Job ID = 14521220 SRX = SRX10468518 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4797829 spots for SRR14094829/SRR14094829.sra Written 4797829 spots for SRR14094829/SRR14094829.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: 00:02:33 4797829 reads; of these: 4797829 (100.00%) were paired; of these: 1585506 (33.05%) aligned concordantly 0 times 2732581 (56.95%) aligned concordantly exactly 1 time 479742 (10.00%) aligned concordantly >1 times ---- 1585506 pairs aligned concordantly 0 times; of these: 36037 (2.27%) aligned discordantly 1 time ---- 1549469 pairs aligned 0 times concordantly or discordantly; of these: 3098938 mates make up the pairs; of these: 2988056 (96.42%) aligned 0 times 81435 (2.63%) aligned exactly 1 time 29447 (0.95%) aligned >1 times 68.86% overall alignment rate Time searching: 00:02:33 Overall time: 00:02:33 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] 140925 / 3225112 = 0.0437 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 20:42:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.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 20:42:43: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:42:43: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:42:49: 1000000 INFO @ Sat, 15 Jan 2022 20:42:55: 2000000 INFO @ Sat, 15 Jan 2022 20:43:01: 3000000 INFO @ Sat, 15 Jan 2022 20:43:06: 4000000 INFO @ Sat, 15 Jan 2022 20:43:11: 5000000 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 20:43:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.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 20:43:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:43:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:43:17: 6000000 INFO @ Sat, 15 Jan 2022 20:43:19: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:43:19: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:43:19: #1 total tags in treatment: 3071725 INFO @ Sat, 15 Jan 2022 20:43:19: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:43:19: #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 20:43:19: #1 tags after filtering in treatment: 2325252 INFO @ Sat, 15 Jan 2022 20:43:19: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 15 Jan 2022 20:43:19: #1 finished! INFO @ Sat, 15 Jan 2022 20:43:19: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:43:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:43:20: #2 number of paired peaks: 432 WARNING @ Sat, 15 Jan 2022 20:43:20: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Sat, 15 Jan 2022 20:43:20: start model_add_line... INFO @ Sat, 15 Jan 2022 20:43:20: start X-correlation... INFO @ Sat, 15 Jan 2022 20:43:20: end of X-cor INFO @ Sat, 15 Jan 2022 20:43:20: #2 finished! INFO @ Sat, 15 Jan 2022 20:43:20: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 20:43:20: #2 alternative fragment length(s) may be 3,30 bps INFO @ Sat, 15 Jan 2022 20:43:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.05_model.r WARNING @ Sat, 15 Jan 2022 20:43:20: #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 20:43:20: #2 You may need to consider one of the other alternative d(s): 3,30 WARNING @ Sat, 15 Jan 2022 20:43:20: #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 20:43:20: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:43:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:43:20: 1000000 INFO @ Sat, 15 Jan 2022 20:43:23: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:43:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:43:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:43:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.05_summits.bed INFO @ Sat, 15 Jan 2022 20:43:25: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:43:27: 2000000 INFO @ Sat, 15 Jan 2022 20:43:33: 3000000 INFO @ Sat, 15 Jan 2022 20:43:40: 4000000 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 20:43:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.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 20:43:43: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:43:43: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:43:46: 5000000 INFO @ Sat, 15 Jan 2022 20:43:50: 1000000 INFO @ Sat, 15 Jan 2022 20:43:54: 6000000 INFO @ Sat, 15 Jan 2022 20:43:56: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:43:56: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:43:56: #1 total tags in treatment: 3071725 INFO @ Sat, 15 Jan 2022 20:43:56: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:43:56: #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 20:43:56: #1 tags after filtering in treatment: 2325252 INFO @ Sat, 15 Jan 2022 20:43:56: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 15 Jan 2022 20:43:56: #1 finished! INFO @ Sat, 15 Jan 2022 20:43:56: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:43:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:43:56: #2 number of paired peaks: 432 WARNING @ Sat, 15 Jan 2022 20:43:56: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Sat, 15 Jan 2022 20:43:56: start model_add_line... INFO @ Sat, 15 Jan 2022 20:43:56: start X-correlation... INFO @ Sat, 15 Jan 2022 20:43:56: end of X-cor INFO @ Sat, 15 Jan 2022 20:43:56: #2 finished! INFO @ Sat, 15 Jan 2022 20:43:56: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 20:43:56: #2 alternative fragment length(s) may be 3,30 bps INFO @ Sat, 15 Jan 2022 20:43:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.10_model.r WARNING @ Sat, 15 Jan 2022 20:43:56: #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 20:43:56: #2 You may need to consider one of the other alternative d(s): 3,30 WARNING @ Sat, 15 Jan 2022 20:43:56: #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 20:43:56: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:43:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:43:58: 2000000 INFO @ Sat, 15 Jan 2022 20:43:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:44:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:44:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:44:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.10_summits.bed INFO @ Sat, 15 Jan 2022 20:44:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:44:04: 3000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:44:10: 4000000 INFO @ Sat, 15 Jan 2022 20:44:17: 5000000 INFO @ Sat, 15 Jan 2022 20:44:23: 6000000 INFO @ Sat, 15 Jan 2022 20:44:25: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:44:25: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:44:25: #1 total tags in treatment: 3071725 INFO @ Sat, 15 Jan 2022 20:44:25: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:44:25: #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 20:44:25: #1 tags after filtering in treatment: 2325252 INFO @ Sat, 15 Jan 2022 20:44:25: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 15 Jan 2022 20:44:25: #1 finished! INFO @ Sat, 15 Jan 2022 20:44:25: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:44:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:44:25: #2 number of paired peaks: 432 WARNING @ Sat, 15 Jan 2022 20:44:25: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Sat, 15 Jan 2022 20:44:25: start model_add_line... INFO @ Sat, 15 Jan 2022 20:44:25: start X-correlation... INFO @ Sat, 15 Jan 2022 20:44:25: end of X-cor INFO @ Sat, 15 Jan 2022 20:44:25: #2 finished! INFO @ Sat, 15 Jan 2022 20:44:25: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 20:44:25: #2 alternative fragment length(s) may be 3,30 bps INFO @ Sat, 15 Jan 2022 20:44:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.20_model.r WARNING @ Sat, 15 Jan 2022 20:44:25: #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 20:44:25: #2 You may need to consider one of the other alternative d(s): 3,30 WARNING @ Sat, 15 Jan 2022 20:44:25: #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 20:44:25: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:44:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:44:29: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:44:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:44:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:44:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468518/SRX10468518.20_summits.bed INFO @ Sat, 15 Jan 2022 20:44:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling