Job ID = 14520645 SRX = SRX7847362 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 31749409 spots for SRR11235544/SRR11235544.sra Written 31749409 spots for SRR11235544/SRR11235544.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: 00:13:18 31749409 reads; of these: 31749409 (100.00%) were paired; of these: 5073024 (15.98%) aligned concordantly 0 times 20936331 (65.94%) aligned concordantly exactly 1 time 5740054 (18.08%) aligned concordantly >1 times ---- 5073024 pairs aligned concordantly 0 times; of these: 87297 (1.72%) aligned discordantly 1 time ---- 4985727 pairs aligned 0 times concordantly or discordantly; of these: 9971454 mates make up the pairs; of these: 8222705 (82.46%) aligned 0 times 1057250 (10.60%) aligned exactly 1 time 691499 (6.93%) aligned >1 times 87.05% overall alignment rate Time searching: 00:13:18 Overall time: 00:13:18 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 16 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] 26101825 / 26724596 = 0.9767 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 19:54:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.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 19:54:50: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:54:50: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:54:55: 1000000 INFO @ Sat, 15 Jan 2022 19:54:59: 2000000 INFO @ Sat, 15 Jan 2022 19:55:03: 3000000 INFO @ Sat, 15 Jan 2022 19:55:04: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 19:55:04: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 19:55:04: #1 total tags in treatment: 646458 INFO @ Sat, 15 Jan 2022 19:55:04: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:55:04: #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 19:55:04: #1 tags after filtering in treatment: 245679 INFO @ Sat, 15 Jan 2022 19:55:04: #1 Redundant rate of treatment: 0.62 INFO @ Sat, 15 Jan 2022 19:55:04: #1 finished! INFO @ Sat, 15 Jan 2022 19:55:04: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:55:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:55:04: #2 number of paired peaks: 720 WARNING @ Sat, 15 Jan 2022 19:55:04: Fewer paired peaks (720) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 720 pairs to build model! INFO @ Sat, 15 Jan 2022 19:55:04: start model_add_line... INFO @ Sat, 15 Jan 2022 19:55:04: start X-correlation... INFO @ Sat, 15 Jan 2022 19:55:04: end of X-cor INFO @ Sat, 15 Jan 2022 19:55:04: #2 finished! INFO @ Sat, 15 Jan 2022 19:55:04: #2 predicted fragment length is 167 bps INFO @ Sat, 15 Jan 2022 19:55:04: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 15 Jan 2022 19:55:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.05_model.r INFO @ Sat, 15 Jan 2022 19:55:04: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:55:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:55:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:55:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:55:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:55:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.05_summits.bed INFO @ Sat, 15 Jan 2022 19:55:06: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (682 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 19:55:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.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 19:55:20: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:55:20: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:55:25: 1000000 INFO @ Sat, 15 Jan 2022 19:55:31: 2000000 INFO @ Sat, 15 Jan 2022 19:55:36: 3000000 INFO @ Sat, 15 Jan 2022 19:55:36: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 19:55:36: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 19:55:36: #1 total tags in treatment: 646458 INFO @ Sat, 15 Jan 2022 19:55:36: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:55:36: #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 19:55:36: #1 tags after filtering in treatment: 245679 INFO @ Sat, 15 Jan 2022 19:55:36: #1 Redundant rate of treatment: 0.62 INFO @ Sat, 15 Jan 2022 19:55:36: #1 finished! INFO @ Sat, 15 Jan 2022 19:55:36: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:55:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:55:36: #2 number of paired peaks: 720 WARNING @ Sat, 15 Jan 2022 19:55:36: Fewer paired peaks (720) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 720 pairs to build model! INFO @ Sat, 15 Jan 2022 19:55:36: start model_add_line... INFO @ Sat, 15 Jan 2022 19:55:37: start X-correlation... INFO @ Sat, 15 Jan 2022 19:55:37: end of X-cor INFO @ Sat, 15 Jan 2022 19:55:37: #2 finished! INFO @ Sat, 15 Jan 2022 19:55:37: #2 predicted fragment length is 167 bps INFO @ Sat, 15 Jan 2022 19:55:37: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 15 Jan 2022 19:55:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.10_model.r INFO @ Sat, 15 Jan 2022 19:55:37: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:55:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:55:38: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:55:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:55:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:55:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.10_summits.bed INFO @ Sat, 15 Jan 2022 19:55:38: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (504 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 19:55:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.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 19:55:50: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:55:50: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:55:54: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:55:59: 2000000 INFO @ Sat, 15 Jan 2022 19:56:03: 3000000 INFO @ Sat, 15 Jan 2022 19:56:03: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 19:56:03: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 19:56:03: #1 total tags in treatment: 646458 INFO @ Sat, 15 Jan 2022 19:56:03: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:56:03: #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 19:56:03: #1 tags after filtering in treatment: 245679 INFO @ Sat, 15 Jan 2022 19:56:03: #1 Redundant rate of treatment: 0.62 INFO @ Sat, 15 Jan 2022 19:56:03: #1 finished! INFO @ Sat, 15 Jan 2022 19:56:03: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:56:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:56:03: #2 number of paired peaks: 720 WARNING @ Sat, 15 Jan 2022 19:56:03: Fewer paired peaks (720) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 720 pairs to build model! INFO @ Sat, 15 Jan 2022 19:56:03: start model_add_line... INFO @ Sat, 15 Jan 2022 19:56:03: start X-correlation... INFO @ Sat, 15 Jan 2022 19:56:03: end of X-cor INFO @ Sat, 15 Jan 2022 19:56:03: #2 finished! INFO @ Sat, 15 Jan 2022 19:56:03: #2 predicted fragment length is 167 bps INFO @ Sat, 15 Jan 2022 19:56:03: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 15 Jan 2022 19:56:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.20_model.r INFO @ Sat, 15 Jan 2022 19:56:03: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:56:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:56:04: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:56:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:56:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:56:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847362/SRX7847362.20_summits.bed INFO @ Sat, 15 Jan 2022 19:56:05: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (320 records, 4 fields): 1 millis CompletedMACS2peakCalling