Job ID = 14520407 SRX = SRX11781133 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5331598 spots for SRR15481076/SRR15481076.sra Written 5331598 spots for SRR15481076/SRR15481076.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: 00:03:17 5331598 reads; of these: 5331598 (100.00%) were paired; of these: 3476228 (65.20%) aligned concordantly 0 times 1697946 (31.85%) aligned concordantly exactly 1 time 157424 (2.95%) aligned concordantly >1 times ---- 3476228 pairs aligned concordantly 0 times; of these: 38058 (1.09%) aligned discordantly 1 time ---- 3438170 pairs aligned 0 times concordantly or discordantly; of these: 6876340 mates make up the pairs; of these: 3833326 (55.75%) aligned 0 times 2723720 (39.61%) aligned exactly 1 time 319294 (4.64%) aligned >1 times 64.05% overall alignment rate Time searching: 00:03:17 Overall time: 00:03:17 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] 271149 / 1892734 = 0.1433 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 19:09:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.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 19:09:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:09:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:09:09: 1000000 INFO @ Sat, 15 Jan 2022 19:09:15: 2000000 INFO @ Sat, 15 Jan 2022 19:09:21: 3000000 INFO @ Sat, 15 Jan 2022 19:09:27: 4000000 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 19:09:33: 5000000 INFO @ Sat, 15 Jan 2022 19:09:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.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 19:09:34: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:09:34: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:09:39: 6000000 INFO @ Sat, 15 Jan 2022 19:09:41: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:09:41: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:09:41: #1 total tags in treatment: 1586969 INFO @ Sat, 15 Jan 2022 19:09:41: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:09:41: #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 19:09:41: #1 tags after filtering in treatment: 1202868 INFO @ Sat, 15 Jan 2022 19:09:41: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 15 Jan 2022 19:09:41: #1 finished! INFO @ Sat, 15 Jan 2022 19:09:41: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:09:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:09:41: 1000000 INFO @ Sat, 15 Jan 2022 19:09:41: #2 number of paired peaks: 178 WARNING @ Sat, 15 Jan 2022 19:09:41: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sat, 15 Jan 2022 19:09:41: start model_add_line... INFO @ Sat, 15 Jan 2022 19:09:41: start X-correlation... INFO @ Sat, 15 Jan 2022 19:09:41: end of X-cor INFO @ Sat, 15 Jan 2022 19:09:41: #2 finished! INFO @ Sat, 15 Jan 2022 19:09:41: #2 predicted fragment length is 248 bps INFO @ Sat, 15 Jan 2022 19:09:41: #2 alternative fragment length(s) may be 1,248,277,587 bps INFO @ Sat, 15 Jan 2022 19:09:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.05_model.r INFO @ Sat, 15 Jan 2022 19:09:41: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:09:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:09:46: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:09:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:09:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:09:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.05_summits.bed INFO @ Sat, 15 Jan 2022 19:09:47: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (23 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:09:48: 2000000 INFO @ Sat, 15 Jan 2022 19:09:55: 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 19:10:02: 4000000 INFO @ Sat, 15 Jan 2022 19:10:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.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 19:10:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:10:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:10:09: 5000000 INFO @ Sat, 15 Jan 2022 19:10:09: 1000000 INFO @ Sat, 15 Jan 2022 19:10:15: 2000000 INFO @ Sat, 15 Jan 2022 19:10:16: 6000000 INFO @ Sat, 15 Jan 2022 19:10:18: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:10:18: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:10:18: #1 total tags in treatment: 1586969 INFO @ Sat, 15 Jan 2022 19:10:18: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:10:18: #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 19:10:18: #1 tags after filtering in treatment: 1202868 INFO @ Sat, 15 Jan 2022 19:10:18: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 15 Jan 2022 19:10:18: #1 finished! INFO @ Sat, 15 Jan 2022 19:10:18: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:10:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:10:18: #2 number of paired peaks: 178 WARNING @ Sat, 15 Jan 2022 19:10:18: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sat, 15 Jan 2022 19:10:18: start model_add_line... INFO @ Sat, 15 Jan 2022 19:10:18: start X-correlation... INFO @ Sat, 15 Jan 2022 19:10:18: end of X-cor INFO @ Sat, 15 Jan 2022 19:10:18: #2 finished! INFO @ Sat, 15 Jan 2022 19:10:18: #2 predicted fragment length is 248 bps INFO @ Sat, 15 Jan 2022 19:10:18: #2 alternative fragment length(s) may be 1,248,277,587 bps INFO @ Sat, 15 Jan 2022 19:10:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.10_model.r INFO @ Sat, 15 Jan 2022 19:10:18: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:10:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:10:20: 3000000 INFO @ Sat, 15 Jan 2022 19:10:23: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:10:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:10:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:10:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.10_summits.bed INFO @ Sat, 15 Jan 2022 19:10:24: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:10:27: 4000000 INFO @ Sat, 15 Jan 2022 19:10:32: 5000000 INFO @ Sat, 15 Jan 2022 19:10:38: 6000000 INFO @ Sat, 15 Jan 2022 19:10:40: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:10:40: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:10:40: #1 total tags in treatment: 1586969 INFO @ Sat, 15 Jan 2022 19:10:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:10:40: #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 19:10:40: #1 tags after filtering in treatment: 1202868 INFO @ Sat, 15 Jan 2022 19:10:40: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 15 Jan 2022 19:10:40: #1 finished! INFO @ Sat, 15 Jan 2022 19:10:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:10:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:10:40: #2 number of paired peaks: 178 WARNING @ Sat, 15 Jan 2022 19:10:40: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sat, 15 Jan 2022 19:10:40: start model_add_line... INFO @ Sat, 15 Jan 2022 19:10:40: start X-correlation... INFO @ Sat, 15 Jan 2022 19:10:40: end of X-cor INFO @ Sat, 15 Jan 2022 19:10:40: #2 finished! INFO @ Sat, 15 Jan 2022 19:10:40: #2 predicted fragment length is 248 bps INFO @ Sat, 15 Jan 2022 19:10:40: #2 alternative fragment length(s) may be 1,248,277,587 bps INFO @ Sat, 15 Jan 2022 19:10:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.20_model.r INFO @ Sat, 15 Jan 2022 19:10:40: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:10:40: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:10:45: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:10:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:10:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:10:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781133/SRX11781133.20_summits.bed INFO @ Sat, 15 Jan 2022 19:10:46: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (5 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。