Job ID = 14521293 SRX = SRX10468535 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2766115 spots for SRR14094846/SRR14094846.sra Written 2766115 spots for SRR14094846/SRR14094846.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: 00:01:09 2766115 reads; of these: 2766115 (100.00%) were paired; of these: 757692 (27.39%) aligned concordantly 0 times 1698927 (61.42%) aligned concordantly exactly 1 time 309496 (11.19%) aligned concordantly >1 times ---- 757692 pairs aligned concordantly 0 times; of these: 15246 (2.01%) aligned discordantly 1 time ---- 742446 pairs aligned 0 times concordantly or discordantly; of these: 1484892 mates make up the pairs; of these: 1435574 (96.68%) aligned 0 times 34260 (2.31%) aligned exactly 1 time 15058 (1.01%) aligned >1 times 74.05% overall alignment rate Time searching: 00:01:09 Overall time: 00:01:09 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] 58315 / 2009692 = 0.0290 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 20:49:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.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 20:49:34: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:49:34: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:49:39: 1000000 INFO @ Sat, 15 Jan 2022 20:49:43: 2000000 INFO @ Sat, 15 Jan 2022 20:49:48: 3000000 INFO @ Sat, 15 Jan 2022 20:49:52: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:49:52: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:49:52: #1 total tags in treatment: 1950130 INFO @ Sat, 15 Jan 2022 20:49:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:49:52: #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 20:49:52: #1 tags after filtering in treatment: 1497585 INFO @ Sat, 15 Jan 2022 20:49:52: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 20:49:52: #1 finished! INFO @ Sat, 15 Jan 2022 20:49:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:49:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:49:52: #2 number of paired peaks: 576 WARNING @ Sat, 15 Jan 2022 20:49:52: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Sat, 15 Jan 2022 20:49:52: start model_add_line... INFO @ Sat, 15 Jan 2022 20:49:52: start X-correlation... INFO @ Sat, 15 Jan 2022 20:49:52: end of X-cor INFO @ Sat, 15 Jan 2022 20:49:52: #2 finished! INFO @ Sat, 15 Jan 2022 20:49:52: #2 predicted fragment length is 55 bps INFO @ Sat, 15 Jan 2022 20:49:52: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sat, 15 Jan 2022 20:49:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.05_model.r INFO @ Sat, 15 Jan 2022 20:49:52: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:49:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:49:55: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:49:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:49:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:49:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.05_summits.bed INFO @ Sat, 15 Jan 2022 20:49:56: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (854 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 20:50:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.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 20:50:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:50:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:50:10: 1000000 INFO @ Sat, 15 Jan 2022 20:50:15: 2000000 INFO @ Sat, 15 Jan 2022 20:50:21: 3000000 INFO @ Sat, 15 Jan 2022 20:50:26: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:50:26: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:50:26: #1 total tags in treatment: 1950130 INFO @ Sat, 15 Jan 2022 20:50:26: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:50:26: #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 20:50:26: #1 tags after filtering in treatment: 1497585 INFO @ Sat, 15 Jan 2022 20:50:26: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 20:50:26: #1 finished! INFO @ Sat, 15 Jan 2022 20:50:26: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:50:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:50:26: #2 number of paired peaks: 576 WARNING @ Sat, 15 Jan 2022 20:50:26: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Sat, 15 Jan 2022 20:50:26: start model_add_line... INFO @ Sat, 15 Jan 2022 20:50:26: start X-correlation... INFO @ Sat, 15 Jan 2022 20:50:26: end of X-cor INFO @ Sat, 15 Jan 2022 20:50:26: #2 finished! INFO @ Sat, 15 Jan 2022 20:50:26: #2 predicted fragment length is 55 bps INFO @ Sat, 15 Jan 2022 20:50:26: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sat, 15 Jan 2022 20:50:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.10_model.r INFO @ Sat, 15 Jan 2022 20:50:26: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:50:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:50:29: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:50:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:50:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:50:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.10_summits.bed INFO @ Sat, 15 Jan 2022 20:50:30: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (474 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 20:50:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.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 20:50:34: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:50:34: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:50:39: 1000000 INFO @ Sat, 15 Jan 2022 20:50:44: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:50:50: 3000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:50:54: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:50:54: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:50:54: #1 total tags in treatment: 1950130 INFO @ Sat, 15 Jan 2022 20:50:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:50:54: #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 20:50:55: #1 tags after filtering in treatment: 1497585 INFO @ Sat, 15 Jan 2022 20:50:55: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 20:50:55: #1 finished! INFO @ Sat, 15 Jan 2022 20:50:55: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:50:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:50:55: #2 number of paired peaks: 576 WARNING @ Sat, 15 Jan 2022 20:50:55: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Sat, 15 Jan 2022 20:50:55: start model_add_line... INFO @ Sat, 15 Jan 2022 20:50:55: start X-correlation... INFO @ Sat, 15 Jan 2022 20:50:55: end of X-cor INFO @ Sat, 15 Jan 2022 20:50:55: #2 finished! INFO @ Sat, 15 Jan 2022 20:50:55: #2 predicted fragment length is 55 bps INFO @ Sat, 15 Jan 2022 20:50:55: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sat, 15 Jan 2022 20:50:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.20_model.r INFO @ Sat, 15 Jan 2022 20:50:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:50:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:50:58: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:50:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:50:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:50:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468535/SRX10468535.20_summits.bed INFO @ Sat, 15 Jan 2022 20:50:59: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (199 records, 4 fields): 1 millis CompletedMACS2peakCalling