Job ID = 7107012 SRX = SRX6911543 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12281072 spots for SRR10191154/SRR10191154.sra Written 12281072 spots for SRR10191154/SRR10191154.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: 00:13:41 12281072 reads; of these: 12281072 (100.00%) were paired; of these: 2647802 (21.56%) aligned concordantly 0 times 8075793 (65.76%) aligned concordantly exactly 1 time 1557477 (12.68%) aligned concordantly >1 times ---- 2647802 pairs aligned concordantly 0 times; of these: 508874 (19.22%) aligned discordantly 1 time ---- 2138928 pairs aligned 0 times concordantly or discordantly; of these: 4277856 mates make up the pairs; of these: 3598509 (84.12%) aligned 0 times 391160 (9.14%) aligned exactly 1 time 288187 (6.74%) aligned >1 times 85.35% overall alignment rate Time searching: 00:13:41 Overall time: 00:13:41 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_sort_core] merging from 12 files... [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] 1418945 / 10141479 = 0.1399 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 13:20:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.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 13:20:26: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:20:26: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:20:33: 1000000 INFO @ Wed, 22 Jul 2020 13:20:40: 2000000 INFO @ Wed, 22 Jul 2020 13:20:47: 3000000 INFO @ Wed, 22 Jul 2020 13:20:54: 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 13:20:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.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 13:20:56: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:20:56: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:21:01: 5000000 INFO @ Wed, 22 Jul 2020 13:21:02: 1000000 INFO @ Wed, 22 Jul 2020 13:21:08: 6000000 INFO @ Wed, 22 Jul 2020 13:21:09: 2000000 INFO @ Wed, 22 Jul 2020 13:21:15: 3000000 INFO @ Wed, 22 Jul 2020 13:21:16: 7000000 INFO @ Wed, 22 Jul 2020 13:21:22: 4000000 INFO @ Wed, 22 Jul 2020 13:21:23: 8000000 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 13:21:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.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 13:21:26: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:21:26: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:21:28: 5000000 INFO @ Wed, 22 Jul 2020 13:21:31: 9000000 INFO @ Wed, 22 Jul 2020 13:21:34: 1000000 INFO @ Wed, 22 Jul 2020 13:21:35: 6000000 INFO @ Wed, 22 Jul 2020 13:21:38: 10000000 INFO @ Wed, 22 Jul 2020 13:21:41: 7000000 INFO @ Wed, 22 Jul 2020 13:21:41: 2000000 INFO @ Wed, 22 Jul 2020 13:21:46: 11000000 INFO @ Wed, 22 Jul 2020 13:21:48: 8000000 INFO @ Wed, 22 Jul 2020 13:21:49: 3000000 INFO @ Wed, 22 Jul 2020 13:21:53: 12000000 INFO @ Wed, 22 Jul 2020 13:21:54: 9000000 INFO @ Wed, 22 Jul 2020 13:21:56: 4000000 INFO @ Wed, 22 Jul 2020 13:22:01: 10000000 INFO @ Wed, 22 Jul 2020 13:22:01: 13000000 INFO @ Wed, 22 Jul 2020 13:22:04: 5000000 INFO @ Wed, 22 Jul 2020 13:22:07: 11000000 INFO @ Wed, 22 Jul 2020 13:22:08: 14000000 INFO @ Wed, 22 Jul 2020 13:22:11: 6000000 INFO @ Wed, 22 Jul 2020 13:22:14: 12000000 INFO @ Wed, 22 Jul 2020 13:22:15: 15000000 INFO @ Wed, 22 Jul 2020 13:22:19: 7000000 INFO @ Wed, 22 Jul 2020 13:22:20: 13000000 INFO @ Wed, 22 Jul 2020 13:22:23: 16000000 INFO @ Wed, 22 Jul 2020 13:22:26: 14000000 INFO @ Wed, 22 Jul 2020 13:22:27: 8000000 INFO @ Wed, 22 Jul 2020 13:22:30: 17000000 INFO @ Wed, 22 Jul 2020 13:22:33: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 13:22:34: 9000000 INFO @ Wed, 22 Jul 2020 13:22:38: 18000000 INFO @ Wed, 22 Jul 2020 13:22:39: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:22:39: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:22:39: #1 total tags in treatment: 8256389 INFO @ Wed, 22 Jul 2020 13:22:39: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:22:39: #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 13:22:39: #1 tags after filtering in treatment: 4317695 INFO @ Wed, 22 Jul 2020 13:22:39: #1 Redundant rate of treatment: 0.48 INFO @ Wed, 22 Jul 2020 13:22:39: #1 finished! INFO @ Wed, 22 Jul 2020 13:22:39: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:22:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:22:39: #2 number of paired peaks: 121 WARNING @ Wed, 22 Jul 2020 13:22:39: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Wed, 22 Jul 2020 13:22:39: start model_add_line... INFO @ Wed, 22 Jul 2020 13:22:39: start X-correlation... INFO @ Wed, 22 Jul 2020 13:22:39: end of X-cor INFO @ Wed, 22 Jul 2020 13:22:39: #2 finished! INFO @ Wed, 22 Jul 2020 13:22:39: #2 predicted fragment length is 41 bps INFO @ Wed, 22 Jul 2020 13:22:39: #2 alternative fragment length(s) may be 41,91,118,165,227,253,265,295,321,358,383,412,414,422,460,481,498,543,551 bps INFO @ Wed, 22 Jul 2020 13:22:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.05_model.r WARNING @ Wed, 22 Jul 2020 13:22:39: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:22:39: #2 You may need to consider one of the other alternative d(s): 41,91,118,165,227,253,265,295,321,358,383,412,414,422,460,481,498,543,551 WARNING @ Wed, 22 Jul 2020 13:22:39: #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 13:22:39: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:22:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:22:39: 16000000 INFO @ Wed, 22 Jul 2020 13:22:42: 10000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 13:22:46: 17000000 INFO @ Wed, 22 Jul 2020 13:22:46: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:22:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.05_peaks.xls INFO @ Wed, 22 Jul 2020 13:22:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:22:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.05_summits.bed INFO @ Wed, 22 Jul 2020 13:22:48: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (65 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 13:22:49: 11000000 INFO @ Wed, 22 Jul 2020 13:22:52: 18000000 INFO @ Wed, 22 Jul 2020 13:22:53: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:22:53: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:22:53: #1 total tags in treatment: 8256389 INFO @ Wed, 22 Jul 2020 13:22:53: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:22:53: #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 13:22:53: #1 tags after filtering in treatment: 4317695 INFO @ Wed, 22 Jul 2020 13:22:53: #1 Redundant rate of treatment: 0.48 INFO @ Wed, 22 Jul 2020 13:22:53: #1 finished! INFO @ Wed, 22 Jul 2020 13:22:53: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:22:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:22:54: #2 number of paired peaks: 121 WARNING @ Wed, 22 Jul 2020 13:22:54: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Wed, 22 Jul 2020 13:22:54: start model_add_line... INFO @ Wed, 22 Jul 2020 13:22:54: start X-correlation... INFO @ Wed, 22 Jul 2020 13:22:54: end of X-cor INFO @ Wed, 22 Jul 2020 13:22:54: #2 finished! INFO @ Wed, 22 Jul 2020 13:22:54: #2 predicted fragment length is 41 bps INFO @ Wed, 22 Jul 2020 13:22:54: #2 alternative fragment length(s) may be 41,91,118,165,227,253,265,295,321,358,383,412,414,422,460,481,498,543,551 bps INFO @ Wed, 22 Jul 2020 13:22:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.10_model.r WARNING @ Wed, 22 Jul 2020 13:22:54: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:22:54: #2 You may need to consider one of the other alternative d(s): 41,91,118,165,227,253,265,295,321,358,383,412,414,422,460,481,498,543,551 WARNING @ Wed, 22 Jul 2020 13:22:54: #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 13:22:54: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:22:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:22:57: 12000000 INFO @ Wed, 22 Jul 2020 13:23:01: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:23:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.10_peaks.xls INFO @ Wed, 22 Jul 2020 13:23:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:23:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.10_summits.bed INFO @ Wed, 22 Jul 2020 13:23:04: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (4 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 13:23:04: 13000000 INFO @ Wed, 22 Jul 2020 13:23:11: 14000000 INFO @ Wed, 22 Jul 2020 13:23:18: 15000000 INFO @ Wed, 22 Jul 2020 13:23:26: 16000000 INFO @ Wed, 22 Jul 2020 13:23:33: 17000000 INFO @ Wed, 22 Jul 2020 13:23:40: 18000000 INFO @ Wed, 22 Jul 2020 13:23:41: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:23:41: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:23:41: #1 total tags in treatment: 8256389 INFO @ Wed, 22 Jul 2020 13:23:41: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:23:41: #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 13:23:41: #1 tags after filtering in treatment: 4317695 INFO @ Wed, 22 Jul 2020 13:23:41: #1 Redundant rate of treatment: 0.48 INFO @ Wed, 22 Jul 2020 13:23:41: #1 finished! INFO @ Wed, 22 Jul 2020 13:23:41: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:23:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:23:42: #2 number of paired peaks: 121 WARNING @ Wed, 22 Jul 2020 13:23:42: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Wed, 22 Jul 2020 13:23:42: start model_add_line... INFO @ Wed, 22 Jul 2020 13:23:42: start X-correlation... INFO @ Wed, 22 Jul 2020 13:23:42: end of X-cor INFO @ Wed, 22 Jul 2020 13:23:42: #2 finished! INFO @ Wed, 22 Jul 2020 13:23:42: #2 predicted fragment length is 41 bps INFO @ Wed, 22 Jul 2020 13:23:42: #2 alternative fragment length(s) may be 41,91,118,165,227,253,265,295,321,358,383,412,414,422,460,481,498,543,551 bps INFO @ Wed, 22 Jul 2020 13:23:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.20_model.r WARNING @ Wed, 22 Jul 2020 13:23:42: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:23:42: #2 You may need to consider one of the other alternative d(s): 41,91,118,165,227,253,265,295,321,358,383,412,414,422,460,481,498,543,551 WARNING @ Wed, 22 Jul 2020 13:23:42: #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 13:23:42: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:23:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:23:48: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:23:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.20_peaks.xls INFO @ Wed, 22 Jul 2020 13:23:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:23:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911543/SRX6911543.20_summits.bed INFO @ Wed, 22 Jul 2020 13:23:51: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling