Job ID = 14519664 SRX = SRX9786324 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9646563 spots for SRR13362156/SRR13362156.sra Written 9646563 spots for SRR13362156/SRR13362156.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: 00:07:15 9646563 reads; of these: 9646563 (100.00%) were paired; of these: 1781375 (18.47%) aligned concordantly 0 times 7195601 (74.59%) aligned concordantly exactly 1 time 669587 (6.94%) aligned concordantly >1 times ---- 1781375 pairs aligned concordantly 0 times; of these: 200347 (11.25%) aligned discordantly 1 time ---- 1581028 pairs aligned 0 times concordantly or discordantly; of these: 3162056 mates make up the pairs; of these: 2044720 (64.66%) aligned 0 times 968327 (30.62%) aligned exactly 1 time 149009 (4.71%) aligned >1 times 89.40% overall alignment rate Time searching: 00:07:15 Overall time: 00:07:15 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] 549287 / 8064648 = 0.0681 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 17:31:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.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 17:31:09: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:31:09: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:31:14: 1000000 INFO @ Sat, 15 Jan 2022 17:31:19: 2000000 INFO @ Sat, 15 Jan 2022 17:31:25: 3000000 INFO @ Sat, 15 Jan 2022 17:31:30: 4000000 INFO @ Sat, 15 Jan 2022 17:31:35: 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 17:31:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.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 17:31:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:31:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:31:40: 6000000 INFO @ Sat, 15 Jan 2022 17:31:46: 7000000 INFO @ Sat, 15 Jan 2022 17:31:46: 1000000 INFO @ Sat, 15 Jan 2022 17:31:52: 8000000 INFO @ Sat, 15 Jan 2022 17:31:53: 2000000 INFO @ Sat, 15 Jan 2022 17:31:58: 9000000 INFO @ Sat, 15 Jan 2022 17:32:00: 3000000 INFO @ Sat, 15 Jan 2022 17:32:04: 10000000 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 17:32:07: 4000000 INFO @ Sat, 15 Jan 2022 17:32:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.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 17:32:09: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:32:09: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:32:10: 11000000 INFO @ Sat, 15 Jan 2022 17:32:14: 5000000 INFO @ Sat, 15 Jan 2022 17:32:15: 1000000 INFO @ Sat, 15 Jan 2022 17:32:16: 12000000 INFO @ Sat, 15 Jan 2022 17:32:21: 6000000 INFO @ Sat, 15 Jan 2022 17:32:22: 13000000 INFO @ Sat, 15 Jan 2022 17:32:22: 2000000 INFO @ Sat, 15 Jan 2022 17:32:28: 14000000 INFO @ Sat, 15 Jan 2022 17:32:28: 7000000 INFO @ Sat, 15 Jan 2022 17:32:29: 3000000 INFO @ Sat, 15 Jan 2022 17:32:34: 15000000 INFO @ Sat, 15 Jan 2022 17:32:36: 8000000 INFO @ Sat, 15 Jan 2022 17:32:36: 4000000 INFO @ Sat, 15 Jan 2022 17:32:40: 16000000 INFO @ Sat, 15 Jan 2022 17:32:41: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:32:41: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:32:41: #1 total tags in treatment: 7322329 INFO @ Sat, 15 Jan 2022 17:32:41: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:32:41: #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 17:32:41: #1 tags after filtering in treatment: 4701532 INFO @ Sat, 15 Jan 2022 17:32:41: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 15 Jan 2022 17:32:41: #1 finished! INFO @ Sat, 15 Jan 2022 17:32:41: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:32:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:32:41: #2 number of paired peaks: 108 WARNING @ Sat, 15 Jan 2022 17:32:41: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Sat, 15 Jan 2022 17:32:41: start model_add_line... INFO @ Sat, 15 Jan 2022 17:32:41: start X-correlation... INFO @ Sat, 15 Jan 2022 17:32:41: end of X-cor INFO @ Sat, 15 Jan 2022 17:32:41: #2 finished! INFO @ Sat, 15 Jan 2022 17:32:41: #2 predicted fragment length is 67 bps INFO @ Sat, 15 Jan 2022 17:32:41: #2 alternative fragment length(s) may be 27,67,108,141,167,190,217,236,295,350,355,379,422,439,492,504,524,576 bps INFO @ Sat, 15 Jan 2022 17:32:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.05_model.r WARNING @ Sat, 15 Jan 2022 17:32:41: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:32:41: #2 You may need to consider one of the other alternative d(s): 27,67,108,141,167,190,217,236,295,350,355,379,422,439,492,504,524,576 WARNING @ Sat, 15 Jan 2022 17:32:41: #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 17:32:41: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:32:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:32:42: 5000000 INFO @ Sat, 15 Jan 2022 17:32:43: 9000000 INFO @ Sat, 15 Jan 2022 17:32:47: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:32:49: 6000000 INFO @ Sat, 15 Jan 2022 17:32:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:32:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:32:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.05_summits.bed INFO @ Sat, 15 Jan 2022 17:32:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (35 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:32:50: 10000000 INFO @ Sat, 15 Jan 2022 17:32:56: 7000000 INFO @ Sat, 15 Jan 2022 17:32:57: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:33:03: 8000000 INFO @ Sat, 15 Jan 2022 17:33:04: 12000000 INFO @ Sat, 15 Jan 2022 17:33:10: 9000000 INFO @ Sat, 15 Jan 2022 17:33:11: 13000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:33:17: 10000000 INFO @ Sat, 15 Jan 2022 17:33:18: 14000000 INFO @ Sat, 15 Jan 2022 17:33:24: 11000000 INFO @ Sat, 15 Jan 2022 17:33:25: 15000000 INFO @ Sat, 15 Jan 2022 17:33:31: 12000000 INFO @ Sat, 15 Jan 2022 17:33:32: 16000000 INFO @ Sat, 15 Jan 2022 17:33:33: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:33:33: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:33:33: #1 total tags in treatment: 7322329 INFO @ Sat, 15 Jan 2022 17:33:33: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:33:33: #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 17:33:34: #1 tags after filtering in treatment: 4701532 INFO @ Sat, 15 Jan 2022 17:33:34: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 15 Jan 2022 17:33:34: #1 finished! INFO @ Sat, 15 Jan 2022 17:33:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:33:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:33:34: #2 number of paired peaks: 108 WARNING @ Sat, 15 Jan 2022 17:33:34: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Sat, 15 Jan 2022 17:33:34: start model_add_line... INFO @ Sat, 15 Jan 2022 17:33:34: start X-correlation... INFO @ Sat, 15 Jan 2022 17:33:34: end of X-cor INFO @ Sat, 15 Jan 2022 17:33:34: #2 finished! INFO @ Sat, 15 Jan 2022 17:33:34: #2 predicted fragment length is 67 bps INFO @ Sat, 15 Jan 2022 17:33:34: #2 alternative fragment length(s) may be 27,67,108,141,167,190,217,236,295,350,355,379,422,439,492,504,524,576 bps INFO @ Sat, 15 Jan 2022 17:33:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.10_model.r WARNING @ Sat, 15 Jan 2022 17:33:34: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:33:34: #2 You may need to consider one of the other alternative d(s): 27,67,108,141,167,190,217,236,295,350,355,379,422,439,492,504,524,576 WARNING @ Sat, 15 Jan 2022 17:33:34: #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 17:33:34: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:33:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:33:38: 13000000 INFO @ Sat, 15 Jan 2022 17:33:40: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:33:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:33:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:33:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.10_summits.bed INFO @ Sat, 15 Jan 2022 17:33:42: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (5 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:33:45: 14000000 INFO @ Sat, 15 Jan 2022 17:33:51: 15000000 INFO @ Sat, 15 Jan 2022 17:33:58: 16000000 INFO @ Sat, 15 Jan 2022 17:33:59: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:33:59: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:33:59: #1 total tags in treatment: 7322329 INFO @ Sat, 15 Jan 2022 17:33:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:33:59: #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 17:33:59: #1 tags after filtering in treatment: 4701532 INFO @ Sat, 15 Jan 2022 17:33:59: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 15 Jan 2022 17:33:59: #1 finished! INFO @ Sat, 15 Jan 2022 17:33:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:33:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:33:59: #2 number of paired peaks: 108 WARNING @ Sat, 15 Jan 2022 17:33:59: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Sat, 15 Jan 2022 17:33:59: start model_add_line... INFO @ Sat, 15 Jan 2022 17:33:59: start X-correlation... INFO @ Sat, 15 Jan 2022 17:33:59: end of X-cor INFO @ Sat, 15 Jan 2022 17:33:59: #2 finished! INFO @ Sat, 15 Jan 2022 17:33:59: #2 predicted fragment length is 67 bps INFO @ Sat, 15 Jan 2022 17:33:59: #2 alternative fragment length(s) may be 27,67,108,141,167,190,217,236,295,350,355,379,422,439,492,504,524,576 bps INFO @ Sat, 15 Jan 2022 17:33:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.20_model.r WARNING @ Sat, 15 Jan 2022 17:33:59: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:33:59: #2 You may need to consider one of the other alternative d(s): 27,67,108,141,167,190,217,236,295,350,355,379,422,439,492,504,524,576 WARNING @ Sat, 15 Jan 2022 17:33:59: #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 17:33:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:33:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:34:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:34:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:34:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:34:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9786324/SRX9786324.20_summits.bed INFO @ Sat, 15 Jan 2022 17:34:07: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling