Job ID = 14521788 SRX = SRX10459803 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1342886 spots for SRR14085602/SRR14085602.sra Written 1342886 spots for SRR14085602/SRR14085602.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: 00:01:22 1342886 reads; of these: 1342886 (100.00%) were paired; of these: 231946 (17.27%) aligned concordantly 0 times 989738 (73.70%) aligned concordantly exactly 1 time 121202 (9.03%) aligned concordantly >1 times ---- 231946 pairs aligned concordantly 0 times; of these: 14769 (6.37%) aligned discordantly 1 time ---- 217177 pairs aligned 0 times concordantly or discordantly; of these: 434354 mates make up the pairs; of these: 377805 (86.98%) aligned 0 times 43397 (9.99%) aligned exactly 1 time 13152 (3.03%) aligned >1 times 85.93% overall alignment rate Time searching: 00:01:22 Overall time: 00:01:22 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] 17873 / 1122876 = 0.0159 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 21:38:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.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 21:38:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:38:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:38:16: 1000000 INFO @ Sat, 15 Jan 2022 21:38:24: 2000000 INFO @ Sat, 15 Jan 2022 21:38:26: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 21:38:26: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 21:38:26: #1 total tags in treatment: 1093196 INFO @ Sat, 15 Jan 2022 21:38:26: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:38:26: #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 21:38:26: #1 tags after filtering in treatment: 997598 INFO @ Sat, 15 Jan 2022 21:38:26: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 15 Jan 2022 21:38:26: #1 finished! INFO @ Sat, 15 Jan 2022 21:38:26: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:38:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:38:26: #2 number of paired peaks: 109 WARNING @ Sat, 15 Jan 2022 21:38:26: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Sat, 15 Jan 2022 21:38:26: start model_add_line... INFO @ Sat, 15 Jan 2022 21:38:26: start X-correlation... INFO @ Sat, 15 Jan 2022 21:38:26: end of X-cor INFO @ Sat, 15 Jan 2022 21:38:26: #2 finished! INFO @ Sat, 15 Jan 2022 21:38:26: #2 predicted fragment length is 201 bps INFO @ Sat, 15 Jan 2022 21:38:26: #2 alternative fragment length(s) may be 3,189,201,217 bps INFO @ Sat, 15 Jan 2022 21:38:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.05_model.r INFO @ Sat, 15 Jan 2022 21:38:27: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:38:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:38:29: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:38:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:38:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:38:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.05_summits.bed INFO @ Sat, 15 Jan 2022 21:38:31: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (57 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 21:38:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.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 21:38:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:38:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:38:46: 1000000 INFO @ Sat, 15 Jan 2022 21:38:55: 2000000 INFO @ Sat, 15 Jan 2022 21:38:57: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 21:38:57: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 21:38:57: #1 total tags in treatment: 1093196 INFO @ Sat, 15 Jan 2022 21:38:57: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:38:57: #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 21:38:57: #1 tags after filtering in treatment: 997598 INFO @ Sat, 15 Jan 2022 21:38:57: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 15 Jan 2022 21:38:57: #1 finished! INFO @ Sat, 15 Jan 2022 21:38:57: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:38:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:38:57: #2 number of paired peaks: 109 WARNING @ Sat, 15 Jan 2022 21:38:57: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Sat, 15 Jan 2022 21:38:57: start model_add_line... INFO @ Sat, 15 Jan 2022 21:38:57: start X-correlation... INFO @ Sat, 15 Jan 2022 21:38:57: end of X-cor INFO @ Sat, 15 Jan 2022 21:38:57: #2 finished! INFO @ Sat, 15 Jan 2022 21:38:57: #2 predicted fragment length is 201 bps INFO @ Sat, 15 Jan 2022 21:38:57: #2 alternative fragment length(s) may be 3,189,201,217 bps INFO @ Sat, 15 Jan 2022 21:38:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.10_model.r INFO @ Sat, 15 Jan 2022 21:38:57: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:38:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:39:00: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:39:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:39:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:39:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.10_summits.bed INFO @ Sat, 15 Jan 2022 21:39:01: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (37 records, 4 fields): 190 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 21:39:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.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 21:39:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:39:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:39:16: 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 21:39:25: 2000000 INFO @ Sat, 15 Jan 2022 21:39:28: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 21:39:28: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 21:39:28: #1 total tags in treatment: 1093196 INFO @ Sat, 15 Jan 2022 21:39:28: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:39:28: #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 21:39:28: #1 tags after filtering in treatment: 997598 INFO @ Sat, 15 Jan 2022 21:39:28: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 15 Jan 2022 21:39:28: #1 finished! INFO @ Sat, 15 Jan 2022 21:39:28: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:39:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:39:28: #2 number of paired peaks: 109 WARNING @ Sat, 15 Jan 2022 21:39:28: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Sat, 15 Jan 2022 21:39:28: start model_add_line... INFO @ Sat, 15 Jan 2022 21:39:28: start X-correlation... INFO @ Sat, 15 Jan 2022 21:39:28: end of X-cor INFO @ Sat, 15 Jan 2022 21:39:28: #2 finished! INFO @ Sat, 15 Jan 2022 21:39:28: #2 predicted fragment length is 201 bps INFO @ Sat, 15 Jan 2022 21:39:28: #2 alternative fragment length(s) may be 3,189,201,217 bps INFO @ Sat, 15 Jan 2022 21:39:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.20_model.r INFO @ Sat, 15 Jan 2022 21:39:28: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:39:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:39:31: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:39:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:39:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:39:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10459803/SRX10459803.20_summits.bed INFO @ Sat, 15 Jan 2022 21:39:32: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (18 records, 4 fields): 2 millis CompletedMACS2peakCalling