Job ID = 14520674 SRX = SRX7847373 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 34090304 spots for SRR11235555/SRR11235555.sra Written 34090304 spots for SRR11235555/SRR11235555.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: 00:15:12 34090304 reads; of these: 34090304 (100.00%) were paired; of these: 5893492 (17.29%) aligned concordantly 0 times 22760941 (66.77%) aligned concordantly exactly 1 time 5435871 (15.95%) aligned concordantly >1 times ---- 5893492 pairs aligned concordantly 0 times; of these: 85289 (1.45%) aligned discordantly 1 time ---- 5808203 pairs aligned 0 times concordantly or discordantly; of these: 11616406 mates make up the pairs; of these: 9570925 (82.39%) aligned 0 times 1224345 (10.54%) aligned exactly 1 time 821136 (7.07%) aligned >1 times 85.96% overall alignment rate Time searching: 00:15:12 Overall time: 00:15:12 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] 27931984 / 28183863 = 0.9911 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 20:00:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.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 20:00:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:00:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:00:53: 1000000 INFO @ Sat, 15 Jan 2022 20:00:58: 2000000 INFO @ Sat, 15 Jan 2022 20:01:01: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 20:01:01: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 20:01:01: #1 total tags in treatment: 342140 INFO @ Sat, 15 Jan 2022 20:01:01: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:01:01: #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 20:01:01: #1 tags after filtering in treatment: 128834 INFO @ Sat, 15 Jan 2022 20:01:01: #1 Redundant rate of treatment: 0.62 INFO @ Sat, 15 Jan 2022 20:01:01: #1 finished! INFO @ Sat, 15 Jan 2022 20:01:01: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:01:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:01:01: #2 number of paired peaks: 563 WARNING @ Sat, 15 Jan 2022 20:01:01: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Sat, 15 Jan 2022 20:01:01: start model_add_line... INFO @ Sat, 15 Jan 2022 20:01:01: start X-correlation... INFO @ Sat, 15 Jan 2022 20:01:01: end of X-cor INFO @ Sat, 15 Jan 2022 20:01:01: #2 finished! INFO @ Sat, 15 Jan 2022 20:01:01: #2 predicted fragment length is 167 bps INFO @ Sat, 15 Jan 2022 20:01:01: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 15 Jan 2022 20:01:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.05_model.r INFO @ Sat, 15 Jan 2022 20:01:01: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:01:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:01:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:01:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:01:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:01:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.05_summits.bed INFO @ Sat, 15 Jan 2022 20:01:02: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (492 records, 4 fields): 2 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 20:01:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.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 20:01:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:01:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:01:23: 1000000 INFO @ Sat, 15 Jan 2022 20:01:27: 2000000 INFO @ Sat, 15 Jan 2022 20:01:30: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 20:01:30: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 20:01:30: #1 total tags in treatment: 342140 INFO @ Sat, 15 Jan 2022 20:01:30: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:01:30: #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 20:01:30: #1 tags after filtering in treatment: 128834 INFO @ Sat, 15 Jan 2022 20:01:30: #1 Redundant rate of treatment: 0.62 INFO @ Sat, 15 Jan 2022 20:01:30: #1 finished! INFO @ Sat, 15 Jan 2022 20:01:30: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:01:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:01:30: #2 number of paired peaks: 563 WARNING @ Sat, 15 Jan 2022 20:01:30: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Sat, 15 Jan 2022 20:01:30: start model_add_line... INFO @ Sat, 15 Jan 2022 20:01:30: start X-correlation... INFO @ Sat, 15 Jan 2022 20:01:30: end of X-cor INFO @ Sat, 15 Jan 2022 20:01:30: #2 finished! INFO @ Sat, 15 Jan 2022 20:01:30: #2 predicted fragment length is 167 bps INFO @ Sat, 15 Jan 2022 20:01:30: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 15 Jan 2022 20:01:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.10_model.r INFO @ Sat, 15 Jan 2022 20:01:30: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:01:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:01:31: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:01:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:01:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:01:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.10_summits.bed INFO @ Sat, 15 Jan 2022 20:01:31: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (336 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 20:01:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.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 20:01:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:01:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:01:53: 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 20:01:57: 2000000 INFO @ Sat, 15 Jan 2022 20:02:00: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 20:02:00: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 20:02:00: #1 total tags in treatment: 342140 INFO @ Sat, 15 Jan 2022 20:02:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:02:00: #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 20:02:00: #1 tags after filtering in treatment: 128834 INFO @ Sat, 15 Jan 2022 20:02:00: #1 Redundant rate of treatment: 0.62 INFO @ Sat, 15 Jan 2022 20:02:00: #1 finished! INFO @ Sat, 15 Jan 2022 20:02:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:02:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:02:01: #2 number of paired peaks: 563 WARNING @ Sat, 15 Jan 2022 20:02:01: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Sat, 15 Jan 2022 20:02:01: start model_add_line... INFO @ Sat, 15 Jan 2022 20:02:01: start X-correlation... INFO @ Sat, 15 Jan 2022 20:02:01: end of X-cor INFO @ Sat, 15 Jan 2022 20:02:01: #2 finished! INFO @ Sat, 15 Jan 2022 20:02:01: #2 predicted fragment length is 167 bps INFO @ Sat, 15 Jan 2022 20:02:01: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 15 Jan 2022 20:02:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.20_model.r INFO @ Sat, 15 Jan 2022 20:02:01: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:02:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:02:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:02:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:02:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:02:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847373/SRX7847373.20_summits.bed INFO @ Sat, 15 Jan 2022 20:02:01: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (173 records, 4 fields): 2 millis CompletedMACS2peakCalling