Job ID = 14521515 SRX = SRX10468493 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4246398 spots for SRR14094804/SRR14094804.sra Written 4246398 spots for SRR14094804/SRR14094804.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: 00:01:42 4246398 reads; of these: 4246398 (100.00%) were paired; of these: 1498896 (35.30%) aligned concordantly 0 times 1755000 (41.33%) aligned concordantly exactly 1 time 992502 (23.37%) aligned concordantly >1 times ---- 1498896 pairs aligned concordantly 0 times; of these: 3524 (0.24%) aligned discordantly 1 time ---- 1495372 pairs aligned 0 times concordantly or discordantly; of these: 2990744 mates make up the pairs; of these: 2928552 (97.92%) aligned 0 times 33512 (1.12%) aligned exactly 1 time 28680 (0.96%) aligned >1 times 65.52% overall alignment rate Time searching: 00:01:42 Overall time: 00:01:42 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] 345042 / 2747835 = 0.1256 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 21:09:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.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 21:09:23: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:09:23: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:09:29: 1000000 INFO @ Sat, 15 Jan 2022 21:09:35: 2000000 INFO @ Sat, 15 Jan 2022 21:09:40: 3000000 INFO @ Sat, 15 Jan 2022 21:09:45: 4000000 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 21:09:50: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 21:09:50: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 21:09:50: #1 total tags in treatment: 2402498 INFO @ Sat, 15 Jan 2022 21:09:50: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:09:50: #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 21:09:50: #1 tags after filtering in treatment: 1661317 INFO @ Sat, 15 Jan 2022 21:09:50: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Jan 2022 21:09:50: #1 finished! INFO @ Sat, 15 Jan 2022 21:09:50: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:09:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:09:50: #2 number of paired peaks: 134 WARNING @ Sat, 15 Jan 2022 21:09:50: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Sat, 15 Jan 2022 21:09:50: start model_add_line... INFO @ Sat, 15 Jan 2022 21:09:50: start X-correlation... INFO @ Sat, 15 Jan 2022 21:09:50: end of X-cor INFO @ Sat, 15 Jan 2022 21:09:50: #2 finished! INFO @ Sat, 15 Jan 2022 21:09:50: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 21:09:50: #2 alternative fragment length(s) may be 3,13,18,31,45,70 bps INFO @ Sat, 15 Jan 2022 21:09:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.05_model.r WARNING @ Sat, 15 Jan 2022 21:09:50: #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 21:09:50: #2 You may need to consider one of the other alternative d(s): 3,13,18,31,45,70 WARNING @ Sat, 15 Jan 2022 21:09:50: #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 21:09:50: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:09:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:09:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.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 21:09:52: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:09:52: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:09:53: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:09:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:09:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:09:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.05_summits.bed INFO @ Sat, 15 Jan 2022 21:09:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:09:58: 1000000 INFO @ Sat, 15 Jan 2022 21:10:04: 2000000 INFO @ Sat, 15 Jan 2022 21:10:09: 3000000 INFO @ Sat, 15 Jan 2022 21:10:14: 4000000 INFO @ Sat, 15 Jan 2022 21:10:18: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 21:10:18: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 21:10:18: #1 total tags in treatment: 2402498 INFO @ Sat, 15 Jan 2022 21:10:18: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:10:18: #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 21:10:18: #1 tags after filtering in treatment: 1661317 INFO @ Sat, 15 Jan 2022 21:10:18: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Jan 2022 21:10:18: #1 finished! INFO @ Sat, 15 Jan 2022 21:10:18: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:10:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:10:19: #2 number of paired peaks: 134 WARNING @ Sat, 15 Jan 2022 21:10:19: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Sat, 15 Jan 2022 21:10:19: start model_add_line... INFO @ Sat, 15 Jan 2022 21:10:19: start X-correlation... INFO @ Sat, 15 Jan 2022 21:10:19: end of X-cor INFO @ Sat, 15 Jan 2022 21:10:19: #2 finished! INFO @ Sat, 15 Jan 2022 21:10:19: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 21:10:19: #2 alternative fragment length(s) may be 3,13,18,31,45,70 bps INFO @ Sat, 15 Jan 2022 21:10:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.10_model.r WARNING @ Sat, 15 Jan 2022 21:10:19: #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 21:10:19: #2 You may need to consider one of the other alternative d(s): 3,13,18,31,45,70 WARNING @ Sat, 15 Jan 2022 21:10:19: #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 21:10:19: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:10:19: #3 Pre-compute pvalue-qvalue table... 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 21:10:21: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:10:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.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 21:10:22: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:10:22: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:10:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:10:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:10:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.10_summits.bed INFO @ Sat, 15 Jan 2022 21:10:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:10:27: 1000000 INFO @ Sat, 15 Jan 2022 21:10:33: 2000000 INFO @ Sat, 15 Jan 2022 21:10:38: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:10:43: 4000000 INFO @ Sat, 15 Jan 2022 21:10:47: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 21:10:47: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 21:10:47: #1 total tags in treatment: 2402498 INFO @ Sat, 15 Jan 2022 21:10:47: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:10:47: #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 21:10:47: #1 tags after filtering in treatment: 1661317 INFO @ Sat, 15 Jan 2022 21:10:47: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Jan 2022 21:10:47: #1 finished! INFO @ Sat, 15 Jan 2022 21:10:47: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:10:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:10:48: #2 number of paired peaks: 134 WARNING @ Sat, 15 Jan 2022 21:10:48: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Sat, 15 Jan 2022 21:10:48: start model_add_line... INFO @ Sat, 15 Jan 2022 21:10:48: start X-correlation... INFO @ Sat, 15 Jan 2022 21:10:48: end of X-cor INFO @ Sat, 15 Jan 2022 21:10:48: #2 finished! INFO @ Sat, 15 Jan 2022 21:10:48: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 21:10:48: #2 alternative fragment length(s) may be 3,13,18,31,45,70 bps INFO @ Sat, 15 Jan 2022 21:10:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.20_model.r WARNING @ Sat, 15 Jan 2022 21:10:48: #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 21:10:48: #2 You may need to consider one of the other alternative d(s): 3,13,18,31,45,70 WARNING @ Sat, 15 Jan 2022 21:10:48: #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 21:10:48: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:10:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:10:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:10:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:10:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:10:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468493/SRX10468493.20_summits.bed INFO @ Sat, 15 Jan 2022 21:10:52: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling