Job ID = 14521923 SRX = SRX11539774 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21521729 spots for SRR15233871/SRR15233871.sra Written 21521729 spots for SRR15233871/SRR15233871.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: 00:10:52 21521729 reads; of these: 21521729 (100.00%) were paired; of these: 20185983 (93.79%) aligned concordantly 0 times 109364 (0.51%) aligned concordantly exactly 1 time 1226382 (5.70%) aligned concordantly >1 times ---- 20185983 pairs aligned concordantly 0 times; of these: 110687 (0.55%) aligned discordantly 1 time ---- 20075296 pairs aligned 0 times concordantly or discordantly; of these: 40150592 mates make up the pairs; of these: 39852199 (99.26%) aligned 0 times 116240 (0.29%) aligned exactly 1 time 182153 (0.45%) aligned >1 times 7.41% overall alignment rate Time searching: 00:10:52 Overall time: 00:10:52 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] 1344218 / 1439137 = 0.9340 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 22:03:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.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 22:03:47: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:03:47: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:03:50: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 22:03:50: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 22:03:50: #1 total tags in treatment: 56533 INFO @ Sat, 15 Jan 2022 22:03:50: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:03:50: #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 22:03:50: #1 tags after filtering in treatment: 47241 INFO @ Sat, 15 Jan 2022 22:03:50: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 15 Jan 2022 22:03:50: #1 finished! INFO @ Sat, 15 Jan 2022 22:03:50: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:03:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:03:50: #2 number of paired peaks: 251 WARNING @ Sat, 15 Jan 2022 22:03:50: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Sat, 15 Jan 2022 22:03:50: start model_add_line... INFO @ Sat, 15 Jan 2022 22:03:50: start X-correlation... INFO @ Sat, 15 Jan 2022 22:03:50: end of X-cor INFO @ Sat, 15 Jan 2022 22:03:50: #2 finished! INFO @ Sat, 15 Jan 2022 22:03:50: #2 predicted fragment length is 55 bps INFO @ Sat, 15 Jan 2022 22:03:50: #2 alternative fragment length(s) may be 1,55,114,151,203,267,299,385,452,509,577 bps INFO @ Sat, 15 Jan 2022 22:03:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.05_model.r WARNING @ Sat, 15 Jan 2022 22:03:50: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 22:03:50: #2 You may need to consider one of the other alternative d(s): 1,55,114,151,203,267,299,385,452,509,577 WARNING @ Sat, 15 Jan 2022 22:03:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 22:03:50: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:03:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:03:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:03:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.05_peaks.xls INFO @ Sat, 15 Jan 2022 22:03:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:03:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.05_summits.bed INFO @ Sat, 15 Jan 2022 22:03:50: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (38 records, 4 fields): 1 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 22:04:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.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 22:04:17: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:04:17: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:04:19: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 22:04:19: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 22:04:19: #1 total tags in treatment: 56533 INFO @ Sat, 15 Jan 2022 22:04:19: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:04:19: #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 22:04:19: #1 tags after filtering in treatment: 47241 INFO @ Sat, 15 Jan 2022 22:04:19: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 15 Jan 2022 22:04:19: #1 finished! INFO @ Sat, 15 Jan 2022 22:04:19: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:04:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:04:19: #2 number of paired peaks: 251 WARNING @ Sat, 15 Jan 2022 22:04:19: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Sat, 15 Jan 2022 22:04:19: start model_add_line... INFO @ Sat, 15 Jan 2022 22:04:19: start X-correlation... INFO @ Sat, 15 Jan 2022 22:04:19: end of X-cor INFO @ Sat, 15 Jan 2022 22:04:19: #2 finished! INFO @ Sat, 15 Jan 2022 22:04:19: #2 predicted fragment length is 55 bps INFO @ Sat, 15 Jan 2022 22:04:19: #2 alternative fragment length(s) may be 1,55,114,151,203,267,299,385,452,509,577 bps INFO @ Sat, 15 Jan 2022 22:04:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.10_model.r WARNING @ Sat, 15 Jan 2022 22:04:19: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 22:04:19: #2 You may need to consider one of the other alternative d(s): 1,55,114,151,203,267,299,385,452,509,577 WARNING @ Sat, 15 Jan 2022 22:04:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 22:04:19: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:04:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:04:20: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:04:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.10_peaks.xls INFO @ Sat, 15 Jan 2022 22:04:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:04:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.10_summits.bed INFO @ Sat, 15 Jan 2022 22:04:20: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (22 records, 4 fields): 1 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 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:04:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.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 22:04:47: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:04:47: #1 read treatment tags... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 22:04:50: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 22:04:50: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 22:04:50: #1 total tags in treatment: 56533 INFO @ Sat, 15 Jan 2022 22:04:50: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:04:50: #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 22:04:50: #1 tags after filtering in treatment: 47241 INFO @ Sat, 15 Jan 2022 22:04:50: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 15 Jan 2022 22:04:50: #1 finished! INFO @ Sat, 15 Jan 2022 22:04:50: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:04:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:04:50: #2 number of paired peaks: 251 WARNING @ Sat, 15 Jan 2022 22:04:50: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Sat, 15 Jan 2022 22:04:50: start model_add_line... INFO @ Sat, 15 Jan 2022 22:04:50: start X-correlation... INFO @ Sat, 15 Jan 2022 22:04:50: end of X-cor INFO @ Sat, 15 Jan 2022 22:04:50: #2 finished! INFO @ Sat, 15 Jan 2022 22:04:50: #2 predicted fragment length is 55 bps INFO @ Sat, 15 Jan 2022 22:04:50: #2 alternative fragment length(s) may be 1,55,114,151,203,267,299,385,452,509,577 bps INFO @ Sat, 15 Jan 2022 22:04:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.20_model.r WARNING @ Sat, 15 Jan 2022 22:04:50: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 22:04:50: #2 You may need to consider one of the other alternative d(s): 1,55,114,151,203,267,299,385,452,509,577 WARNING @ Sat, 15 Jan 2022 22:04:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 22:04:50: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:04:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:04:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:04:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.20_peaks.xls INFO @ Sat, 15 Jan 2022 22:04:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:04:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11539774/SRX11539774.20_summits.bed INFO @ Sat, 15 Jan 2022 22:04:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling