Job ID = 14519923 SRX = SRX8829421 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15357999 spots for SRR12329201/SRR12329201.sra Written 15357999 spots for SRR12329201/SRR12329201.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: 00:12:23 15357999 reads; of these: 15357999 (100.00%) were paired; of these: 3675297 (23.93%) aligned concordantly 0 times 7824169 (50.95%) aligned concordantly exactly 1 time 3858533 (25.12%) aligned concordantly >1 times ---- 3675297 pairs aligned concordantly 0 times; of these: 110544 (3.01%) aligned discordantly 1 time ---- 3564753 pairs aligned 0 times concordantly or discordantly; of these: 7129506 mates make up the pairs; of these: 6239290 (87.51%) aligned 0 times 505983 (7.10%) aligned exactly 1 time 384233 (5.39%) aligned >1 times 79.69% overall alignment rate Time searching: 00:12:24 Overall time: 00:12:24 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 12 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] 10726733 / 11767590 = 0.9115 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 18:21:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.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 18:21:32: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:21:32: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:21:40: 1000000 INFO @ Sat, 15 Jan 2022 18:21:48: 2000000 INFO @ Sat, 15 Jan 2022 18:21:56: 3000000 INFO @ Sat, 15 Jan 2022 18:21:56: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:21:56: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:21:56: #1 total tags in treatment: 1032859 INFO @ Sat, 15 Jan 2022 18:21:56: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:21:56: #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 18:21:56: #1 tags after filtering in treatment: 691634 INFO @ Sat, 15 Jan 2022 18:21:56: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 15 Jan 2022 18:21:56: #1 finished! INFO @ Sat, 15 Jan 2022 18:21:56: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:21:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:21:56: #2 number of paired peaks: 319 WARNING @ Sat, 15 Jan 2022 18:21:56: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Sat, 15 Jan 2022 18:21:56: start model_add_line... INFO @ Sat, 15 Jan 2022 18:21:56: start X-correlation... INFO @ Sat, 15 Jan 2022 18:21:56: end of X-cor INFO @ Sat, 15 Jan 2022 18:21:56: #2 finished! INFO @ Sat, 15 Jan 2022 18:21:56: #2 predicted fragment length is 123 bps INFO @ Sat, 15 Jan 2022 18:21:56: #2 alternative fragment length(s) may be 1,60,90,112,123,141,162,229,456,496,526,584 bps INFO @ Sat, 15 Jan 2022 18:21:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.05_model.r INFO @ Sat, 15 Jan 2022 18:21:56: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:21:56: #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 18:21:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:22:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.05_peaks.xls INFO @ Sat, 15 Jan 2022 18:22:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:22:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.05_summits.bed INFO @ Sat, 15 Jan 2022 18:22:00: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (207 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 18:22:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.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 18:22:01: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:22:01: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:22:09: 1000000 INFO @ Sat, 15 Jan 2022 18:22:16: 2000000 INFO @ Sat, 15 Jan 2022 18:22:24: 3000000 INFO @ Sat, 15 Jan 2022 18:22:24: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:22:24: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:22:24: #1 total tags in treatment: 1032859 INFO @ Sat, 15 Jan 2022 18:22:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:22:24: #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 18:22:24: #1 tags after filtering in treatment: 691634 INFO @ Sat, 15 Jan 2022 18:22:24: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 15 Jan 2022 18:22:24: #1 finished! INFO @ Sat, 15 Jan 2022 18:22:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:22:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:22:24: #2 number of paired peaks: 319 WARNING @ Sat, 15 Jan 2022 18:22:24: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Sat, 15 Jan 2022 18:22:24: start model_add_line... INFO @ Sat, 15 Jan 2022 18:22:24: start X-correlation... INFO @ Sat, 15 Jan 2022 18:22:24: end of X-cor INFO @ Sat, 15 Jan 2022 18:22:24: #2 finished! INFO @ Sat, 15 Jan 2022 18:22:24: #2 predicted fragment length is 123 bps INFO @ Sat, 15 Jan 2022 18:22:24: #2 alternative fragment length(s) may be 1,60,90,112,123,141,162,229,456,496,526,584 bps INFO @ Sat, 15 Jan 2022 18:22:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.10_model.r INFO @ Sat, 15 Jan 2022 18:22:24: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:22:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:22:27: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:22:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.10_peaks.xls INFO @ Sat, 15 Jan 2022 18:22:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:22:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.10_summits.bed INFO @ Sat, 15 Jan 2022 18:22:28: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (35 records, 4 fields): 3 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 18:22:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.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 18:22:31: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:22:31: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:22:40: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 18:22:49: 2000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 18:22:57: 3000000 INFO @ Sat, 15 Jan 2022 18:22:57: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:22:57: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:22:57: #1 total tags in treatment: 1032859 INFO @ Sat, 15 Jan 2022 18:22:57: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:22:57: #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 18:22:57: #1 tags after filtering in treatment: 691634 INFO @ Sat, 15 Jan 2022 18:22:57: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 15 Jan 2022 18:22:57: #1 finished! INFO @ Sat, 15 Jan 2022 18:22:57: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:22:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:22:57: #2 number of paired peaks: 319 WARNING @ Sat, 15 Jan 2022 18:22:57: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Sat, 15 Jan 2022 18:22:57: start model_add_line... INFO @ Sat, 15 Jan 2022 18:22:57: start X-correlation... INFO @ Sat, 15 Jan 2022 18:22:57: end of X-cor INFO @ Sat, 15 Jan 2022 18:22:57: #2 finished! INFO @ Sat, 15 Jan 2022 18:22:57: #2 predicted fragment length is 123 bps INFO @ Sat, 15 Jan 2022 18:22:57: #2 alternative fragment length(s) may be 1,60,90,112,123,141,162,229,456,496,526,584 bps INFO @ Sat, 15 Jan 2022 18:22:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.20_model.r INFO @ Sat, 15 Jan 2022 18:22:57: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:22:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:23:00: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:23:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.20_peaks.xls INFO @ Sat, 15 Jan 2022 18:23:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:23:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8829421/SRX8829421.20_summits.bed INFO @ Sat, 15 Jan 2022 18:23:01: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (8 records, 4 fields): 12 millis CompletedMACS2peakCalling