Job ID = 14521314 SRX = SRX10468543 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7607202 spots for SRR14094854/SRR14094854.sra Written 7607202 spots for SRR14094854/SRR14094854.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: 00:03:48 7607202 reads; of these: 7607202 (100.00%) were paired; of these: 969590 (12.75%) aligned concordantly 0 times 5721392 (75.21%) aligned concordantly exactly 1 time 916220 (12.04%) aligned concordantly >1 times ---- 969590 pairs aligned concordantly 0 times; of these: 166566 (17.18%) aligned discordantly 1 time ---- 803024 pairs aligned 0 times concordantly or discordantly; of these: 1606048 mates make up the pairs; of these: 1380416 (85.95%) aligned 0 times 136788 (8.52%) aligned exactly 1 time 88844 (5.53%) aligned >1 times 90.93% overall alignment rate Time searching: 00:03:48 Overall time: 00:03:48 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] 388472 / 6668423 = 0.0583 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 20:56:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.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 20:56:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:56:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:56:46: 1000000 INFO @ Sat, 15 Jan 2022 20:56:50: 2000000 INFO @ Sat, 15 Jan 2022 20:56:54: 3000000 INFO @ Sat, 15 Jan 2022 20:56:57: 4000000 INFO @ Sat, 15 Jan 2022 20:57:01: 5000000 INFO @ Sat, 15 Jan 2022 20:57:05: 6000000 INFO @ Sat, 15 Jan 2022 20:57:09: 7000000 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 20:57:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.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 20:57:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:57:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:57:13: 8000000 INFO @ Sat, 15 Jan 2022 20:57:16: 1000000 INFO @ Sat, 15 Jan 2022 20:57:17: 9000000 INFO @ Sat, 15 Jan 2022 20:57:20: 2000000 INFO @ Sat, 15 Jan 2022 20:57:21: 10000000 INFO @ Sat, 15 Jan 2022 20:57:24: 3000000 INFO @ Sat, 15 Jan 2022 20:57:25: 11000000 INFO @ Sat, 15 Jan 2022 20:57:28: 4000000 INFO @ Sat, 15 Jan 2022 20:57:29: 12000000 INFO @ Sat, 15 Jan 2022 20:57:33: 5000000 INFO @ Sat, 15 Jan 2022 20:57:33: 13000000 INFO @ Sat, 15 Jan 2022 20:57:33: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:57:33: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:57:33: #1 total tags in treatment: 6250164 INFO @ Sat, 15 Jan 2022 20:57:33: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:57:33: #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 20:57:33: #1 tags after filtering in treatment: 3953535 INFO @ Sat, 15 Jan 2022 20:57:33: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 15 Jan 2022 20:57:33: #1 finished! INFO @ Sat, 15 Jan 2022 20:57:33: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:57:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:57:34: #2 number of paired peaks: 225 WARNING @ Sat, 15 Jan 2022 20:57:34: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Sat, 15 Jan 2022 20:57:34: start model_add_line... INFO @ Sat, 15 Jan 2022 20:57:34: start X-correlation... INFO @ Sat, 15 Jan 2022 20:57:34: end of X-cor INFO @ Sat, 15 Jan 2022 20:57:34: #2 finished! INFO @ Sat, 15 Jan 2022 20:57:34: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 20:57:34: #2 alternative fragment length(s) may be 3,15 bps INFO @ Sat, 15 Jan 2022 20:57:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.05_model.r WARNING @ Sat, 15 Jan 2022 20:57:34: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:57:34: #2 You may need to consider one of the other alternative d(s): 3,15 WARNING @ Sat, 15 Jan 2022 20:57:34: #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 20:57:34: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:57:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:57:37: 6000000 INFO @ Sat, 15 Jan 2022 20:57:39: #3 Call peaks for each chromosome... 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 20:57:40: 7000000 INFO @ Sat, 15 Jan 2022 20:57:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:57:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:57:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.05_summits.bed INFO @ Sat, 15 Jan 2022 20:57:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:57:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.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 20:57:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:57:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:57:44: 8000000 INFO @ Sat, 15 Jan 2022 20:57:46: 1000000 INFO @ Sat, 15 Jan 2022 20:57:48: 9000000 INFO @ Sat, 15 Jan 2022 20:57:50: 2000000 INFO @ Sat, 15 Jan 2022 20:57:52: 10000000 INFO @ Sat, 15 Jan 2022 20:57:54: 3000000 INFO @ Sat, 15 Jan 2022 20:57:56: 11000000 INFO @ Sat, 15 Jan 2022 20:57:58: 4000000 INFO @ Sat, 15 Jan 2022 20:58:00: 12000000 INFO @ Sat, 15 Jan 2022 20:58:03: 5000000 INFO @ Sat, 15 Jan 2022 20:58:05: 13000000 INFO @ Sat, 15 Jan 2022 20:58:05: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:58:05: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:58:05: #1 total tags in treatment: 6250164 INFO @ Sat, 15 Jan 2022 20:58:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:58:05: #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 20:58:05: #1 tags after filtering in treatment: 3953535 INFO @ Sat, 15 Jan 2022 20:58:05: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 15 Jan 2022 20:58:05: #1 finished! INFO @ Sat, 15 Jan 2022 20:58:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:58:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:58:05: #2 number of paired peaks: 225 WARNING @ Sat, 15 Jan 2022 20:58:05: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Sat, 15 Jan 2022 20:58:05: start model_add_line... INFO @ Sat, 15 Jan 2022 20:58:05: start X-correlation... INFO @ Sat, 15 Jan 2022 20:58:05: end of X-cor INFO @ Sat, 15 Jan 2022 20:58:05: #2 finished! INFO @ Sat, 15 Jan 2022 20:58:05: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 20:58:05: #2 alternative fragment length(s) may be 3,15 bps INFO @ Sat, 15 Jan 2022 20:58:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.10_model.r WARNING @ Sat, 15 Jan 2022 20:58:05: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:58:05: #2 You may need to consider one of the other alternative d(s): 3,15 WARNING @ Sat, 15 Jan 2022 20:58:05: #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 20:58:05: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:58:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:58:07: 6000000 INFO @ Sat, 15 Jan 2022 20:58:10: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:58:11: 7000000 INFO @ Sat, 15 Jan 2022 20:58:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:58:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:58:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.10_summits.bed INFO @ Sat, 15 Jan 2022 20:58:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:58:14: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:58:18: 9000000 INFO @ Sat, 15 Jan 2022 20:58:22: 10000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:58:26: 11000000 INFO @ Sat, 15 Jan 2022 20:58:30: 12000000 INFO @ Sat, 15 Jan 2022 20:58:34: 13000000 INFO @ Sat, 15 Jan 2022 20:58:34: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:58:34: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:58:34: #1 total tags in treatment: 6250164 INFO @ Sat, 15 Jan 2022 20:58:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:58:34: #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 20:58:34: #1 tags after filtering in treatment: 3953535 INFO @ Sat, 15 Jan 2022 20:58:34: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 15 Jan 2022 20:58:34: #1 finished! INFO @ Sat, 15 Jan 2022 20:58:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:58:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:58:34: #2 number of paired peaks: 225 WARNING @ Sat, 15 Jan 2022 20:58:34: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Sat, 15 Jan 2022 20:58:34: start model_add_line... INFO @ Sat, 15 Jan 2022 20:58:34: start X-correlation... INFO @ Sat, 15 Jan 2022 20:58:34: end of X-cor INFO @ Sat, 15 Jan 2022 20:58:34: #2 finished! INFO @ Sat, 15 Jan 2022 20:58:34: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 20:58:34: #2 alternative fragment length(s) may be 3,15 bps INFO @ Sat, 15 Jan 2022 20:58:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.20_model.r WARNING @ Sat, 15 Jan 2022 20:58:34: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:58:34: #2 You may need to consider one of the other alternative d(s): 3,15 WARNING @ Sat, 15 Jan 2022 20:58:34: #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 20:58:34: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:58:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:58:39: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:58:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:58:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:58:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468543/SRX10468543.20_summits.bed INFO @ Sat, 15 Jan 2022 20:58:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling