Job ID = 14520826 SRX = SRX8245533 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9427516 spots for SRR11684744/SRR11684744.sra Written 9427516 spots for SRR11684744/SRR11684744.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: 00:11:47 9427516 reads; of these: 9427516 (100.00%) were paired; of these: 4998322 (53.02%) aligned concordantly 0 times 3902206 (41.39%) aligned concordantly exactly 1 time 526988 (5.59%) aligned concordantly >1 times ---- 4998322 pairs aligned concordantly 0 times; of these: 94059 (1.88%) aligned discordantly 1 time ---- 4904263 pairs aligned 0 times concordantly or discordantly; of these: 9808526 mates make up the pairs; of these: 6292768 (64.16%) aligned 0 times 3027399 (30.86%) aligned exactly 1 time 488359 (4.98%) aligned >1 times 66.63% overall alignment rate Time searching: 00:11:47 Overall time: 00:11:47 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 8 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] 335799 / 4522498 = 0.0743 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 20:12:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.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 20:12:29: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:12:29: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:12:34: 1000000 INFO @ Sat, 15 Jan 2022 20:12:38: 2000000 INFO @ Sat, 15 Jan 2022 20:12:43: 3000000 INFO @ Sat, 15 Jan 2022 20:12:47: 4000000 INFO @ Sat, 15 Jan 2022 20:12:51: 5000000 INFO @ Sat, 15 Jan 2022 20:12:56: 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 20:12:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.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 20:12:59: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:12:59: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:13:00: 7000000 INFO @ Sat, 15 Jan 2022 20:13:04: 1000000 INFO @ Sat, 15 Jan 2022 20:13:05: 8000000 INFO @ Sat, 15 Jan 2022 20:13:09: 2000000 INFO @ Sat, 15 Jan 2022 20:13:09: 9000000 INFO @ Sat, 15 Jan 2022 20:13:13: 3000000 INFO @ Sat, 15 Jan 2022 20:13:14: 10000000 INFO @ Sat, 15 Jan 2022 20:13:18: 4000000 INFO @ Sat, 15 Jan 2022 20:13:19: 11000000 INFO @ Sat, 15 Jan 2022 20:13:22: 5000000 INFO @ Sat, 15 Jan 2022 20:13:23: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:13:23: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:13:23: #1 total tags in treatment: 4096460 INFO @ Sat, 15 Jan 2022 20:13:23: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:13:23: #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 20:13:23: #1 tags after filtering in treatment: 2648569 INFO @ Sat, 15 Jan 2022 20:13:23: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 20:13:23: #1 finished! INFO @ Sat, 15 Jan 2022 20:13:23: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:13:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:13:23: #2 number of paired peaks: 169 WARNING @ Sat, 15 Jan 2022 20:13:23: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 15 Jan 2022 20:13:23: start model_add_line... INFO @ Sat, 15 Jan 2022 20:13:23: start X-correlation... INFO @ Sat, 15 Jan 2022 20:13:23: end of X-cor INFO @ Sat, 15 Jan 2022 20:13:23: #2 finished! INFO @ Sat, 15 Jan 2022 20:13:23: #2 predicted fragment length is 53 bps INFO @ Sat, 15 Jan 2022 20:13:23: #2 alternative fragment length(s) may be 24,53,99,116,179,185,204,216,240,267,309,325,353,387,402,455,475,490,518,538,575 bps INFO @ Sat, 15 Jan 2022 20:13:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.05_model.r WARNING @ Sat, 15 Jan 2022 20:13:23: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:13:23: #2 You may need to consider one of the other alternative d(s): 24,53,99,116,179,185,204,216,240,267,309,325,353,387,402,455,475,490,518,538,575 WARNING @ Sat, 15 Jan 2022 20:13:23: #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 20:13:23: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:13:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:13:26: 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 20:13:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:13:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.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 20:13:29: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:13:29: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:13:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:13:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:13:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.05_summits.bed INFO @ Sat, 15 Jan 2022 20:13:30: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (22 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:13:31: 7000000 INFO @ Sat, 15 Jan 2022 20:13:35: 1000000 INFO @ Sat, 15 Jan 2022 20:13:36: 8000000 INFO @ Sat, 15 Jan 2022 20:13:40: 2000000 INFO @ Sat, 15 Jan 2022 20:13:41: 9000000 INFO @ Sat, 15 Jan 2022 20:13:45: 3000000 INFO @ Sat, 15 Jan 2022 20:13:46: 10000000 INFO @ Sat, 15 Jan 2022 20:13:50: 4000000 INFO @ Sat, 15 Jan 2022 20:13:50: 11000000 INFO @ Sat, 15 Jan 2022 20:13:55: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:13:55: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:13:55: #1 total tags in treatment: 4096460 INFO @ Sat, 15 Jan 2022 20:13:55: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:13:55: #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 20:13:55: #1 tags after filtering in treatment: 2648569 INFO @ Sat, 15 Jan 2022 20:13:55: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 20:13:55: #1 finished! INFO @ Sat, 15 Jan 2022 20:13:55: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:13:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:13:55: #2 number of paired peaks: 169 WARNING @ Sat, 15 Jan 2022 20:13:55: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 15 Jan 2022 20:13:55: start model_add_line... INFO @ Sat, 15 Jan 2022 20:13:55: start X-correlation... INFO @ Sat, 15 Jan 2022 20:13:55: end of X-cor INFO @ Sat, 15 Jan 2022 20:13:55: #2 finished! INFO @ Sat, 15 Jan 2022 20:13:55: #2 predicted fragment length is 53 bps INFO @ Sat, 15 Jan 2022 20:13:55: #2 alternative fragment length(s) may be 24,53,99,116,179,185,204,216,240,267,309,325,353,387,402,455,475,490,518,538,575 bps INFO @ Sat, 15 Jan 2022 20:13:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.10_model.r WARNING @ Sat, 15 Jan 2022 20:13:55: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:13:55: #2 You may need to consider one of the other alternative d(s): 24,53,99,116,179,185,204,216,240,267,309,325,353,387,402,455,475,490,518,538,575 WARNING @ Sat, 15 Jan 2022 20:13:55: #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 20:13:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:13:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:13:55: 5000000 INFO @ Sat, 15 Jan 2022 20:13:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:14:00: 6000000 INFO @ Sat, 15 Jan 2022 20:14:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:14:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:14:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.10_summits.bed INFO @ Sat, 15 Jan 2022 20:14:01: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:14:05: 7000000 INFO @ Sat, 15 Jan 2022 20:14:11: 8000000 INFO @ Sat, 15 Jan 2022 20:14:16: 9000000 INFO @ Sat, 15 Jan 2022 20:14:21: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:14:26: 11000000 INFO @ Sat, 15 Jan 2022 20:14:31: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:14:31: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:14:31: #1 total tags in treatment: 4096460 INFO @ Sat, 15 Jan 2022 20:14:31: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:14:31: #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 20:14:31: #1 tags after filtering in treatment: 2648569 INFO @ Sat, 15 Jan 2022 20:14:31: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 20:14:31: #1 finished! INFO @ Sat, 15 Jan 2022 20:14:31: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:14:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:14:31: #2 number of paired peaks: 169 WARNING @ Sat, 15 Jan 2022 20:14:31: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 15 Jan 2022 20:14:31: start model_add_line... INFO @ Sat, 15 Jan 2022 20:14:31: start X-correlation... INFO @ Sat, 15 Jan 2022 20:14:31: end of X-cor INFO @ Sat, 15 Jan 2022 20:14:31: #2 finished! INFO @ Sat, 15 Jan 2022 20:14:31: #2 predicted fragment length is 53 bps INFO @ Sat, 15 Jan 2022 20:14:31: #2 alternative fragment length(s) may be 24,53,99,116,179,185,204,216,240,267,309,325,353,387,402,455,475,490,518,538,575 bps INFO @ Sat, 15 Jan 2022 20:14:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.20_model.r WARNING @ Sat, 15 Jan 2022 20:14:31: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:14:31: #2 You may need to consider one of the other alternative d(s): 24,53,99,116,179,185,204,216,240,267,309,325,353,387,402,455,475,490,518,538,575 WARNING @ Sat, 15 Jan 2022 20:14:31: #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 20:14:31: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:14:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:14:35: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:14:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:14:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:14:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245533/SRX8245533.20_summits.bed INFO @ Sat, 15 Jan 2022 20:14:37: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling