Job ID = 14520863 SRX = SRX8245542 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10484638 spots for SRR11684753/SRR11684753.sra Written 10484638 spots for SRR11684753/SRR11684753.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: 00:07:42 10484638 reads; of these: 10484638 (100.00%) were paired; of these: 5368331 (51.20%) aligned concordantly 0 times 4548249 (43.38%) aligned concordantly exactly 1 time 568058 (5.42%) aligned concordantly >1 times ---- 5368331 pairs aligned concordantly 0 times; of these: 76041 (1.42%) aligned discordantly 1 time ---- 5292290 pairs aligned 0 times concordantly or discordantly; of these: 10584580 mates make up the pairs; of these: 6542986 (61.82%) aligned 0 times 3519416 (33.25%) aligned exactly 1 time 522178 (4.93%) aligned >1 times 68.80% overall alignment rate Time searching: 00:07:42 Overall time: 00:07:42 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_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] 332413 / 5191546 = 0.0640 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 20:15:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.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 20:15:21: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:15:21: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:15:27: 1000000 INFO @ Sat, 15 Jan 2022 20:15:33: 2000000 INFO @ Sat, 15 Jan 2022 20:15:39: 3000000 INFO @ Sat, 15 Jan 2022 20:15:45: 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 20:15:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.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 20:15:50: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:15:50: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:15:51: 5000000 INFO @ Sat, 15 Jan 2022 20:15:57: 1000000 INFO @ Sat, 15 Jan 2022 20:15:57: 6000000 INFO @ Sat, 15 Jan 2022 20:16:04: 2000000 INFO @ Sat, 15 Jan 2022 20:16:04: 7000000 INFO @ Sat, 15 Jan 2022 20:16:11: 3000000 INFO @ Sat, 15 Jan 2022 20:16:11: 8000000 INFO @ Sat, 15 Jan 2022 20:16:17: 4000000 INFO @ Sat, 15 Jan 2022 20:16:18: 9000000 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 20:16:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.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 20:16:20: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:16:20: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:16:24: 5000000 INFO @ Sat, 15 Jan 2022 20:16:25: 10000000 INFO @ Sat, 15 Jan 2022 20:16:29: 1000000 INFO @ Sat, 15 Jan 2022 20:16:30: 6000000 INFO @ Sat, 15 Jan 2022 20:16:31: 11000000 INFO @ Sat, 15 Jan 2022 20:16:37: 7000000 INFO @ Sat, 15 Jan 2022 20:16:38: 2000000 INFO @ Sat, 15 Jan 2022 20:16:38: 12000000 INFO @ Sat, 15 Jan 2022 20:16:44: 8000000 INFO @ Sat, 15 Jan 2022 20:16:45: 13000000 INFO @ Sat, 15 Jan 2022 20:16:46: 3000000 INFO @ Sat, 15 Jan 2022 20:16:50: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:16:50: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:16:50: #1 total tags in treatment: 4785795 INFO @ Sat, 15 Jan 2022 20:16:50: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:16:50: #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 20:16:51: #1 tags after filtering in treatment: 3140599 INFO @ Sat, 15 Jan 2022 20:16:51: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 15 Jan 2022 20:16:51: #1 finished! INFO @ Sat, 15 Jan 2022 20:16:51: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:16:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:16:51: #2 number of paired peaks: 169 WARNING @ Sat, 15 Jan 2022 20:16:51: 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 20:16:51: start model_add_line... INFO @ Sat, 15 Jan 2022 20:16:51: start X-correlation... INFO @ Sat, 15 Jan 2022 20:16:51: end of X-cor INFO @ Sat, 15 Jan 2022 20:16:51: #2 finished! INFO @ Sat, 15 Jan 2022 20:16:51: #2 predicted fragment length is 27 bps INFO @ Sat, 15 Jan 2022 20:16:51: #2 alternative fragment length(s) may be 27,36,100,116,147,185,211,235,257,289,312,345,359,367,390,408,433,450,482,513,520,526,532,539,545,561,573,587 bps INFO @ Sat, 15 Jan 2022 20:16:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.05_model.r WARNING @ Sat, 15 Jan 2022 20:16:51: #2 Since the d (27) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:16:51: #2 You may need to consider one of the other alternative d(s): 27,36,100,116,147,185,211,235,257,289,312,345,359,367,390,408,433,450,482,513,520,526,532,539,545,561,573,587 WARNING @ Sat, 15 Jan 2022 20:16:51: #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 20:16:51: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:16:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:16:51: 9000000 INFO @ Sat, 15 Jan 2022 20:16:54: 4000000 INFO @ Sat, 15 Jan 2022 20:16:55: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:16:57: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:16:57: 10000000 INFO @ Sat, 15 Jan 2022 20:16:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:16:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.05_summits.bed INFO @ Sat, 15 Jan 2022 20:16:58: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:17:03: 5000000 INFO @ Sat, 15 Jan 2022 20:17:04: 11000000 INFO @ Sat, 15 Jan 2022 20:17:10: 6000000 INFO @ Sat, 15 Jan 2022 20:17:11: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:17:17: 13000000 INFO @ Sat, 15 Jan 2022 20:17:19: 7000000 INFO @ Sat, 15 Jan 2022 20:17:22: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:17:22: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:17:22: #1 total tags in treatment: 4785795 INFO @ Sat, 15 Jan 2022 20:17:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:17:22: #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 20:17:22: #1 tags after filtering in treatment: 3140599 INFO @ Sat, 15 Jan 2022 20:17:22: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 15 Jan 2022 20:17:22: #1 finished! INFO @ Sat, 15 Jan 2022 20:17:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:17:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:17:22: #2 number of paired peaks: 169 WARNING @ Sat, 15 Jan 2022 20:17:22: 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 20:17:22: start model_add_line... INFO @ Sat, 15 Jan 2022 20:17:22: start X-correlation... INFO @ Sat, 15 Jan 2022 20:17:22: end of X-cor INFO @ Sat, 15 Jan 2022 20:17:22: #2 finished! INFO @ Sat, 15 Jan 2022 20:17:22: #2 predicted fragment length is 27 bps INFO @ Sat, 15 Jan 2022 20:17:22: #2 alternative fragment length(s) may be 27,36,100,116,147,185,211,235,257,289,312,345,359,367,390,408,433,450,482,513,520,526,532,539,545,561,573,587 bps INFO @ Sat, 15 Jan 2022 20:17:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.10_model.r WARNING @ Sat, 15 Jan 2022 20:17:22: #2 Since the d (27) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:17:22: #2 You may need to consider one of the other alternative d(s): 27,36,100,116,147,185,211,235,257,289,312,345,359,367,390,408,433,450,482,513,520,526,532,539,545,561,573,587 WARNING @ Sat, 15 Jan 2022 20:17:22: #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 20:17:22: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:17:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:17:27: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:17:27: 8000000 INFO @ Sat, 15 Jan 2022 20:17:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:17:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:17:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.10_summits.bed INFO @ Sat, 15 Jan 2022 20:17:29: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 178 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:17:36: 9000000 INFO @ Sat, 15 Jan 2022 20:17:44: 10000000 INFO @ Sat, 15 Jan 2022 20:17:52: 11000000 INFO @ Sat, 15 Jan 2022 20:18:01: 12000000 INFO @ Sat, 15 Jan 2022 20:18:09: 13000000 INFO @ Sat, 15 Jan 2022 20:18:14: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:18:14: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:18:14: #1 total tags in treatment: 4785795 INFO @ Sat, 15 Jan 2022 20:18:14: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:18:14: #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 20:18:14: #1 tags after filtering in treatment: 3140599 INFO @ Sat, 15 Jan 2022 20:18:14: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 15 Jan 2022 20:18:14: #1 finished! INFO @ Sat, 15 Jan 2022 20:18:14: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:18:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:18:15: #2 number of paired peaks: 169 WARNING @ Sat, 15 Jan 2022 20:18:15: 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 20:18:15: start model_add_line... INFO @ Sat, 15 Jan 2022 20:18:15: start X-correlation... INFO @ Sat, 15 Jan 2022 20:18:15: end of X-cor INFO @ Sat, 15 Jan 2022 20:18:15: #2 finished! INFO @ Sat, 15 Jan 2022 20:18:15: #2 predicted fragment length is 27 bps INFO @ Sat, 15 Jan 2022 20:18:15: #2 alternative fragment length(s) may be 27,36,100,116,147,185,211,235,257,289,312,345,359,367,390,408,433,450,482,513,520,526,532,539,545,561,573,587 bps INFO @ Sat, 15 Jan 2022 20:18:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.20_model.r WARNING @ Sat, 15 Jan 2022 20:18:15: #2 Since the d (27) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:18:15: #2 You may need to consider one of the other alternative d(s): 27,36,100,116,147,185,211,235,257,289,312,345,359,367,390,408,433,450,482,513,520,526,532,539,545,561,573,587 WARNING @ Sat, 15 Jan 2022 20:18:15: #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 20:18:15: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:18:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:18:19: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:18:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:18:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:18:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245542/SRX8245542.20_summits.bed INFO @ Sat, 15 Jan 2022 20:18:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling