Job ID = 14521217 SRX = SRX10468515 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4347412 spots for SRR14094826/SRR14094826.sra Written 4347412 spots for SRR14094826/SRR14094826.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: 00:02:42 4347412 reads; of these: 4347412 (100.00%) were paired; of these: 901420 (20.73%) aligned concordantly 0 times 2928908 (67.37%) aligned concordantly exactly 1 time 517084 (11.89%) aligned concordantly >1 times ---- 901420 pairs aligned concordantly 0 times; of these: 30901 (3.43%) aligned discordantly 1 time ---- 870519 pairs aligned 0 times concordantly or discordantly; of these: 1741038 mates make up the pairs; of these: 1663685 (95.56%) aligned 0 times 55800 (3.20%) aligned exactly 1 time 21553 (1.24%) aligned >1 times 80.87% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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] 206190 / 3459341 = 0.0596 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 20:43:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.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 20:43:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:43:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:43:18: 1000000 INFO @ Sat, 15 Jan 2022 20:43:23: 2000000 INFO @ Sat, 15 Jan 2022 20:43:28: 3000000 INFO @ Sat, 15 Jan 2022 20:43:33: 4000000 INFO @ Sat, 15 Jan 2022 20:43:38: 5000000 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 20:43:42: 6000000 INFO @ Sat, 15 Jan 2022 20:43:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.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 20:43:43: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:43:43: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:43:46: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:43:46: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:43:46: #1 total tags in treatment: 3240183 INFO @ Sat, 15 Jan 2022 20:43:46: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:43:46: #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 20:43:46: #1 tags after filtering in treatment: 2322707 INFO @ Sat, 15 Jan 2022 20:43:46: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 20:43:46: #1 finished! INFO @ Sat, 15 Jan 2022 20:43:46: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:43:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:43:46: #2 number of paired peaks: 561 WARNING @ Sat, 15 Jan 2022 20:43:46: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Sat, 15 Jan 2022 20:43:46: start model_add_line... INFO @ Sat, 15 Jan 2022 20:43:46: start X-correlation... INFO @ Sat, 15 Jan 2022 20:43:46: end of X-cor INFO @ Sat, 15 Jan 2022 20:43:46: #2 finished! INFO @ Sat, 15 Jan 2022 20:43:46: #2 predicted fragment length is 42 bps INFO @ Sat, 15 Jan 2022 20:43:46: #2 alternative fragment length(s) may be 3,42 bps INFO @ Sat, 15 Jan 2022 20:43:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.05_model.r WARNING @ Sat, 15 Jan 2022 20:43:46: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:43:46: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Sat, 15 Jan 2022 20:43:46: #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 20:43:46: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:43:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:43:50: 1000000 INFO @ Sat, 15 Jan 2022 20:43:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:43:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:43:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:43:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.05_summits.bed INFO @ Sat, 15 Jan 2022 20:43:52: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1044 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:43:57: 2000000 INFO @ Sat, 15 Jan 2022 20:44:03: 3000000 INFO @ Sat, 15 Jan 2022 20:44:10: 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 20:44:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.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 20:44:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:44:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:44:16: 5000000 INFO @ Sat, 15 Jan 2022 20:44:20: 1000000 INFO @ Sat, 15 Jan 2022 20:44:23: 6000000 INFO @ Sat, 15 Jan 2022 20:44:26: 2000000 INFO @ Sat, 15 Jan 2022 20:44:27: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:44:27: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:44:27: #1 total tags in treatment: 3240183 INFO @ Sat, 15 Jan 2022 20:44:27: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:44:27: #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 20:44:27: #1 tags after filtering in treatment: 2322707 INFO @ Sat, 15 Jan 2022 20:44:27: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 20:44:27: #1 finished! INFO @ Sat, 15 Jan 2022 20:44:27: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:44:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:44:28: #2 number of paired peaks: 561 WARNING @ Sat, 15 Jan 2022 20:44:28: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Sat, 15 Jan 2022 20:44:28: start model_add_line... INFO @ Sat, 15 Jan 2022 20:44:28: start X-correlation... INFO @ Sat, 15 Jan 2022 20:44:28: end of X-cor INFO @ Sat, 15 Jan 2022 20:44:28: #2 finished! INFO @ Sat, 15 Jan 2022 20:44:28: #2 predicted fragment length is 42 bps INFO @ Sat, 15 Jan 2022 20:44:28: #2 alternative fragment length(s) may be 3,42 bps INFO @ Sat, 15 Jan 2022 20:44:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.10_model.r WARNING @ Sat, 15 Jan 2022 20:44:28: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:44:28: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Sat, 15 Jan 2022 20:44:28: #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 20:44:28: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:44:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:44:32: 3000000 INFO @ Sat, 15 Jan 2022 20:44:32: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:44:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:44:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:44:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.10_summits.bed INFO @ Sat, 15 Jan 2022 20:44:34: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (590 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:44:37: 4000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:44:43: 5000000 INFO @ Sat, 15 Jan 2022 20:44:48: 6000000 INFO @ Sat, 15 Jan 2022 20:44:51: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:44:51: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:44:51: #1 total tags in treatment: 3240183 INFO @ Sat, 15 Jan 2022 20:44:51: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:44:51: #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 20:44:51: #1 tags after filtering in treatment: 2322707 INFO @ Sat, 15 Jan 2022 20:44:51: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 20:44:51: #1 finished! INFO @ Sat, 15 Jan 2022 20:44:51: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:44:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:44:52: #2 number of paired peaks: 561 WARNING @ Sat, 15 Jan 2022 20:44:52: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Sat, 15 Jan 2022 20:44:52: start model_add_line... INFO @ Sat, 15 Jan 2022 20:44:52: start X-correlation... INFO @ Sat, 15 Jan 2022 20:44:52: end of X-cor INFO @ Sat, 15 Jan 2022 20:44:52: #2 finished! INFO @ Sat, 15 Jan 2022 20:44:52: #2 predicted fragment length is 42 bps INFO @ Sat, 15 Jan 2022 20:44:52: #2 alternative fragment length(s) may be 3,42 bps INFO @ Sat, 15 Jan 2022 20:44:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.20_model.r WARNING @ Sat, 15 Jan 2022 20:44:52: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:44:52: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Sat, 15 Jan 2022 20:44:52: #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 20:44:52: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:44:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:44:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:44:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:44:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:44:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468515/SRX10468515.20_summits.bed INFO @ Sat, 15 Jan 2022 20:44:58: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (246 records, 4 fields): 1 millis CompletedMACS2peakCalling