Job ID = 14521452 SRX = SRX10468476 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3802385 spots for SRR14094888/SRR14094888.sra Written 3802385 spots for SRR14094888/SRR14094888.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: 00:00:52 3802385 reads; of these: 3802385 (100.00%) were paired; of these: 1727320 (45.43%) aligned concordantly 0 times 1527627 (40.18%) aligned concordantly exactly 1 time 547438 (14.40%) aligned concordantly >1 times ---- 1727320 pairs aligned concordantly 0 times; of these: 5451 (0.32%) aligned discordantly 1 time ---- 1721869 pairs aligned 0 times concordantly or discordantly; of these: 3443738 mates make up the pairs; of these: 3376631 (98.05%) aligned 0 times 41777 (1.21%) aligned exactly 1 time 25330 (0.74%) aligned >1 times 55.60% overall alignment rate Time searching: 00:00:52 Overall time: 00:00:52 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] 107301 / 2075578 = 0.0517 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 21:01:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.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 21:01:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:01:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:01:43: 1000000 INFO @ Sat, 15 Jan 2022 21:01:48: 2000000 INFO @ Sat, 15 Jan 2022 21:01:53: 3000000 INFO @ Sat, 15 Jan 2022 21:01:58: 4000000 INFO @ Sat, 15 Jan 2022 21:01:58: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 21:01:58: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 21:01:58: #1 total tags in treatment: 1967789 INFO @ Sat, 15 Jan 2022 21:01:58: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:01:58: #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 21:01:58: #1 tags after filtering in treatment: 1536003 INFO @ Sat, 15 Jan 2022 21:01:58: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Jan 2022 21:01:58: #1 finished! INFO @ Sat, 15 Jan 2022 21:01:58: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:01:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:01:59: #2 number of paired peaks: 100 WARNING @ Sat, 15 Jan 2022 21:01:59: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Sat, 15 Jan 2022 21:01:59: start model_add_line... INFO @ Sat, 15 Jan 2022 21:01:59: start X-correlation... INFO @ Sat, 15 Jan 2022 21:01:59: end of X-cor INFO @ Sat, 15 Jan 2022 21:01:59: #2 finished! INFO @ Sat, 15 Jan 2022 21:01:59: #2 predicted fragment length is 85 bps INFO @ Sat, 15 Jan 2022 21:01:59: #2 alternative fragment length(s) may be 3,85 bps INFO @ Sat, 15 Jan 2022 21:01:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.05_model.r INFO @ Sat, 15 Jan 2022 21:01:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:01:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:02:02: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:02:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:02:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:02:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.05_summits.bed INFO @ Sat, 15 Jan 2022 21:02:03: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (577 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 21:02:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.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 21:02:08: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:02:08: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:02:13: 1000000 INFO @ Sat, 15 Jan 2022 21:02:18: 2000000 INFO @ Sat, 15 Jan 2022 21:02:23: 3000000 INFO @ Sat, 15 Jan 2022 21:02:28: 4000000 INFO @ Sat, 15 Jan 2022 21:02:28: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 21:02:28: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 21:02:28: #1 total tags in treatment: 1967789 INFO @ Sat, 15 Jan 2022 21:02:28: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:02:28: #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 21:02:28: #1 tags after filtering in treatment: 1536003 INFO @ Sat, 15 Jan 2022 21:02:28: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Jan 2022 21:02:28: #1 finished! INFO @ Sat, 15 Jan 2022 21:02:28: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:02:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:02:28: #2 number of paired peaks: 100 WARNING @ Sat, 15 Jan 2022 21:02:28: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Sat, 15 Jan 2022 21:02:28: start model_add_line... INFO @ Sat, 15 Jan 2022 21:02:28: start X-correlation... INFO @ Sat, 15 Jan 2022 21:02:29: end of X-cor INFO @ Sat, 15 Jan 2022 21:02:29: #2 finished! INFO @ Sat, 15 Jan 2022 21:02:29: #2 predicted fragment length is 85 bps INFO @ Sat, 15 Jan 2022 21:02:29: #2 alternative fragment length(s) may be 3,85 bps INFO @ Sat, 15 Jan 2022 21:02:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.10_model.r INFO @ Sat, 15 Jan 2022 21:02:29: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:02:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:02:31: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:02:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:02:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:02:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.10_summits.bed INFO @ Sat, 15 Jan 2022 21:02:33: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (224 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 21:02:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.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 21:02:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:02:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:02:43: 1000000 INFO @ Sat, 15 Jan 2022 21:02:48: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:02:53: 3000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:02:58: 4000000 INFO @ Sat, 15 Jan 2022 21:02:58: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 21:02:58: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 21:02:58: #1 total tags in treatment: 1967789 INFO @ Sat, 15 Jan 2022 21:02:58: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:02:58: #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 21:02:58: #1 tags after filtering in treatment: 1536003 INFO @ Sat, 15 Jan 2022 21:02:58: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Jan 2022 21:02:58: #1 finished! INFO @ Sat, 15 Jan 2022 21:02:58: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:02:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:02:58: #2 number of paired peaks: 100 WARNING @ Sat, 15 Jan 2022 21:02:58: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Sat, 15 Jan 2022 21:02:58: start model_add_line... INFO @ Sat, 15 Jan 2022 21:02:58: start X-correlation... INFO @ Sat, 15 Jan 2022 21:02:58: end of X-cor INFO @ Sat, 15 Jan 2022 21:02:58: #2 finished! INFO @ Sat, 15 Jan 2022 21:02:58: #2 predicted fragment length is 85 bps INFO @ Sat, 15 Jan 2022 21:02:58: #2 alternative fragment length(s) may be 3,85 bps INFO @ Sat, 15 Jan 2022 21:02:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.20_model.r INFO @ Sat, 15 Jan 2022 21:02:58: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:02:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:03:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:03:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:03:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:03:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468476/SRX10468476.20_summits.bed INFO @ Sat, 15 Jan 2022 21:03:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (78 records, 4 fields): 1 millis CompletedMACS2peakCalling