Job ID = 14520651 SRX = SRX7847368 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 32741791 spots for SRR11235550/SRR11235550.sra Written 32741791 spots for SRR11235550/SRR11235550.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: 00:16:35 32741791 reads; of these: 32741791 (100.00%) were paired; of these: 4220097 (12.89%) aligned concordantly 0 times 20512699 (62.65%) aligned concordantly exactly 1 time 8008995 (24.46%) aligned concordantly >1 times ---- 4220097 pairs aligned concordantly 0 times; of these: 72768 (1.72%) aligned discordantly 1 time ---- 4147329 pairs aligned 0 times concordantly or discordantly; of these: 8294658 mates make up the pairs; of these: 6606107 (79.64%) aligned 0 times 962652 (11.61%) aligned exactly 1 time 725899 (8.75%) aligned >1 times 89.91% overall alignment rate Time searching: 00:16:35 Overall time: 00:16:35 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 16 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] 28260392 / 28569375 = 0.9892 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 19:58:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.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 19:58:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:58:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:58:47: 1000000 INFO @ Sat, 15 Jan 2022 19:58:52: 2000000 INFO @ Sat, 15 Jan 2022 19:58:54: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 19:58:54: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 19:58:54: #1 total tags in treatment: 322662 INFO @ Sat, 15 Jan 2022 19:58:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:58:54: #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 19:58:54: #1 tags after filtering in treatment: 144824 INFO @ Sat, 15 Jan 2022 19:58:54: #1 Redundant rate of treatment: 0.55 INFO @ Sat, 15 Jan 2022 19:58:54: #1 finished! INFO @ Sat, 15 Jan 2022 19:58:54: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:58:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:58:54: #2 number of paired peaks: 541 WARNING @ Sat, 15 Jan 2022 19:58:54: Fewer paired peaks (541) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 541 pairs to build model! INFO @ Sat, 15 Jan 2022 19:58:54: start model_add_line... INFO @ Sat, 15 Jan 2022 19:58:54: start X-correlation... INFO @ Sat, 15 Jan 2022 19:58:54: end of X-cor INFO @ Sat, 15 Jan 2022 19:58:54: #2 finished! INFO @ Sat, 15 Jan 2022 19:58:54: #2 predicted fragment length is 166 bps INFO @ Sat, 15 Jan 2022 19:58:54: #2 alternative fragment length(s) may be 166 bps INFO @ Sat, 15 Jan 2022 19:58:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.05_model.r INFO @ Sat, 15 Jan 2022 19:58:54: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:58:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:58:54: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:58:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:58:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:58:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.05_summits.bed INFO @ Sat, 15 Jan 2022 19:58:55: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (384 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 19:59:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.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 19:59:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:59:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:59:17: 1000000 INFO @ Sat, 15 Jan 2022 19:59:22: 2000000 INFO @ Sat, 15 Jan 2022 19:59:24: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 19:59:24: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 19:59:24: #1 total tags in treatment: 322662 INFO @ Sat, 15 Jan 2022 19:59:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:59:24: #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 19:59:24: #1 tags after filtering in treatment: 144824 INFO @ Sat, 15 Jan 2022 19:59:24: #1 Redundant rate of treatment: 0.55 INFO @ Sat, 15 Jan 2022 19:59:24: #1 finished! INFO @ Sat, 15 Jan 2022 19:59:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:59:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:59:24: #2 number of paired peaks: 541 WARNING @ Sat, 15 Jan 2022 19:59:24: Fewer paired peaks (541) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 541 pairs to build model! INFO @ Sat, 15 Jan 2022 19:59:24: start model_add_line... INFO @ Sat, 15 Jan 2022 19:59:24: start X-correlation... INFO @ Sat, 15 Jan 2022 19:59:24: end of X-cor INFO @ Sat, 15 Jan 2022 19:59:24: #2 finished! INFO @ Sat, 15 Jan 2022 19:59:24: #2 predicted fragment length is 166 bps INFO @ Sat, 15 Jan 2022 19:59:24: #2 alternative fragment length(s) may be 166 bps INFO @ Sat, 15 Jan 2022 19:59:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.10_model.r INFO @ Sat, 15 Jan 2022 19:59:24: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:59:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:59:25: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:59:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:59:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:59:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.10_summits.bed INFO @ Sat, 15 Jan 2022 19:59:25: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (248 records, 4 fields): 20 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 19:59:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.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 19:59:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:59:42: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:59:46: 1000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:59:50: 2000000 INFO @ Sat, 15 Jan 2022 19:59:52: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 19:59:52: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 19:59:52: #1 total tags in treatment: 322662 INFO @ Sat, 15 Jan 2022 19:59:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:59:52: #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 19:59:52: #1 tags after filtering in treatment: 144824 INFO @ Sat, 15 Jan 2022 19:59:52: #1 Redundant rate of treatment: 0.55 INFO @ Sat, 15 Jan 2022 19:59:52: #1 finished! INFO @ Sat, 15 Jan 2022 19:59:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:59:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:59:52: #2 number of paired peaks: 541 WARNING @ Sat, 15 Jan 2022 19:59:52: Fewer paired peaks (541) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 541 pairs to build model! INFO @ Sat, 15 Jan 2022 19:59:52: start model_add_line... INFO @ Sat, 15 Jan 2022 19:59:52: start X-correlation... INFO @ Sat, 15 Jan 2022 19:59:52: end of X-cor INFO @ Sat, 15 Jan 2022 19:59:52: #2 finished! INFO @ Sat, 15 Jan 2022 19:59:52: #2 predicted fragment length is 166 bps INFO @ Sat, 15 Jan 2022 19:59:52: #2 alternative fragment length(s) may be 166 bps INFO @ Sat, 15 Jan 2022 19:59:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.20_model.r INFO @ Sat, 15 Jan 2022 19:59:52: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:59:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:59:53: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:59:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:59:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:59:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847368/SRX7847368.20_summits.bed INFO @ Sat, 15 Jan 2022 19:59:53: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (112 records, 4 fields): 11 millis CompletedMACS2peakCalling