Job ID = 14521044 SRX = SRX8245465 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13385725 spots for SRR11684676/SRR11684676.sra Written 13385725 spots for SRR11684676/SRR11684676.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: 00:06:51 13385725 reads; of these: 13385725 (100.00%) were paired; of these: 6196868 (46.29%) aligned concordantly 0 times 6534917 (48.82%) aligned concordantly exactly 1 time 653940 (4.89%) aligned concordantly >1 times ---- 6196868 pairs aligned concordantly 0 times; of these: 38395 (0.62%) aligned discordantly 1 time ---- 6158473 pairs aligned 0 times concordantly or discordantly; of these: 12316946 mates make up the pairs; of these: 7250367 (58.86%) aligned 0 times 4456896 (36.19%) aligned exactly 1 time 609683 (4.95%) aligned >1 times 72.92% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 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] 592117 / 7226126 = 0.0819 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 20:33:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.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 20:33:50: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:33:50: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:33:55: 1000000 INFO @ Sat, 15 Jan 2022 20:34:00: 2000000 INFO @ Sat, 15 Jan 2022 20:34:05: 3000000 INFO @ Sat, 15 Jan 2022 20:34:10: 4000000 INFO @ Sat, 15 Jan 2022 20:34:15: 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 20:34:20: 6000000 INFO @ Sat, 15 Jan 2022 20:34:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.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 20:34:20: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:34:20: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:34:26: 7000000 INFO @ Sat, 15 Jan 2022 20:34:27: 1000000 INFO @ Sat, 15 Jan 2022 20:34:31: 8000000 INFO @ Sat, 15 Jan 2022 20:34:33: 2000000 INFO @ Sat, 15 Jan 2022 20:34:37: 9000000 INFO @ Sat, 15 Jan 2022 20:34:39: 3000000 INFO @ Sat, 15 Jan 2022 20:34:42: 10000000 INFO @ Sat, 15 Jan 2022 20:34:45: 4000000 INFO @ Sat, 15 Jan 2022 20:34:48: 11000000 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 20:34:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.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 20:34:50: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:34:50: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:34:51: 5000000 INFO @ Sat, 15 Jan 2022 20:34:54: 12000000 INFO @ Sat, 15 Jan 2022 20:34:57: 1000000 INFO @ Sat, 15 Jan 2022 20:34:58: 6000000 INFO @ Sat, 15 Jan 2022 20:35:00: 13000000 INFO @ Sat, 15 Jan 2022 20:35:04: 2000000 INFO @ Sat, 15 Jan 2022 20:35:04: 7000000 INFO @ Sat, 15 Jan 2022 20:35:07: 14000000 INFO @ Sat, 15 Jan 2022 20:35:11: 3000000 INFO @ Sat, 15 Jan 2022 20:35:11: 8000000 INFO @ Sat, 15 Jan 2022 20:35:13: 15000000 INFO @ Sat, 15 Jan 2022 20:35:17: 4000000 INFO @ Sat, 15 Jan 2022 20:35:17: 9000000 INFO @ Sat, 15 Jan 2022 20:35:20: 16000000 INFO @ Sat, 15 Jan 2022 20:35:24: 5000000 INFO @ Sat, 15 Jan 2022 20:35:24: 10000000 INFO @ Sat, 15 Jan 2022 20:35:26: 17000000 INFO @ Sat, 15 Jan 2022 20:35:30: 11000000 INFO @ Sat, 15 Jan 2022 20:35:31: 6000000 INFO @ Sat, 15 Jan 2022 20:35:33: 18000000 INFO @ Sat, 15 Jan 2022 20:35:35: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:35:35: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:35:35: #1 total tags in treatment: 6598285 INFO @ Sat, 15 Jan 2022 20:35:35: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:35:35: #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 20:35:35: #1 tags after filtering in treatment: 3405989 INFO @ Sat, 15 Jan 2022 20:35:35: #1 Redundant rate of treatment: 0.48 INFO @ Sat, 15 Jan 2022 20:35:35: #1 finished! INFO @ Sat, 15 Jan 2022 20:35:35: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:35:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:35:35: #2 number of paired peaks: 167 WARNING @ Sat, 15 Jan 2022 20:35:35: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Sat, 15 Jan 2022 20:35:35: start model_add_line... INFO @ Sat, 15 Jan 2022 20:35:35: start X-correlation... INFO @ Sat, 15 Jan 2022 20:35:35: end of X-cor INFO @ Sat, 15 Jan 2022 20:35:35: #2 finished! INFO @ Sat, 15 Jan 2022 20:35:35: #2 predicted fragment length is 54 bps INFO @ Sat, 15 Jan 2022 20:35:35: #2 alternative fragment length(s) may be 54,93,130,193,248,264,329,352,379,420,443,467,481,495,524,550,572 bps INFO @ Sat, 15 Jan 2022 20:35:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.05_model.r WARNING @ Sat, 15 Jan 2022 20:35:35: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:35:35: #2 You may need to consider one of the other alternative d(s): 54,93,130,193,248,264,329,352,379,420,443,467,481,495,524,550,572 WARNING @ Sat, 15 Jan 2022 20:35:35: #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 20:35:35: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:35:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:35:37: 12000000 INFO @ Sat, 15 Jan 2022 20:35:38: 7000000 INFO @ Sat, 15 Jan 2022 20:35:40: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:35:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:35:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:35:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.05_summits.bed INFO @ Sat, 15 Jan 2022 20:35:42: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (306 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:35:43: 13000000 INFO @ Sat, 15 Jan 2022 20:35:45: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:35:49: 14000000 INFO @ Sat, 15 Jan 2022 20:35:52: 9000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:35:56: 15000000 INFO @ Sat, 15 Jan 2022 20:35:59: 10000000 INFO @ Sat, 15 Jan 2022 20:36:02: 16000000 INFO @ Sat, 15 Jan 2022 20:36:05: 11000000 INFO @ Sat, 15 Jan 2022 20:36:08: 17000000 INFO @ Sat, 15 Jan 2022 20:36:13: 12000000 INFO @ Sat, 15 Jan 2022 20:36:15: 18000000 INFO @ Sat, 15 Jan 2022 20:36:17: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:36:17: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:36:17: #1 total tags in treatment: 6598285 INFO @ Sat, 15 Jan 2022 20:36:17: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:36:17: #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 20:36:17: #1 tags after filtering in treatment: 3405989 INFO @ Sat, 15 Jan 2022 20:36:17: #1 Redundant rate of treatment: 0.48 INFO @ Sat, 15 Jan 2022 20:36:17: #1 finished! INFO @ Sat, 15 Jan 2022 20:36:17: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:36:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:36:17: #2 number of paired peaks: 167 WARNING @ Sat, 15 Jan 2022 20:36:17: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Sat, 15 Jan 2022 20:36:17: start model_add_line... INFO @ Sat, 15 Jan 2022 20:36:17: start X-correlation... INFO @ Sat, 15 Jan 2022 20:36:17: end of X-cor INFO @ Sat, 15 Jan 2022 20:36:17: #2 finished! INFO @ Sat, 15 Jan 2022 20:36:17: #2 predicted fragment length is 54 bps INFO @ Sat, 15 Jan 2022 20:36:17: #2 alternative fragment length(s) may be 54,93,130,193,248,264,329,352,379,420,443,467,481,495,524,550,572 bps INFO @ Sat, 15 Jan 2022 20:36:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.10_model.r WARNING @ Sat, 15 Jan 2022 20:36:17: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:36:17: #2 You may need to consider one of the other alternative d(s): 54,93,130,193,248,264,329,352,379,420,443,467,481,495,524,550,572 WARNING @ Sat, 15 Jan 2022 20:36:17: #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 20:36:17: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:36:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:36:19: 13000000 INFO @ Sat, 15 Jan 2022 20:36:22: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:36:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:36:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:36:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.10_summits.bed INFO @ Sat, 15 Jan 2022 20:36:24: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (26 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:36:26: 14000000 INFO @ Sat, 15 Jan 2022 20:36:33: 15000000 INFO @ Sat, 15 Jan 2022 20:36:39: 16000000 INFO @ Sat, 15 Jan 2022 20:36:46: 17000000 INFO @ Sat, 15 Jan 2022 20:36:52: 18000000 INFO @ Sat, 15 Jan 2022 20:36:54: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:36:54: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:36:54: #1 total tags in treatment: 6598285 INFO @ Sat, 15 Jan 2022 20:36:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:36:54: #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 20:36:55: #1 tags after filtering in treatment: 3405989 INFO @ Sat, 15 Jan 2022 20:36:55: #1 Redundant rate of treatment: 0.48 INFO @ Sat, 15 Jan 2022 20:36:55: #1 finished! INFO @ Sat, 15 Jan 2022 20:36:55: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:36:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:36:55: #2 number of paired peaks: 167 WARNING @ Sat, 15 Jan 2022 20:36:55: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Sat, 15 Jan 2022 20:36:55: start model_add_line... INFO @ Sat, 15 Jan 2022 20:36:55: start X-correlation... INFO @ Sat, 15 Jan 2022 20:36:55: end of X-cor INFO @ Sat, 15 Jan 2022 20:36:55: #2 finished! INFO @ Sat, 15 Jan 2022 20:36:55: #2 predicted fragment length is 54 bps INFO @ Sat, 15 Jan 2022 20:36:55: #2 alternative fragment length(s) may be 54,93,130,193,248,264,329,352,379,420,443,467,481,495,524,550,572 bps INFO @ Sat, 15 Jan 2022 20:36:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.20_model.r WARNING @ Sat, 15 Jan 2022 20:36:55: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:36:55: #2 You may need to consider one of the other alternative d(s): 54,93,130,193,248,264,329,352,379,420,443,467,481,495,524,550,572 WARNING @ Sat, 15 Jan 2022 20:36:55: #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 20:36:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:36:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:36:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:37:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:37:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:37:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245465/SRX8245465.20_summits.bed INFO @ Sat, 15 Jan 2022 20:37:01: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling