligned concordantly exactly 1 time 118489 (2.05%) aligned concordantly >1 times ---- 3922147 pairs aligned concordantly 0 times; of these: 49035 (1.25%) aligned discordantly 1 time ---- 3873112 pairs aligned 0 times concordantly or discordantly; of these: 7746224 mates make up the pairs; of these: 4431039 (57.20%) aligned 0 times 3002095 (38.76%) aligned exactly 1 time 313090 (4.04%) aligned >1 times 61.58% overall alignment rate Time searching: 00:02:27 Overall time: 00:02:27 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] 347382 / 1892038 = 0.1836 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 19:06:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.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 19:06:16: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:06:16: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:06:20: 1000000 INFO @ Sat, 15 Jan 2022 19:06:24: 2000000 INFO @ Sat, 15 Jan 2022 19:06:28: 3000000 INFO @ Sat, 15 Jan 2022 19:06:32: 4000000 INFO @ Sat, 15 Jan 2022 19:06:36: 5000000 INFO @ Sat, 15 Jan 2022 19:06:40: 6000000 INFO @ Sat, 15 Jan 2022 19:06:42: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:06:42: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:06:42: #1 total tags in treatment: 1501135 INFO @ Sat, 15 Jan 2022 19:06:42: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:06:42: #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 19:06:42: #1 tags after filtering in treatment: 909413 INFO @ Sat, 15 Jan 2022 19:06:42: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 15 Jan 2022 19:06:42: #1 finished! INFO @ Sat, 15 Jan 2022 19:06:42: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:06:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:06:42: #2 number of paired peaks: 163 WARNING @ Sat, 15 Jan 2022 19:06:42: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Sat, 15 Jan 2022 19:06:42: start model_add_line... INFO @ Sat, 15 Jan 2022 19:06:42: start X-correlation... INFO @ Sat, 15 Jan 2022 19:06:42: end of X-cor INFO @ Sat, 15 Jan 2022 19:06:42: #2 finished! INFO @ Sat, 15 Jan 2022 19:06:42: #2 predicted fragment length is 228 bps INFO @ Sat, 15 Jan 2022 19:06:42: #2 alternative fragment length(s) may be 45,183,214,228,238,242,252,256,272,333 bps INFO @ Sat, 15 Jan 2022 19:06:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.05_model.r INFO @ Sat, 15 Jan 2022 19:06:42: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:06:42: #3 Pre-compute pvalue-qvalue table... 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 19:06:44: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:06:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:06:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:06:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.05_summits.bed INFO @ Sat, 15 Jan 2022 19:06:45: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (20 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:06:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.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 19:06:46: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:06:46: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:06:50: 1000000 INFO @ Sat, 15 Jan 2022 19:06:54: 2000000 INFO @ Sat, 15 Jan 2022 19:06:58: 3000000 INFO @ Sat, 15 Jan 2022 19:07:02: 4000000 INFO @ Sat, 15 Jan 2022 19:07:06: 5000000 INFO @ Sat, 15 Jan 2022 19:07:10: 6000000 INFO @ Sat, 15 Jan 2022 19:07:12: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:07:12: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:07:12: #1 total tags in treatment: 1501135 INFO @ Sat, 15 Jan 2022 19:07:12: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:07:12: #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 19:07:12: #1 tags after filtering in treatment: 909413 INFO @ Sat, 15 Jan 2022 19:07:12: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 15 Jan 2022 19:07:12: #1 finished! INFO @ Sat, 15 Jan 2022 19:07:12: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:07:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:07:12: #2 number of paired peaks: 163 WARNING @ Sat, 15 Jan 2022 19:07:12: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Sat, 15 Jan 2022 19:07:12: start model_add_line... INFO @ Sat, 15 Jan 2022 19:07:12: start X-correlation... INFO @ Sat, 15 Jan 2022 19:07:12: end of X-cor INFO @ Sat, 15 Jan 2022 19:07:12: #2 finished! INFO @ Sat, 15 Jan 2022 19:07:12: #2 predicted fragment length is 228 bps INFO @ Sat, 15 Jan 2022 19:07:12: #2 alternative fragment length(s) may be 45,183,214,228,238,242,252,256,272,333 bps INFO @ Sat, 15 Jan 2022 19:07:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.10_model.r INFO @ Sat, 15 Jan 2022 19:07:12: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:07:12: #3 Pre-compute pvalue-qvalue table... 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 19:07:14: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:07:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:07:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:07:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.10_summits.bed INFO @ Sat, 15 Jan 2022 19:07:15: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (16 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:07:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.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 19:07:16: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:07:16: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:07:20: 1000000 INFO @ Sat, 15 Jan 2022 19:07:24: 2000000 INFO @ Sat, 15 Jan 2022 19:07:28: 3000000 INFO @ Sat, 15 Jan 2022 19:07:32: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:07:37: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:07:41: 6000000 INFO @ Sat, 15 Jan 2022 19:07:43: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:07:43: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:07:43: #1 total tags in treatment: 1501135 INFO @ Sat, 15 Jan 2022 19:07:43: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:07:43: #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 19:07:43: #1 tags after filtering in treatment: 909413 INFO @ Sat, 15 Jan 2022 19:07:43: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 15 Jan 2022 19:07:43: #1 finished! INFO @ Sat, 15 Jan 2022 19:07:43: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:07:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:07:43: #2 number of paired peaks: 163 WARNING @ Sat, 15 Jan 2022 19:07:43: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Sat, 15 Jan 2022 19:07:43: start model_add_line... INFO @ Sat, 15 Jan 2022 19:07:43: start X-correlation... INFO @ Sat, 15 Jan 2022 19:07:43: end of X-cor INFO @ Sat, 15 Jan 2022 19:07:43: #2 finished! INFO @ Sat, 15 Jan 2022 19:07:43: #2 predicted fragment length is 228 bps INFO @ Sat, 15 Jan 2022 19:07:43: #2 alternative fragment length(s) may be 45,183,214,228,238,242,252,256,272,333 bps INFO @ Sat, 15 Jan 2022 19:07:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.20_model.r INFO @ Sat, 15 Jan 2022 19:07:43: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:07:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:07:45: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:07:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:07:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:07:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781121/SRX11781121.20_summits.bed INFO @ Sat, 15 Jan 2022 19:07:46: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling