Job ID = 7099273 SRX = SRX6911500 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7915866 spots for SRR10191127/SRR10191127.sra Written 7915866 spots for SRR10191127/SRR10191127.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: 00:05:49 7915866 reads; of these: 7915866 (100.00%) were paired; of these: 4468644 (56.45%) aligned concordantly 0 times 2826122 (35.70%) aligned concordantly exactly 1 time 621100 (7.85%) aligned concordantly >1 times ---- 4468644 pairs aligned concordantly 0 times; of these: 558405 (12.50%) aligned discordantly 1 time ---- 3910239 pairs aligned 0 times concordantly or discordantly; of these: 7820478 mates make up the pairs; of these: 6727858 (86.03%) aligned 0 times 706037 (9.03%) aligned exactly 1 time 386583 (4.94%) aligned >1 times 57.50% overall alignment rate Time searching: 00:05:49 Overall time: 00:05:49 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] 1212870 / 4003273 = 0.3030 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 12:11:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.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 @ Wed, 22 Jul 2020 12:11:24: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:11:24: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:11:31: 1000000 INFO @ Wed, 22 Jul 2020 12:11:37: 2000000 INFO @ Wed, 22 Jul 2020 12:11:43: 3000000 INFO @ Wed, 22 Jul 2020 12:11:50: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 12:11:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.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 @ Wed, 22 Jul 2020 12:11:54: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:11:54: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:11:57: 5000000 INFO @ Wed, 22 Jul 2020 12:12:01: 1000000 INFO @ Wed, 22 Jul 2020 12:12:04: 6000000 INFO @ Wed, 22 Jul 2020 12:12:09: 2000000 INFO @ Wed, 22 Jul 2020 12:12:09: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:12:09: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:12:09: #1 total tags in treatment: 2404379 INFO @ Wed, 22 Jul 2020 12:12:09: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:12:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:12:09: #1 tags after filtering in treatment: 742685 INFO @ Wed, 22 Jul 2020 12:12:09: #1 Redundant rate of treatment: 0.69 INFO @ Wed, 22 Jul 2020 12:12:09: #1 finished! INFO @ Wed, 22 Jul 2020 12:12:09: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:12:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:12:10: #2 number of paired peaks: 830 WARNING @ Wed, 22 Jul 2020 12:12:10: Fewer paired peaks (830) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 830 pairs to build model! INFO @ Wed, 22 Jul 2020 12:12:10: start model_add_line... INFO @ Wed, 22 Jul 2020 12:12:10: start X-correlation... INFO @ Wed, 22 Jul 2020 12:12:10: end of X-cor INFO @ Wed, 22 Jul 2020 12:12:10: #2 finished! INFO @ Wed, 22 Jul 2020 12:12:10: #2 predicted fragment length is 153 bps INFO @ Wed, 22 Jul 2020 12:12:10: #2 alternative fragment length(s) may be 2,82,153,182 bps INFO @ Wed, 22 Jul 2020 12:12:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.05_model.r WARNING @ Wed, 22 Jul 2020 12:12:10: #2 Since the d (153) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:12:10: #2 You may need to consider one of the other alternative d(s): 2,82,153,182 WARNING @ Wed, 22 Jul 2020 12:12:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 12:12:10: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:12:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:12:12: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:12:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.05_peaks.xls INFO @ Wed, 22 Jul 2020 12:12:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:12:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.05_summits.bed INFO @ Wed, 22 Jul 2020 12:12:13: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (309 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 12:12:16: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 12:12:23: 4000000 INFO @ Wed, 22 Jul 2020 12:12:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.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 @ Wed, 22 Jul 2020 12:12:24: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:12:24: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:12:30: 5000000 INFO @ Wed, 22 Jul 2020 12:12:33: 1000000 INFO @ Wed, 22 Jul 2020 12:12:38: 6000000 INFO @ Wed, 22 Jul 2020 12:12:42: 2000000 INFO @ Wed, 22 Jul 2020 12:12:44: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:12:44: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:12:44: #1 total tags in treatment: 2404379 INFO @ Wed, 22 Jul 2020 12:12:44: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:12:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:12:44: #1 tags after filtering in treatment: 742685 INFO @ Wed, 22 Jul 2020 12:12:44: #1 Redundant rate of treatment: 0.69 INFO @ Wed, 22 Jul 2020 12:12:44: #1 finished! INFO @ Wed, 22 Jul 2020 12:12:44: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:12:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:12:44: #2 number of paired peaks: 830 WARNING @ Wed, 22 Jul 2020 12:12:44: Fewer paired peaks (830) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 830 pairs to build model! INFO @ Wed, 22 Jul 2020 12:12:44: start model_add_line... INFO @ Wed, 22 Jul 2020 12:12:44: start X-correlation... INFO @ Wed, 22 Jul 2020 12:12:44: end of X-cor INFO @ Wed, 22 Jul 2020 12:12:44: #2 finished! INFO @ Wed, 22 Jul 2020 12:12:44: #2 predicted fragment length is 153 bps INFO @ Wed, 22 Jul 2020 12:12:44: #2 alternative fragment length(s) may be 2,82,153,182 bps INFO @ Wed, 22 Jul 2020 12:12:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.10_model.r WARNING @ Wed, 22 Jul 2020 12:12:44: #2 Since the d (153) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:12:44: #2 You may need to consider one of the other alternative d(s): 2,82,153,182 WARNING @ Wed, 22 Jul 2020 12:12:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 12:12:44: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:12:44: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 12:12:47: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:12:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.10_peaks.xls INFO @ Wed, 22 Jul 2020 12:12:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:12:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.10_summits.bed INFO @ Wed, 22 Jul 2020 12:12:47: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (269 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 12:12:51: 3000000 INFO @ Wed, 22 Jul 2020 12:12:59: 4000000 INFO @ Wed, 22 Jul 2020 12:13:08: 5000000 INFO @ Wed, 22 Jul 2020 12:13:16: 6000000 INFO @ Wed, 22 Jul 2020 12:13:21: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:13:21: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:13:21: #1 total tags in treatment: 2404379 INFO @ Wed, 22 Jul 2020 12:13:21: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:13:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:13:21: #1 tags after filtering in treatment: 742685 INFO @ Wed, 22 Jul 2020 12:13:21: #1 Redundant rate of treatment: 0.69 INFO @ Wed, 22 Jul 2020 12:13:21: #1 finished! INFO @ Wed, 22 Jul 2020 12:13:21: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:13:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:13:22: #2 number of paired peaks: 830 WARNING @ Wed, 22 Jul 2020 12:13:22: Fewer paired peaks (830) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 830 pairs to build model! INFO @ Wed, 22 Jul 2020 12:13:22: start model_add_line... INFO @ Wed, 22 Jul 2020 12:13:22: start X-correlation... INFO @ Wed, 22 Jul 2020 12:13:22: end of X-cor INFO @ Wed, 22 Jul 2020 12:13:22: #2 finished! INFO @ Wed, 22 Jul 2020 12:13:22: #2 predicted fragment length is 153 bps INFO @ Wed, 22 Jul 2020 12:13:22: #2 alternative fragment length(s) may be 2,82,153,182 bps INFO @ Wed, 22 Jul 2020 12:13:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.20_model.r WARNING @ Wed, 22 Jul 2020 12:13:22: #2 Since the d (153) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:13:22: #2 You may need to consider one of the other alternative d(s): 2,82,153,182 WARNING @ Wed, 22 Jul 2020 12:13:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 12:13:22: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:13:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:13:25: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:13:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.20_peaks.xls INFO @ Wed, 22 Jul 2020 12:13:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:13:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911500/SRX6911500.20_summits.bed INFO @ Wed, 22 Jul 2020 12:13:25: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (221 records, 4 fields): 2 millis CompletedMACS2peakCalling