Job ID = 14521312 SRX = SRX10468541 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5973331 spots for SRR14094852/SRR14094852.sra Written 5973331 spots for SRR14094852/SRR14094852.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: 00:02:38 5973331 reads; of these: 5973331 (100.00%) were paired; of these: 551698 (9.24%) aligned concordantly 0 times 4658399 (77.99%) aligned concordantly exactly 1 time 763234 (12.78%) aligned concordantly >1 times ---- 551698 pairs aligned concordantly 0 times; of these: 123555 (22.40%) aligned discordantly 1 time ---- 428143 pairs aligned 0 times concordantly or discordantly; of these: 856286 mates make up the pairs; of these: 693112 (80.94%) aligned 0 times 96996 (11.33%) aligned exactly 1 time 66178 (7.73%) aligned >1 times 94.20% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 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] 256386 / 5449473 = 0.0470 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 20:54:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.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 20:54:08: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:54:08: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:54:13: 1000000 INFO @ Sat, 15 Jan 2022 20:54:17: 2000000 INFO @ Sat, 15 Jan 2022 20:54:21: 3000000 INFO @ Sat, 15 Jan 2022 20:54:25: 4000000 INFO @ Sat, 15 Jan 2022 20:54:30: 5000000 INFO @ Sat, 15 Jan 2022 20:54:34: 6000000 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 20:54:38: 7000000 INFO @ Sat, 15 Jan 2022 20:54:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.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 20:54:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:54:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:54:42: 8000000 INFO @ Sat, 15 Jan 2022 20:54:43: 1000000 INFO @ Sat, 15 Jan 2022 20:54:47: 9000000 INFO @ Sat, 15 Jan 2022 20:54:47: 2000000 INFO @ Sat, 15 Jan 2022 20:54:51: 10000000 INFO @ Sat, 15 Jan 2022 20:54:52: 3000000 INFO @ Sat, 15 Jan 2022 20:54:54: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:54:54: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:54:54: #1 total tags in treatment: 5165991 INFO @ Sat, 15 Jan 2022 20:54:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:54:54: #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 20:54:55: #1 tags after filtering in treatment: 3417626 INFO @ Sat, 15 Jan 2022 20:54:55: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 15 Jan 2022 20:54:55: #1 finished! INFO @ Sat, 15 Jan 2022 20:54:55: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:54:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:54:55: #2 number of paired peaks: 317 WARNING @ Sat, 15 Jan 2022 20:54:55: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Sat, 15 Jan 2022 20:54:55: start model_add_line... INFO @ Sat, 15 Jan 2022 20:54:55: start X-correlation... INFO @ Sat, 15 Jan 2022 20:54:55: end of X-cor INFO @ Sat, 15 Jan 2022 20:54:55: #2 finished! INFO @ Sat, 15 Jan 2022 20:54:55: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 20:54:55: #2 alternative fragment length(s) may be 3,32,49 bps INFO @ Sat, 15 Jan 2022 20:54:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.05_model.r WARNING @ Sat, 15 Jan 2022 20:54:55: #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 20:54:55: #2 You may need to consider one of the other alternative d(s): 3,32,49 WARNING @ Sat, 15 Jan 2022 20:54:55: #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 20:54:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:54:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:54:56: 4000000 INFO @ Sat, 15 Jan 2022 20:54:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:55:00: 5000000 INFO @ Sat, 15 Jan 2022 20:55:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:55:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:55:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.05_summits.bed INFO @ Sat, 15 Jan 2022 20:55:01: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:55:05: 6000000 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 20:55:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.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 20:55:08: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:55:08: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:55:09: 7000000 INFO @ Sat, 15 Jan 2022 20:55:13: 1000000 INFO @ Sat, 15 Jan 2022 20:55:13: 8000000 INFO @ Sat, 15 Jan 2022 20:55:17: 2000000 INFO @ Sat, 15 Jan 2022 20:55:18: 9000000 INFO @ Sat, 15 Jan 2022 20:55:22: 3000000 INFO @ Sat, 15 Jan 2022 20:55:22: 10000000 INFO @ Sat, 15 Jan 2022 20:55:25: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:55:25: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:55:25: #1 total tags in treatment: 5165991 INFO @ Sat, 15 Jan 2022 20:55:25: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:55:25: #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 20:55:25: #1 tags after filtering in treatment: 3417626 INFO @ Sat, 15 Jan 2022 20:55:25: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 15 Jan 2022 20:55:25: #1 finished! INFO @ Sat, 15 Jan 2022 20:55:25: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:55:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:55:26: #2 number of paired peaks: 317 WARNING @ Sat, 15 Jan 2022 20:55:26: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Sat, 15 Jan 2022 20:55:26: start model_add_line... INFO @ Sat, 15 Jan 2022 20:55:26: start X-correlation... INFO @ Sat, 15 Jan 2022 20:55:26: end of X-cor INFO @ Sat, 15 Jan 2022 20:55:26: #2 finished! INFO @ Sat, 15 Jan 2022 20:55:26: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 20:55:26: #2 alternative fragment length(s) may be 3,32,49 bps INFO @ Sat, 15 Jan 2022 20:55:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.10_model.r WARNING @ Sat, 15 Jan 2022 20:55:26: #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 20:55:26: #2 You may need to consider one of the other alternative d(s): 3,32,49 WARNING @ Sat, 15 Jan 2022 20:55:26: #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 20:55:26: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:55:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:55:26: 4000000 INFO @ Sat, 15 Jan 2022 20:55:30: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:55:30: 5000000 INFO @ Sat, 15 Jan 2022 20:55:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:55:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:55:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.10_summits.bed INFO @ Sat, 15 Jan 2022 20:55:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:55:35: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:55:39: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:55:44: 8000000 INFO @ Sat, 15 Jan 2022 20:55:48: 9000000 INFO @ Sat, 15 Jan 2022 20:55:52: 10000000 INFO @ Sat, 15 Jan 2022 20:55:56: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:55:56: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:55:56: #1 total tags in treatment: 5165991 INFO @ Sat, 15 Jan 2022 20:55:56: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:55:56: #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 20:55:56: #1 tags after filtering in treatment: 3417626 INFO @ Sat, 15 Jan 2022 20:55:56: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 15 Jan 2022 20:55:56: #1 finished! INFO @ Sat, 15 Jan 2022 20:55:56: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:55:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:55:56: #2 number of paired peaks: 317 WARNING @ Sat, 15 Jan 2022 20:55:56: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Sat, 15 Jan 2022 20:55:56: start model_add_line... INFO @ Sat, 15 Jan 2022 20:55:56: start X-correlation... INFO @ Sat, 15 Jan 2022 20:55:56: end of X-cor INFO @ Sat, 15 Jan 2022 20:55:56: #2 finished! INFO @ Sat, 15 Jan 2022 20:55:56: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 20:55:56: #2 alternative fragment length(s) may be 3,32,49 bps INFO @ Sat, 15 Jan 2022 20:55:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.20_model.r WARNING @ Sat, 15 Jan 2022 20:55:56: #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 20:55:56: #2 You may need to consider one of the other alternative d(s): 3,32,49 WARNING @ Sat, 15 Jan 2022 20:55:56: #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 20:55:56: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:55:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:56:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:56:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:56:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:56:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468541/SRX10468541.20_summits.bed INFO @ Sat, 15 Jan 2022 20:56:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling