Job ID = 14520632 SRX = SRX7847359 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22899361 spots for SRR11235541/SRR11235541.sra Written 22899361 spots for SRR11235541/SRR11235541.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: 00:15:35 22899361 reads; of these: 22899361 (100.00%) were paired; of these: 4981177 (21.75%) aligned concordantly 0 times 15147694 (66.15%) aligned concordantly exactly 1 time 2770490 (12.10%) aligned concordantly >1 times ---- 4981177 pairs aligned concordantly 0 times; of these: 82366 (1.65%) aligned discordantly 1 time ---- 4898811 pairs aligned 0 times concordantly or discordantly; of these: 9797622 mates make up the pairs; of these: 8468514 (86.43%) aligned 0 times 875315 (8.93%) aligned exactly 1 time 453793 (4.63%) aligned >1 times 81.51% overall alignment rate Time searching: 00:15:35 Overall time: 00:15:35 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] 17392653 / 17972424 = 0.9677 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 19:56:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.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 19:56:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:56:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:56:10: 1000000 INFO @ Sat, 15 Jan 2022 19:56:17: 2000000 INFO @ Sat, 15 Jan 2022 19:56:20: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 19:56:20: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 19:56:20: #1 total tags in treatment: 594616 INFO @ Sat, 15 Jan 2022 19:56:20: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:56:20: #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 19:56:20: #1 tags after filtering in treatment: 244644 INFO @ Sat, 15 Jan 2022 19:56:20: #1 Redundant rate of treatment: 0.59 INFO @ Sat, 15 Jan 2022 19:56:20: #1 finished! INFO @ Sat, 15 Jan 2022 19:56:20: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:56:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:56:20: #2 number of paired peaks: 749 WARNING @ Sat, 15 Jan 2022 19:56:20: Fewer paired peaks (749) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 749 pairs to build model! INFO @ Sat, 15 Jan 2022 19:56:20: start model_add_line... INFO @ Sat, 15 Jan 2022 19:56:20: start X-correlation... INFO @ Sat, 15 Jan 2022 19:56:21: end of X-cor INFO @ Sat, 15 Jan 2022 19:56:21: #2 finished! INFO @ Sat, 15 Jan 2022 19:56:21: #2 predicted fragment length is 178 bps INFO @ Sat, 15 Jan 2022 19:56:21: #2 alternative fragment length(s) may be 178 bps INFO @ Sat, 15 Jan 2022 19:56:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.05_model.r INFO @ Sat, 15 Jan 2022 19:56:21: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:56:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:56:22: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:56:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:56:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:56:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.05_summits.bed INFO @ Sat, 15 Jan 2022 19:56:23: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (716 records, 4 fields): 7 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 19:56:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.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 19:56:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:56:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:56:40: 1000000 INFO @ Sat, 15 Jan 2022 19:56:48: 2000000 INFO @ Sat, 15 Jan 2022 19:56:52: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 19:56:52: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 19:56:52: #1 total tags in treatment: 594616 INFO @ Sat, 15 Jan 2022 19:56:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:56:52: #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 19:56:52: #1 tags after filtering in treatment: 244644 INFO @ Sat, 15 Jan 2022 19:56:52: #1 Redundant rate of treatment: 0.59 INFO @ Sat, 15 Jan 2022 19:56:52: #1 finished! INFO @ Sat, 15 Jan 2022 19:56:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:56:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:56:52: #2 number of paired peaks: 749 WARNING @ Sat, 15 Jan 2022 19:56:52: Fewer paired peaks (749) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 749 pairs to build model! INFO @ Sat, 15 Jan 2022 19:56:52: start model_add_line... INFO @ Sat, 15 Jan 2022 19:56:52: start X-correlation... INFO @ Sat, 15 Jan 2022 19:56:52: end of X-cor INFO @ Sat, 15 Jan 2022 19:56:52: #2 finished! INFO @ Sat, 15 Jan 2022 19:56:52: #2 predicted fragment length is 178 bps INFO @ Sat, 15 Jan 2022 19:56:52: #2 alternative fragment length(s) may be 178 bps INFO @ Sat, 15 Jan 2022 19:56:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.10_model.r INFO @ Sat, 15 Jan 2022 19:56:52: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:56:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:56:54: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:56:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:56:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:56:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.10_summits.bed INFO @ Sat, 15 Jan 2022 19:56:54: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (537 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 19:57:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.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 19:57:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:57:03: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:57:11: 1000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:57:18: 2000000 INFO @ Sat, 15 Jan 2022 19:57:22: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 19:57:22: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 19:57:22: #1 total tags in treatment: 594616 INFO @ Sat, 15 Jan 2022 19:57:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:57:22: #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 19:57:22: #1 tags after filtering in treatment: 244644 INFO @ Sat, 15 Jan 2022 19:57:22: #1 Redundant rate of treatment: 0.59 INFO @ Sat, 15 Jan 2022 19:57:22: #1 finished! INFO @ Sat, 15 Jan 2022 19:57:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:57:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:57:22: #2 number of paired peaks: 749 WARNING @ Sat, 15 Jan 2022 19:57:22: Fewer paired peaks (749) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 749 pairs to build model! INFO @ Sat, 15 Jan 2022 19:57:22: start model_add_line... INFO @ Sat, 15 Jan 2022 19:57:22: start X-correlation... INFO @ Sat, 15 Jan 2022 19:57:22: end of X-cor INFO @ Sat, 15 Jan 2022 19:57:22: #2 finished! INFO @ Sat, 15 Jan 2022 19:57:22: #2 predicted fragment length is 178 bps INFO @ Sat, 15 Jan 2022 19:57:22: #2 alternative fragment length(s) may be 178 bps INFO @ Sat, 15 Jan 2022 19:57:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.20_model.r INFO @ Sat, 15 Jan 2022 19:57:22: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:57:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:57:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:57:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:57:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:57:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847359/SRX7847359.20_summits.bed INFO @ Sat, 15 Jan 2022 19:57:24: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (368 records, 4 fields): 5 millis CompletedMACS2peakCalling