Job ID = 14520792 SRX = SRX8245520 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8238393 spots for SRR11684731/SRR11684731.sra Written 8238393 spots for SRR11684731/SRR11684731.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: 00:03:12 8238393 reads; of these: 8238393 (100.00%) were paired; of these: 5635834 (68.41%) aligned concordantly 0 times 2371078 (28.78%) aligned concordantly exactly 1 time 231481 (2.81%) aligned concordantly >1 times ---- 5635834 pairs aligned concordantly 0 times; of these: 28753 (0.51%) aligned discordantly 1 time ---- 5607081 pairs aligned 0 times concordantly or discordantly; of these: 11214162 mates make up the pairs; of these: 8231467 (73.40%) aligned 0 times 2643521 (23.57%) aligned exactly 1 time 339174 (3.02%) aligned >1 times 50.04% overall alignment rate Time searching: 00:03:12 Overall time: 00:03:12 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] 191663 / 2630897 = 0.0729 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 19:58:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.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 19:58:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:58:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:58:10: 1000000 INFO @ Sat, 15 Jan 2022 19:58:15: 2000000 INFO @ Sat, 15 Jan 2022 19:58:19: 3000000 INFO @ Sat, 15 Jan 2022 19:58:24: 4000000 INFO @ Sat, 15 Jan 2022 19:58:29: 5000000 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 19:58:34: 6000000 INFO @ Sat, 15 Jan 2022 19:58:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.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 19:58:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:58:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:58:39: 7000000 INFO @ Sat, 15 Jan 2022 19:58:41: 1000000 INFO @ Sat, 15 Jan 2022 19:58:43: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:58:43: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:58:43: #1 total tags in treatment: 2411805 INFO @ Sat, 15 Jan 2022 19:58:43: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:58:43: #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 19:58:43: #1 tags after filtering in treatment: 1374939 INFO @ Sat, 15 Jan 2022 19:58:43: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 19:58:43: #1 finished! INFO @ Sat, 15 Jan 2022 19:58:43: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:58:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:58:44: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 19:58:44: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 19:58:44: start model_add_line... INFO @ Sat, 15 Jan 2022 19:58:44: start X-correlation... INFO @ Sat, 15 Jan 2022 19:58:44: end of X-cor INFO @ Sat, 15 Jan 2022 19:58:44: #2 finished! INFO @ Sat, 15 Jan 2022 19:58:44: #2 predicted fragment length is 133 bps INFO @ Sat, 15 Jan 2022 19:58:44: #2 alternative fragment length(s) may be 11,56,87,133,166,186,200,229,253,280,313,355,375,394,407,458,479,508,538,570 bps INFO @ Sat, 15 Jan 2022 19:58:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.05_model.r INFO @ Sat, 15 Jan 2022 19:58:44: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:58:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:58:46: 2000000 INFO @ Sat, 15 Jan 2022 19:58:46: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:58:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:58:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:58:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.05_summits.bed INFO @ Sat, 15 Jan 2022 19:58:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (51 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:58:51: 3000000 INFO @ Sat, 15 Jan 2022 19:58:56: 4000000 INFO @ Sat, 15 Jan 2022 19:59:00: 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 19:59:05: 6000000 INFO @ Sat, 15 Jan 2022 19:59:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.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 19:59:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:59:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:59:11: 7000000 INFO @ Sat, 15 Jan 2022 19:59:11: 1000000 INFO @ Sat, 15 Jan 2022 19:59:15: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:59:15: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:59:15: #1 total tags in treatment: 2411805 INFO @ Sat, 15 Jan 2022 19:59:15: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:59:15: #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 19:59:15: #1 tags after filtering in treatment: 1374939 INFO @ Sat, 15 Jan 2022 19:59:15: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 19:59:15: #1 finished! INFO @ Sat, 15 Jan 2022 19:59:15: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:59:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:59:15: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 19:59:15: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 19:59:15: start model_add_line... INFO @ Sat, 15 Jan 2022 19:59:15: start X-correlation... INFO @ Sat, 15 Jan 2022 19:59:15: end of X-cor INFO @ Sat, 15 Jan 2022 19:59:15: #2 finished! INFO @ Sat, 15 Jan 2022 19:59:15: #2 predicted fragment length is 133 bps INFO @ Sat, 15 Jan 2022 19:59:15: #2 alternative fragment length(s) may be 11,56,87,133,166,186,200,229,253,280,313,355,375,394,407,458,479,508,538,570 bps INFO @ Sat, 15 Jan 2022 19:59:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.10_model.r INFO @ Sat, 15 Jan 2022 19:59:15: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:59:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:59:16: 2000000 INFO @ Sat, 15 Jan 2022 19:59:18: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:59:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:59:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:59:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.10_summits.bed INFO @ Sat, 15 Jan 2022 19:59:19: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:59:21: 3000000 INFO @ Sat, 15 Jan 2022 19:59:26: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:59:31: 5000000 INFO @ Sat, 15 Jan 2022 19:59:37: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:59:42: 7000000 INFO @ Sat, 15 Jan 2022 19:59:46: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:59:46: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:59:46: #1 total tags in treatment: 2411805 INFO @ Sat, 15 Jan 2022 19:59:46: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:59:46: #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 19:59:46: #1 tags after filtering in treatment: 1374939 INFO @ Sat, 15 Jan 2022 19:59:46: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 19:59:46: #1 finished! INFO @ Sat, 15 Jan 2022 19:59:46: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:59:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:59:46: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 19:59:46: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 19:59:46: start model_add_line... INFO @ Sat, 15 Jan 2022 19:59:46: start X-correlation... INFO @ Sat, 15 Jan 2022 19:59:46: end of X-cor INFO @ Sat, 15 Jan 2022 19:59:46: #2 finished! INFO @ Sat, 15 Jan 2022 19:59:46: #2 predicted fragment length is 133 bps INFO @ Sat, 15 Jan 2022 19:59:46: #2 alternative fragment length(s) may be 11,56,87,133,166,186,200,229,253,280,313,355,375,394,407,458,479,508,538,570 bps INFO @ Sat, 15 Jan 2022 19:59:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.20_model.r INFO @ Sat, 15 Jan 2022 19:59:46: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:59:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:59:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:59:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:59:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:59:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245520/SRX8245520.20_summits.bed INFO @ Sat, 15 Jan 2022 19:59:50: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (3 records, 4 fields): 4 millis CompletedMACS2peakCalling