Job ID = 14521359 SRX = SRX8952645 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7186367 spots for SRR12458241/SRR12458241.sra Written 7186367 spots for SRR12458241/SRR12458241.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: 00:02:08 7186367 reads; of these: 7186367 (100.00%) were paired; of these: 5966683 (83.03%) aligned concordantly 0 times 1060764 (14.76%) aligned concordantly exactly 1 time 158920 (2.21%) aligned concordantly >1 times ---- 5966683 pairs aligned concordantly 0 times; of these: 298462 (5.00%) aligned discordantly 1 time ---- 5668221 pairs aligned 0 times concordantly or discordantly; of these: 11336442 mates make up the pairs; of these: 10232663 (90.26%) aligned 0 times 941318 (8.30%) aligned exactly 1 time 162461 (1.43%) aligned >1 times 28.81% overall alignment rate Time searching: 00:02:08 Overall time: 00:02:08 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] 523317 / 1505551 = 0.3476 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 20:57:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.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 20:57:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:57:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:57:11: 1000000 INFO @ Sat, 15 Jan 2022 20:57:16: 2000000 INFO @ Sat, 15 Jan 2022 20:57:21: 3000000 INFO @ Sat, 15 Jan 2022 20:57:22: #1 tag size is determined as 41 bps INFO @ Sat, 15 Jan 2022 20:57:22: #1 tag size = 41 INFO @ Sat, 15 Jan 2022 20:57:22: #1 total tags in treatment: 891506 INFO @ Sat, 15 Jan 2022 20:57:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:57:22: #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 20:57:22: #1 tags after filtering in treatment: 813171 INFO @ Sat, 15 Jan 2022 20:57:22: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 15 Jan 2022 20:57:22: #1 finished! INFO @ Sat, 15 Jan 2022 20:57:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:57:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:57:22: #2 number of paired peaks: 185 WARNING @ Sat, 15 Jan 2022 20:57:22: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sat, 15 Jan 2022 20:57:22: start model_add_line... INFO @ Sat, 15 Jan 2022 20:57:22: start X-correlation... INFO @ Sat, 15 Jan 2022 20:57:22: end of X-cor INFO @ Sat, 15 Jan 2022 20:57:22: #2 finished! INFO @ Sat, 15 Jan 2022 20:57:22: #2 predicted fragment length is 214 bps INFO @ Sat, 15 Jan 2022 20:57:22: #2 alternative fragment length(s) may be 2,214,234,251 bps INFO @ Sat, 15 Jan 2022 20:57:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.05_model.r INFO @ Sat, 15 Jan 2022 20:57:22: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:57:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:57:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:57:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:57:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:57:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.05_summits.bed INFO @ Sat, 15 Jan 2022 20:57:25: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (203 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 20:57:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.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 20:57:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:57:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:57:40: 1000000 INFO @ Sat, 15 Jan 2022 20:57:45: 2000000 INFO @ Sat, 15 Jan 2022 20:57:50: 3000000 INFO @ Sat, 15 Jan 2022 20:57:50: #1 tag size is determined as 41 bps INFO @ Sat, 15 Jan 2022 20:57:50: #1 tag size = 41 INFO @ Sat, 15 Jan 2022 20:57:50: #1 total tags in treatment: 891506 INFO @ Sat, 15 Jan 2022 20:57:50: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:57:50: #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 20:57:50: #1 tags after filtering in treatment: 813171 INFO @ Sat, 15 Jan 2022 20:57:50: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 15 Jan 2022 20:57:50: #1 finished! INFO @ Sat, 15 Jan 2022 20:57:50: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:57:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:57:50: #2 number of paired peaks: 185 WARNING @ Sat, 15 Jan 2022 20:57:50: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sat, 15 Jan 2022 20:57:50: start model_add_line... INFO @ Sat, 15 Jan 2022 20:57:50: start X-correlation... INFO @ Sat, 15 Jan 2022 20:57:50: end of X-cor INFO @ Sat, 15 Jan 2022 20:57:50: #2 finished! INFO @ Sat, 15 Jan 2022 20:57:50: #2 predicted fragment length is 214 bps INFO @ Sat, 15 Jan 2022 20:57:50: #2 alternative fragment length(s) may be 2,214,234,251 bps INFO @ Sat, 15 Jan 2022 20:57:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.10_model.r INFO @ Sat, 15 Jan 2022 20:57:50: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:57:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:57:53: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:57:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:57:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:57:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.10_summits.bed INFO @ Sat, 15 Jan 2022 20:57:54: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (94 records, 4 fields): 3 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 20:58:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.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 20:58:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:58:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:58:11: 1000000 INFO @ Sat, 15 Jan 2022 20:58:16: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:58:21: 3000000 INFO @ Sat, 15 Jan 2022 20:58:22: #1 tag size is determined as 41 bps INFO @ Sat, 15 Jan 2022 20:58:22: #1 tag size = 41 INFO @ Sat, 15 Jan 2022 20:58:22: #1 total tags in treatment: 891506 INFO @ Sat, 15 Jan 2022 20:58:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:58:22: #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 20:58:22: #1 tags after filtering in treatment: 813171 INFO @ Sat, 15 Jan 2022 20:58:22: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 15 Jan 2022 20:58:22: #1 finished! INFO @ Sat, 15 Jan 2022 20:58:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:58:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:58:22: #2 number of paired peaks: 185 WARNING @ Sat, 15 Jan 2022 20:58:22: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sat, 15 Jan 2022 20:58:22: start model_add_line... INFO @ Sat, 15 Jan 2022 20:58:22: start X-correlation... INFO @ Sat, 15 Jan 2022 20:58:22: end of X-cor INFO @ Sat, 15 Jan 2022 20:58:22: #2 finished! INFO @ Sat, 15 Jan 2022 20:58:22: #2 predicted fragment length is 214 bps INFO @ Sat, 15 Jan 2022 20:58:22: #2 alternative fragment length(s) may be 2,214,234,251 bps INFO @ Sat, 15 Jan 2022 20:58:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.20_model.r INFO @ Sat, 15 Jan 2022 20:58:22: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:58:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:58:24: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:58:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:58:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:58:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952645/SRX8952645.20_summits.bed INFO @ Sat, 15 Jan 2022 20:58:25: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (48 records, 4 fields): 2 millis CompletedMACS2peakCalling