Job ID = 14521218 SRX = SRX10468516 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4380637 spots for SRR14094827/SRR14094827.sra Written 4380637 spots for SRR14094827/SRR14094827.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: 00:02:23 4380637 reads; of these: 4380637 (100.00%) were paired; of these: 1666619 (38.05%) aligned concordantly 0 times 2320801 (52.98%) aligned concordantly exactly 1 time 393217 (8.98%) aligned concordantly >1 times ---- 1666619 pairs aligned concordantly 0 times; of these: 23001 (1.38%) aligned discordantly 1 time ---- 1643618 pairs aligned 0 times concordantly or discordantly; of these: 3287236 mates make up the pairs; of these: 3213364 (97.75%) aligned 0 times 55274 (1.68%) aligned exactly 1 time 18598 (0.57%) aligned >1 times 63.32% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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] 139770 / 2723797 = 0.0513 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 20:42:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.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 20:42:14: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:42:14: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:42:20: 1000000 INFO @ Sat, 15 Jan 2022 20:42:26: 2000000 INFO @ Sat, 15 Jan 2022 20:42:32: 3000000 INFO @ Sat, 15 Jan 2022 20:42:38: 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 20:42:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.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 20:42:44: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:42:44: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:42:44: 5000000 INFO @ Sat, 15 Jan 2022 20:42:46: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:42:46: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:42:46: #1 total tags in treatment: 2574511 INFO @ Sat, 15 Jan 2022 20:42:46: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:42:46: #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 20:42:46: #1 tags after filtering in treatment: 1952830 INFO @ Sat, 15 Jan 2022 20:42:46: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 15 Jan 2022 20:42:46: #1 finished! INFO @ Sat, 15 Jan 2022 20:42:46: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:42:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:42:46: #2 number of paired peaks: 559 WARNING @ Sat, 15 Jan 2022 20:42:46: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Sat, 15 Jan 2022 20:42:46: start model_add_line... INFO @ Sat, 15 Jan 2022 20:42:46: start X-correlation... INFO @ Sat, 15 Jan 2022 20:42:46: end of X-cor INFO @ Sat, 15 Jan 2022 20:42:46: #2 finished! INFO @ Sat, 15 Jan 2022 20:42:46: #2 predicted fragment length is 55 bps INFO @ Sat, 15 Jan 2022 20:42:46: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sat, 15 Jan 2022 20:42:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.05_model.r WARNING @ Sat, 15 Jan 2022 20:42:46: #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 20:42:46: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Sat, 15 Jan 2022 20:42:46: #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 20:42:46: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:42:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:42:50: 1000000 INFO @ Sat, 15 Jan 2022 20:42:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:42:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:42:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:42:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.05_summits.bed INFO @ Sat, 15 Jan 2022 20:42:52: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (975 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:42:56: 2000000 INFO @ Sat, 15 Jan 2022 20:43:02: 3000000 INFO @ Sat, 15 Jan 2022 20:43:08: 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 20:43:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.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 20:43:14: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:43:14: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:43:14: 5000000 INFO @ Sat, 15 Jan 2022 20:43:15: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:43:15: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:43:15: #1 total tags in treatment: 2574511 INFO @ Sat, 15 Jan 2022 20:43:15: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:43:15: #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 20:43:16: #1 tags after filtering in treatment: 1952830 INFO @ Sat, 15 Jan 2022 20:43:16: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 15 Jan 2022 20:43:16: #1 finished! INFO @ Sat, 15 Jan 2022 20:43:16: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:43:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:43:16: #2 number of paired peaks: 559 WARNING @ Sat, 15 Jan 2022 20:43:16: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Sat, 15 Jan 2022 20:43:16: start model_add_line... INFO @ Sat, 15 Jan 2022 20:43:16: start X-correlation... INFO @ Sat, 15 Jan 2022 20:43:16: end of X-cor INFO @ Sat, 15 Jan 2022 20:43:16: #2 finished! INFO @ Sat, 15 Jan 2022 20:43:16: #2 predicted fragment length is 55 bps INFO @ Sat, 15 Jan 2022 20:43:16: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sat, 15 Jan 2022 20:43:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.10_model.r WARNING @ Sat, 15 Jan 2022 20:43:16: #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 20:43:16: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Sat, 15 Jan 2022 20:43:16: #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 20:43:16: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:43:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:43:20: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:43:20: 1000000 INFO @ Sat, 15 Jan 2022 20:43:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:43:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:43:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.10_summits.bed INFO @ Sat, 15 Jan 2022 20:43:22: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (570 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:43:27: 2000000 INFO @ Sat, 15 Jan 2022 20:43:33: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:43:39: 4000000 INFO @ Sat, 15 Jan 2022 20:43:46: 5000000 INFO @ Sat, 15 Jan 2022 20:43:47: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:43:47: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:43:47: #1 total tags in treatment: 2574511 INFO @ Sat, 15 Jan 2022 20:43:47: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:43:47: #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 20:43:47: #1 tags after filtering in treatment: 1952830 INFO @ Sat, 15 Jan 2022 20:43:47: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 15 Jan 2022 20:43:47: #1 finished! INFO @ Sat, 15 Jan 2022 20:43:47: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:43:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:43:47: #2 number of paired peaks: 559 WARNING @ Sat, 15 Jan 2022 20:43:47: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Sat, 15 Jan 2022 20:43:47: start model_add_line... INFO @ Sat, 15 Jan 2022 20:43:47: start X-correlation... INFO @ Sat, 15 Jan 2022 20:43:47: end of X-cor INFO @ Sat, 15 Jan 2022 20:43:47: #2 finished! INFO @ Sat, 15 Jan 2022 20:43:47: #2 predicted fragment length is 55 bps INFO @ Sat, 15 Jan 2022 20:43:47: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sat, 15 Jan 2022 20:43:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.20_model.r WARNING @ Sat, 15 Jan 2022 20:43:47: #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 20:43:47: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Sat, 15 Jan 2022 20:43:47: #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 20:43:47: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:43:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:43:52: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:43:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:43:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:43:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468516/SRX10468516.20_summits.bed INFO @ Sat, 15 Jan 2022 20:43:54: Done! BigWig に変換しました。 pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (308 records, 4 fields): 2 millis CompletedMACS2peakCalling