Job ID = 14520630 SRX = SRX7847357 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 36090197 spots for SRR11235539/SRR11235539.sra Written 36090197 spots for SRR11235539/SRR11235539.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: 00:22:49 36090197 reads; of these: 36090197 (100.00%) were paired; of these: 5349152 (14.82%) aligned concordantly 0 times 26277035 (72.81%) aligned concordantly exactly 1 time 4464010 (12.37%) aligned concordantly >1 times ---- 5349152 pairs aligned concordantly 0 times; of these: 152852 (2.86%) aligned discordantly 1 time ---- 5196300 pairs aligned 0 times concordantly or discordantly; of these: 10392600 mates make up the pairs; of these: 7900773 (76.02%) aligned 0 times 1698120 (16.34%) aligned exactly 1 time 793707 (7.64%) aligned >1 times 89.05% overall alignment rate Time searching: 00:22:49 Overall time: 00:22:49 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_sort_core] merging from 20 files... [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] 29632550 / 30860146 = 0.9602 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 20:16:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.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 20:16:59: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:16:59: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:17:05: 1000000 INFO @ Sat, 15 Jan 2022 20:17:10: 2000000 INFO @ Sat, 15 Jan 2022 20:17:16: 3000000 INFO @ Sat, 15 Jan 2022 20:17:22: 4000000 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 20:17:28: 5000000 INFO @ Sat, 15 Jan 2022 20:17:28: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 20:17:28: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 20:17:28: #1 total tags in treatment: 1240792 INFO @ Sat, 15 Jan 2022 20:17:28: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:17:28: #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 20:17:29: #1 tags after filtering in treatment: 465330 INFO @ Sat, 15 Jan 2022 20:17:29: #1 Redundant rate of treatment: 0.62 INFO @ Sat, 15 Jan 2022 20:17:29: #1 finished! INFO @ Sat, 15 Jan 2022 20:17:29: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:17:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:17:29: #2 number of paired peaks: 774 WARNING @ Sat, 15 Jan 2022 20:17:29: Fewer paired peaks (774) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 774 pairs to build model! INFO @ Sat, 15 Jan 2022 20:17:29: start model_add_line... INFO @ Sat, 15 Jan 2022 20:17:29: start X-correlation... INFO @ Sat, 15 Jan 2022 20:17:29: end of X-cor INFO @ Sat, 15 Jan 2022 20:17:29: #2 finished! INFO @ Sat, 15 Jan 2022 20:17:29: #2 predicted fragment length is 178 bps INFO @ Sat, 15 Jan 2022 20:17:29: #2 alternative fragment length(s) may be 178 bps INFO @ Sat, 15 Jan 2022 20:17:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.05_model.r INFO @ Sat, 15 Jan 2022 20:17:29: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:17:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:17:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.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 20:17:29: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:17:29: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:17:31: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:17:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:17:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:17:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.05_summits.bed INFO @ Sat, 15 Jan 2022 20:17:32: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (869 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:17:35: 1000000 INFO @ Sat, 15 Jan 2022 20:17:41: 2000000 INFO @ Sat, 15 Jan 2022 20:17:46: 3000000 INFO @ Sat, 15 Jan 2022 20:17:52: 4000000 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 20:17:58: 5000000 INFO @ Sat, 15 Jan 2022 20:17:58: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 20:17:58: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 20:17:58: #1 total tags in treatment: 1240792 INFO @ Sat, 15 Jan 2022 20:17:58: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:17:58: #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 20:17:58: #1 tags after filtering in treatment: 465330 INFO @ Sat, 15 Jan 2022 20:17:58: #1 Redundant rate of treatment: 0.62 INFO @ Sat, 15 Jan 2022 20:17:58: #1 finished! INFO @ Sat, 15 Jan 2022 20:17:58: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:17:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:17:59: #2 number of paired peaks: 774 WARNING @ Sat, 15 Jan 2022 20:17:59: Fewer paired peaks (774) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 774 pairs to build model! INFO @ Sat, 15 Jan 2022 20:17:59: start model_add_line... INFO @ Sat, 15 Jan 2022 20:17:59: start X-correlation... INFO @ Sat, 15 Jan 2022 20:17:59: end of X-cor INFO @ Sat, 15 Jan 2022 20:17:59: #2 finished! INFO @ Sat, 15 Jan 2022 20:17:59: #2 predicted fragment length is 178 bps INFO @ Sat, 15 Jan 2022 20:17:59: #2 alternative fragment length(s) may be 178 bps INFO @ Sat, 15 Jan 2022 20:17:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.10_model.r INFO @ Sat, 15 Jan 2022 20:17:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:17:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:17:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.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 20:17:59: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:17:59: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:18:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:18:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:18:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:18:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.10_summits.bed INFO @ Sat, 15 Jan 2022 20:18:02: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (665 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:18:04: 1000000 INFO @ Sat, 15 Jan 2022 20:18:08: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:18:12: 3000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:18:17: 4000000 INFO @ Sat, 15 Jan 2022 20:18:21: 5000000 INFO @ Sat, 15 Jan 2022 20:18:21: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 20:18:21: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 20:18:21: #1 total tags in treatment: 1240792 INFO @ Sat, 15 Jan 2022 20:18:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:18:21: #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 20:18:21: #1 tags after filtering in treatment: 465330 INFO @ Sat, 15 Jan 2022 20:18:21: #1 Redundant rate of treatment: 0.62 INFO @ Sat, 15 Jan 2022 20:18:21: #1 finished! INFO @ Sat, 15 Jan 2022 20:18:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:18:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:18:21: #2 number of paired peaks: 774 WARNING @ Sat, 15 Jan 2022 20:18:21: Fewer paired peaks (774) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 774 pairs to build model! INFO @ Sat, 15 Jan 2022 20:18:21: start model_add_line... INFO @ Sat, 15 Jan 2022 20:18:21: start X-correlation... INFO @ Sat, 15 Jan 2022 20:18:21: end of X-cor INFO @ Sat, 15 Jan 2022 20:18:21: #2 finished! INFO @ Sat, 15 Jan 2022 20:18:21: #2 predicted fragment length is 178 bps INFO @ Sat, 15 Jan 2022 20:18:21: #2 alternative fragment length(s) may be 178 bps INFO @ Sat, 15 Jan 2022 20:18:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.20_model.r INFO @ Sat, 15 Jan 2022 20:18:21: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:18:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:18:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:18:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:18:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:18:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847357/SRX7847357.20_summits.bed INFO @ Sat, 15 Jan 2022 20:18:24: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (478 records, 4 fields): 4 millis CompletedMACS2peakCalling