Job ID = 14520747 SRX = SRX8245508 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9093941 spots for SRR11684719/SRR11684719.sra Written 9093941 spots for SRR11684719/SRR11684719.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: 00:03:27 9093941 reads; of these: 9093941 (100.00%) were paired; of these: 5956109 (65.50%) aligned concordantly 0 times 2889744 (31.78%) aligned concordantly exactly 1 time 248088 (2.73%) aligned concordantly >1 times ---- 5956109 pairs aligned concordantly 0 times; of these: 31713 (0.53%) aligned discordantly 1 time ---- 5924396 pairs aligned 0 times concordantly or discordantly; of these: 11848792 mates make up the pairs; of these: 8614516 (72.70%) aligned 0 times 2898508 (24.46%) aligned exactly 1 time 335768 (2.83%) aligned >1 times 52.64% overall alignment rate Time searching: 00:03:27 Overall time: 00:03:27 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] 277679 / 3169030 = 0.0876 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 19:53:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.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 19:53:00: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:53:00: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:53:05: 1000000 INFO @ Sat, 15 Jan 2022 19:53:09: 2000000 INFO @ Sat, 15 Jan 2022 19:53:13: 3000000 INFO @ Sat, 15 Jan 2022 19:53:18: 4000000 INFO @ Sat, 15 Jan 2022 19:53:22: 5000000 INFO @ Sat, 15 Jan 2022 19:53:27: 6000000 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 19:53:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.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 19:53:30: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:53:30: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:53:31: 7000000 INFO @ Sat, 15 Jan 2022 19:53:35: 1000000 INFO @ Sat, 15 Jan 2022 19:53:36: 8000000 INFO @ Sat, 15 Jan 2022 19:53:40: 2000000 INFO @ Sat, 15 Jan 2022 19:53:40: 9000000 INFO @ Sat, 15 Jan 2022 19:53:40: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:53:40: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:53:40: #1 total tags in treatment: 2860983 INFO @ Sat, 15 Jan 2022 19:53:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:53:40: #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 19:53:41: #1 tags after filtering in treatment: 1655754 INFO @ Sat, 15 Jan 2022 19:53:41: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 15 Jan 2022 19:53:41: #1 finished! INFO @ Sat, 15 Jan 2022 19:53:41: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:53:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:53:41: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 19:53:41: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 19:53:41: start model_add_line... INFO @ Sat, 15 Jan 2022 19:53:41: start X-correlation... INFO @ Sat, 15 Jan 2022 19:53:41: end of X-cor INFO @ Sat, 15 Jan 2022 19:53:41: #2 finished! INFO @ Sat, 15 Jan 2022 19:53:41: #2 predicted fragment length is 64 bps INFO @ Sat, 15 Jan 2022 19:53:41: #2 alternative fragment length(s) may be 10,33,53,64,90,134,193,208,241,249,278,340,346,375,396,415,477,509,558,576 bps INFO @ Sat, 15 Jan 2022 19:53:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.05_model.r WARNING @ Sat, 15 Jan 2022 19:53:41: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:53:41: #2 You may need to consider one of the other alternative d(s): 10,33,53,64,90,134,193,208,241,249,278,340,346,375,396,415,477,509,558,576 WARNING @ Sat, 15 Jan 2022 19:53:41: #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 19:53:41: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:53:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:53:44: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:53:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:53:45: 3000000 INFO @ Sat, 15 Jan 2022 19:53:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:53:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.05_summits.bed INFO @ Sat, 15 Jan 2022 19:53:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (11 records, 4 fields): 56 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:53:50: 4000000 INFO @ Sat, 15 Jan 2022 19:53:54: 5000000 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 19:53:59: 6000000 INFO @ Sat, 15 Jan 2022 19:54:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.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 19:54:00: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:54:00: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:54:05: 7000000 INFO @ Sat, 15 Jan 2022 19:54:05: 1000000 INFO @ Sat, 15 Jan 2022 19:54:10: 2000000 INFO @ Sat, 15 Jan 2022 19:54:10: 8000000 INFO @ Sat, 15 Jan 2022 19:54:15: 3000000 INFO @ Sat, 15 Jan 2022 19:54:15: 9000000 INFO @ Sat, 15 Jan 2022 19:54:15: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:54:15: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:54:15: #1 total tags in treatment: 2860983 INFO @ Sat, 15 Jan 2022 19:54:15: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:54:15: #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 19:54:15: #1 tags after filtering in treatment: 1655754 INFO @ Sat, 15 Jan 2022 19:54:15: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 15 Jan 2022 19:54:15: #1 finished! INFO @ Sat, 15 Jan 2022 19:54:15: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:54:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:54:15: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 19:54:15: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 19:54:15: start model_add_line... INFO @ Sat, 15 Jan 2022 19:54:15: start X-correlation... INFO @ Sat, 15 Jan 2022 19:54:15: end of X-cor INFO @ Sat, 15 Jan 2022 19:54:15: #2 finished! INFO @ Sat, 15 Jan 2022 19:54:15: #2 predicted fragment length is 64 bps INFO @ Sat, 15 Jan 2022 19:54:15: #2 alternative fragment length(s) may be 10,33,53,64,90,134,193,208,241,249,278,340,346,375,396,415,477,509,558,576 bps INFO @ Sat, 15 Jan 2022 19:54:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.10_model.r WARNING @ Sat, 15 Jan 2022 19:54:15: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:54:15: #2 You may need to consider one of the other alternative d(s): 10,33,53,64,90,134,193,208,241,249,278,340,346,375,396,415,477,509,558,576 WARNING @ Sat, 15 Jan 2022 19:54:15: #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 19:54:15: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:54:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:54:18: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:54:19: 4000000 INFO @ Sat, 15 Jan 2022 19:54:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:54:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:54:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.10_summits.bed INFO @ Sat, 15 Jan 2022 19:54:19: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:54:24: 5000000 INFO @ Sat, 15 Jan 2022 19:54:30: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:54:35: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:54:41: 8000000 INFO @ Sat, 15 Jan 2022 19:54:46: 9000000 INFO @ Sat, 15 Jan 2022 19:54:46: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:54:46: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:54:46: #1 total tags in treatment: 2860983 INFO @ Sat, 15 Jan 2022 19:54:46: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:54:46: #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 19:54:46: #1 tags after filtering in treatment: 1655754 INFO @ Sat, 15 Jan 2022 19:54:46: #1 Redundant rate of treatment: 0.42 INFO @ Sat, 15 Jan 2022 19:54:46: #1 finished! INFO @ Sat, 15 Jan 2022 19:54:46: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:54:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:54:47: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 19:54:47: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 19:54:47: start model_add_line... INFO @ Sat, 15 Jan 2022 19:54:47: start X-correlation... INFO @ Sat, 15 Jan 2022 19:54:47: end of X-cor INFO @ Sat, 15 Jan 2022 19:54:47: #2 finished! INFO @ Sat, 15 Jan 2022 19:54:47: #2 predicted fragment length is 64 bps INFO @ Sat, 15 Jan 2022 19:54:47: #2 alternative fragment length(s) may be 10,33,53,64,90,134,193,208,241,249,278,340,346,375,396,415,477,509,558,576 bps INFO @ Sat, 15 Jan 2022 19:54:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.20_model.r WARNING @ Sat, 15 Jan 2022 19:54:47: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:54:47: #2 You may need to consider one of the other alternative d(s): 10,33,53,64,90,134,193,208,241,249,278,340,346,375,396,415,477,509,558,576 WARNING @ Sat, 15 Jan 2022 19:54:47: #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 19:54:47: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:54:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:54:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:54:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:54:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:54:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245508/SRX8245508.20_summits.bed INFO @ Sat, 15 Jan 2022 19:54:51: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 308 millis CompletedMACS2peakCalling