Job ID = 14521392 SRX = SRX8952654 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9404756 spots for SRR12458232/SRR12458232.sra Written 9404756 spots for SRR12458232/SRR12458232.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: 00:02:23 9404756 reads; of these: 9404756 (100.00%) were paired; of these: 6583279 (70.00%) aligned concordantly 0 times 2486360 (26.44%) aligned concordantly exactly 1 time 335117 (3.56%) aligned concordantly >1 times ---- 6583279 pairs aligned concordantly 0 times; of these: 271507 (4.12%) aligned discordantly 1 time ---- 6311772 pairs aligned 0 times concordantly or discordantly; of these: 12623544 mates make up the pairs; of these: 11280417 (89.36%) aligned 0 times 1162450 (9.21%) aligned exactly 1 time 180677 (1.43%) aligned >1 times 40.03% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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] 365341 / 3083255 = 0.1185 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 21:01:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.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 21:01:27: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:01:27: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:01:31: 1000000 INFO @ Sat, 15 Jan 2022 21:01:35: 2000000 INFO @ Sat, 15 Jan 2022 21:01:39: 3000000 INFO @ Sat, 15 Jan 2022 21:01:43: 4000000 INFO @ Sat, 15 Jan 2022 21:01:48: 5000000 INFO @ Sat, 15 Jan 2022 21:01:52: 6000000 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 21:01:55: #1 tag size is determined as 44 bps INFO @ Sat, 15 Jan 2022 21:01:55: #1 tag size = 44 INFO @ Sat, 15 Jan 2022 21:01:55: #1 total tags in treatment: 2587815 INFO @ Sat, 15 Jan 2022 21:01:55: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:01:55: #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 21:01:55: #1 tags after filtering in treatment: 2236464 INFO @ Sat, 15 Jan 2022 21:01:55: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Jan 2022 21:01:55: #1 finished! INFO @ Sat, 15 Jan 2022 21:01:55: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:01:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:01:55: #2 number of paired peaks: 184 WARNING @ Sat, 15 Jan 2022 21:01:55: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Sat, 15 Jan 2022 21:01:55: start model_add_line... INFO @ Sat, 15 Jan 2022 21:01:55: start X-correlation... INFO @ Sat, 15 Jan 2022 21:01:55: end of X-cor INFO @ Sat, 15 Jan 2022 21:01:55: #2 finished! INFO @ Sat, 15 Jan 2022 21:01:55: #2 predicted fragment length is 217 bps INFO @ Sat, 15 Jan 2022 21:01:55: #2 alternative fragment length(s) may be 1,140,162,186,190,206,217 bps INFO @ Sat, 15 Jan 2022 21:01:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.05_model.r INFO @ Sat, 15 Jan 2022 21:01:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:01:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:01:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.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 21:01:57: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:01:57: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:02:00: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:02:02: 1000000 INFO @ Sat, 15 Jan 2022 21:02:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:02:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:02:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.05_summits.bed INFO @ Sat, 15 Jan 2022 21:02:02: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (378 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:02:06: 2000000 INFO @ Sat, 15 Jan 2022 21:02:11: 3000000 INFO @ Sat, 15 Jan 2022 21:02:16: 4000000 INFO @ Sat, 15 Jan 2022 21:02:21: 5000000 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 21:02:26: 6000000 INFO @ Sat, 15 Jan 2022 21:02:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.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 21:02:27: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:02:27: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:02:30: #1 tag size is determined as 44 bps INFO @ Sat, 15 Jan 2022 21:02:30: #1 tag size = 44 INFO @ Sat, 15 Jan 2022 21:02:30: #1 total tags in treatment: 2587815 INFO @ Sat, 15 Jan 2022 21:02:30: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:02:30: #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 21:02:30: #1 tags after filtering in treatment: 2236464 INFO @ Sat, 15 Jan 2022 21:02:30: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Jan 2022 21:02:30: #1 finished! INFO @ Sat, 15 Jan 2022 21:02:30: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:02:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:02:31: #2 number of paired peaks: 184 WARNING @ Sat, 15 Jan 2022 21:02:31: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Sat, 15 Jan 2022 21:02:31: start model_add_line... INFO @ Sat, 15 Jan 2022 21:02:31: start X-correlation... INFO @ Sat, 15 Jan 2022 21:02:31: end of X-cor INFO @ Sat, 15 Jan 2022 21:02:31: #2 finished! INFO @ Sat, 15 Jan 2022 21:02:31: #2 predicted fragment length is 217 bps INFO @ Sat, 15 Jan 2022 21:02:31: #2 alternative fragment length(s) may be 1,140,162,186,190,206,217 bps INFO @ Sat, 15 Jan 2022 21:02:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.10_model.r INFO @ Sat, 15 Jan 2022 21:02:31: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:02:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:02:32: 1000000 INFO @ Sat, 15 Jan 2022 21:02:35: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:02:37: 2000000 INFO @ Sat, 15 Jan 2022 21:02:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:02:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:02:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.10_summits.bed INFO @ Sat, 15 Jan 2022 21:02:37: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (216 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:02:42: 3000000 INFO @ Sat, 15 Jan 2022 21:02:47: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:02:52: 5000000 INFO @ Sat, 15 Jan 2022 21:02:57: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:03:01: #1 tag size is determined as 44 bps INFO @ Sat, 15 Jan 2022 21:03:01: #1 tag size = 44 INFO @ Sat, 15 Jan 2022 21:03:01: #1 total tags in treatment: 2587815 INFO @ Sat, 15 Jan 2022 21:03:01: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:03:01: #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 21:03:01: #1 tags after filtering in treatment: 2236464 INFO @ Sat, 15 Jan 2022 21:03:01: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Jan 2022 21:03:01: #1 finished! INFO @ Sat, 15 Jan 2022 21:03:01: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:03:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:03:01: #2 number of paired peaks: 184 WARNING @ Sat, 15 Jan 2022 21:03:01: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Sat, 15 Jan 2022 21:03:01: start model_add_line... INFO @ Sat, 15 Jan 2022 21:03:01: start X-correlation... INFO @ Sat, 15 Jan 2022 21:03:01: end of X-cor INFO @ Sat, 15 Jan 2022 21:03:01: #2 finished! INFO @ Sat, 15 Jan 2022 21:03:01: #2 predicted fragment length is 217 bps INFO @ Sat, 15 Jan 2022 21:03:01: #2 alternative fragment length(s) may be 1,140,162,186,190,206,217 bps INFO @ Sat, 15 Jan 2022 21:03:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.20_model.r INFO @ Sat, 15 Jan 2022 21:03:01: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:03:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:03:06: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:03:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:03:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:03:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952654/SRX8952654.20_summits.bed INFO @ Sat, 15 Jan 2022 21:03:08: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (106 records, 4 fields): 2 millis CompletedMACS2peakCalling