Job ID = 14520831 SRX = SRX8245538 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5800457 spots for SRR11684749/SRR11684749.sra Written 5800457 spots for SRR11684749/SRR11684749.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: 00:03:54 5800457 reads; of these: 5800457 (100.00%) were paired; of these: 3656517 (63.04%) aligned concordantly 0 times 1925978 (33.20%) aligned concordantly exactly 1 time 217962 (3.76%) aligned concordantly >1 times ---- 3656517 pairs aligned concordantly 0 times; of these: 6394 (0.17%) aligned discordantly 1 time ---- 3650123 pairs aligned 0 times concordantly or discordantly; of these: 7300246 mates make up the pairs; of these: 5130350 (70.28%) aligned 0 times 1909730 (26.16%) aligned exactly 1 time 260166 (3.56%) aligned >1 times 55.78% overall alignment rate Time searching: 00:03:54 Overall time: 00:03:54 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] 137708 / 2149968 = 0.0641 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 20:04:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.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 20:04:04: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:04:04: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:04:12: 1000000 INFO @ Sat, 15 Jan 2022 20:04:21: 2000000 INFO @ Sat, 15 Jan 2022 20:04:28: 3000000 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 20:04:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.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 20:04:34: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:04:34: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:04:36: 4000000 INFO @ Sat, 15 Jan 2022 20:04:42: 1000000 INFO @ Sat, 15 Jan 2022 20:04:43: 5000000 INFO @ Sat, 15 Jan 2022 20:04:51: 2000000 INFO @ Sat, 15 Jan 2022 20:04:52: 6000000 INFO @ Sat, 15 Jan 2022 20:04:53: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:04:53: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:04:53: #1 total tags in treatment: 2006338 INFO @ Sat, 15 Jan 2022 20:04:53: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:04:53: #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 20:04:53: #1 tags after filtering in treatment: 1281886 INFO @ Sat, 15 Jan 2022 20:04:53: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 15 Jan 2022 20:04:53: #1 finished! INFO @ Sat, 15 Jan 2022 20:04:53: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:04:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:04:53: #2 number of paired peaks: 178 WARNING @ Sat, 15 Jan 2022 20:04:53: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sat, 15 Jan 2022 20:04:53: start model_add_line... INFO @ Sat, 15 Jan 2022 20:04:53: start X-correlation... INFO @ Sat, 15 Jan 2022 20:04:54: end of X-cor INFO @ Sat, 15 Jan 2022 20:04:54: #2 finished! INFO @ Sat, 15 Jan 2022 20:04:54: #2 predicted fragment length is 130 bps INFO @ Sat, 15 Jan 2022 20:04:54: #2 alternative fragment length(s) may be 62,130,146,164,213,244,248,280 bps INFO @ Sat, 15 Jan 2022 20:04:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.05_model.r INFO @ Sat, 15 Jan 2022 20:04:54: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:04:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:04:57: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:04:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:04:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:04:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.05_summits.bed INFO @ Sat, 15 Jan 2022 20:04:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (65 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:04:59: 3000000 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 20:05:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.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 20:05:04: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:05:04: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:05:07: 4000000 INFO @ Sat, 15 Jan 2022 20:05:12: 1000000 INFO @ Sat, 15 Jan 2022 20:05:15: 5000000 INFO @ Sat, 15 Jan 2022 20:05:19: 2000000 INFO @ Sat, 15 Jan 2022 20:05:23: 6000000 INFO @ Sat, 15 Jan 2022 20:05:24: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:05:24: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:05:24: #1 total tags in treatment: 2006338 INFO @ Sat, 15 Jan 2022 20:05:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:05:24: #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 20:05:24: #1 tags after filtering in treatment: 1281886 INFO @ Sat, 15 Jan 2022 20:05:24: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 15 Jan 2022 20:05:24: #1 finished! INFO @ Sat, 15 Jan 2022 20:05:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:05:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:05:25: #2 number of paired peaks: 178 WARNING @ Sat, 15 Jan 2022 20:05:25: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sat, 15 Jan 2022 20:05:25: start model_add_line... INFO @ Sat, 15 Jan 2022 20:05:25: start X-correlation... INFO @ Sat, 15 Jan 2022 20:05:25: end of X-cor INFO @ Sat, 15 Jan 2022 20:05:25: #2 finished! INFO @ Sat, 15 Jan 2022 20:05:25: #2 predicted fragment length is 130 bps INFO @ Sat, 15 Jan 2022 20:05:25: #2 alternative fragment length(s) may be 62,130,146,164,213,244,248,280 bps INFO @ Sat, 15 Jan 2022 20:05:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.10_model.r INFO @ Sat, 15 Jan 2022 20:05:25: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:05:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:05:26: 3000000 INFO @ Sat, 15 Jan 2022 20:05:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:05:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:05:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:05:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.10_summits.bed INFO @ Sat, 15 Jan 2022 20:05:29: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (24 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:05:33: 4000000 INFO @ Sat, 15 Jan 2022 20:05:40: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:05:48: 6000000 INFO @ Sat, 15 Jan 2022 20:05:49: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:05:49: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:05:49: #1 total tags in treatment: 2006338 INFO @ Sat, 15 Jan 2022 20:05:49: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:05:49: #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 20:05:49: #1 tags after filtering in treatment: 1281886 INFO @ Sat, 15 Jan 2022 20:05:49: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 15 Jan 2022 20:05:49: #1 finished! INFO @ Sat, 15 Jan 2022 20:05:49: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:05:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:05:49: #2 number of paired peaks: 178 WARNING @ Sat, 15 Jan 2022 20:05:49: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sat, 15 Jan 2022 20:05:49: start model_add_line... INFO @ Sat, 15 Jan 2022 20:05:49: start X-correlation... INFO @ Sat, 15 Jan 2022 20:05:49: end of X-cor INFO @ Sat, 15 Jan 2022 20:05:49: #2 finished! INFO @ Sat, 15 Jan 2022 20:05:49: #2 predicted fragment length is 130 bps INFO @ Sat, 15 Jan 2022 20:05:49: #2 alternative fragment length(s) may be 62,130,146,164,213,244,248,280 bps INFO @ Sat, 15 Jan 2022 20:05:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.20_model.r INFO @ Sat, 15 Jan 2022 20:05:49: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:05:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:05:52: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:05:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:05:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:05:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245538/SRX8245538.20_summits.bed INFO @ Sat, 15 Jan 2022 20:05:53: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling