Job ID = 12531520 SRX = SRX2997374 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8632122 spots for SRR5819449/SRR5819449.sra Written 8632122 spots for SRR5819449/SRR5819449.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: 00:07:33 8632122 reads; of these: 8632122 (100.00%) were paired; of these: 4375859 (50.69%) aligned concordantly 0 times 2905934 (33.66%) aligned concordantly exactly 1 time 1350329 (15.64%) aligned concordantly >1 times ---- 4375859 pairs aligned concordantly 0 times; of these: 665553 (15.21%) aligned discordantly 1 time ---- 3710306 pairs aligned 0 times concordantly or discordantly; of these: 7420612 mates make up the pairs; of these: 6490996 (87.47%) aligned 0 times 178758 (2.41%) aligned exactly 1 time 750858 (10.12%) aligned >1 times 62.40% overall alignment rate Time searching: 00:07:33 Overall time: 00:07:33 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_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] 1287222 / 4866210 = 0.2645 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 08:13:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.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, 17 Apr 2021 08:13:29: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:13:29: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:13:38: 1000000 INFO @ Sat, 17 Apr 2021 08:13:48: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 08:13:57: 3000000 INFO @ Sat, 17 Apr 2021 08:13:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.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, 17 Apr 2021 08:13:59: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:13:59: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:14:06: 4000000 INFO @ Sat, 17 Apr 2021 08:14:09: 1000000 INFO @ Sat, 17 Apr 2021 08:14:15: 5000000 INFO @ Sat, 17 Apr 2021 08:14:18: 2000000 INFO @ Sat, 17 Apr 2021 08:14:25: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 08:14:28: 3000000 INFO @ Sat, 17 Apr 2021 08:14:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.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, 17 Apr 2021 08:14:29: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:14:29: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:14:34: 7000000 INFO @ Sat, 17 Apr 2021 08:14:38: 1000000 INFO @ Sat, 17 Apr 2021 08:14:38: 4000000 INFO @ Sat, 17 Apr 2021 08:14:44: 8000000 INFO @ Sat, 17 Apr 2021 08:14:46: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 08:14:46: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 08:14:46: #1 total tags in treatment: 3125425 INFO @ Sat, 17 Apr 2021 08:14:46: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:14:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 08:14:46: #1 tags after filtering in treatment: 1548008 INFO @ Sat, 17 Apr 2021 08:14:46: #1 Redundant rate of treatment: 0.50 INFO @ Sat, 17 Apr 2021 08:14:46: #1 finished! INFO @ Sat, 17 Apr 2021 08:14:46: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:14:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:14:46: #2 number of paired peaks: 288 WARNING @ Sat, 17 Apr 2021 08:14:46: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Sat, 17 Apr 2021 08:14:46: start model_add_line... INFO @ Sat, 17 Apr 2021 08:14:46: start X-correlation... INFO @ Sat, 17 Apr 2021 08:14:46: end of X-cor INFO @ Sat, 17 Apr 2021 08:14:46: #2 finished! INFO @ Sat, 17 Apr 2021 08:14:46: #2 predicted fragment length is 84 bps INFO @ Sat, 17 Apr 2021 08:14:46: #2 alternative fragment length(s) may be 4,63,84 bps INFO @ Sat, 17 Apr 2021 08:14:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.05_model.r WARNING @ Sat, 17 Apr 2021 08:14:46: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:14:46: #2 You may need to consider one of the other alternative d(s): 4,63,84 WARNING @ Sat, 17 Apr 2021 08:14:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:14:46: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:14:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:14:47: 2000000 INFO @ Sat, 17 Apr 2021 08:14:48: 5000000 INFO @ Sat, 17 Apr 2021 08:14:50: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:14:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.05_peaks.xls INFO @ Sat, 17 Apr 2021 08:14:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:14:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.05_summits.bed INFO @ Sat, 17 Apr 2021 08:14:52: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (2362 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:14:55: 3000000 INFO @ Sat, 17 Apr 2021 08:14:58: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 08:15:04: 4000000 INFO @ Sat, 17 Apr 2021 08:15:07: 7000000 BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 08:15:13: 5000000 INFO @ Sat, 17 Apr 2021 08:15:16: 8000000 INFO @ Sat, 17 Apr 2021 08:15:18: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 08:15:18: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 08:15:18: #1 total tags in treatment: 3125425 INFO @ Sat, 17 Apr 2021 08:15:18: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:15:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 08:15:18: #1 tags after filtering in treatment: 1548008 INFO @ Sat, 17 Apr 2021 08:15:18: #1 Redundant rate of treatment: 0.50 INFO @ Sat, 17 Apr 2021 08:15:18: #1 finished! INFO @ Sat, 17 Apr 2021 08:15:18: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:15:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:15:18: #2 number of paired peaks: 288 WARNING @ Sat, 17 Apr 2021 08:15:18: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Sat, 17 Apr 2021 08:15:18: start model_add_line... INFO @ Sat, 17 Apr 2021 08:15:18: start X-correlation... INFO @ Sat, 17 Apr 2021 08:15:18: end of X-cor INFO @ Sat, 17 Apr 2021 08:15:18: #2 finished! INFO @ Sat, 17 Apr 2021 08:15:18: #2 predicted fragment length is 84 bps INFO @ Sat, 17 Apr 2021 08:15:18: #2 alternative fragment length(s) may be 4,63,84 bps INFO @ Sat, 17 Apr 2021 08:15:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.10_model.r WARNING @ Sat, 17 Apr 2021 08:15:18: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:15:18: #2 You may need to consider one of the other alternative d(s): 4,63,84 WARNING @ Sat, 17 Apr 2021 08:15:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:15:18: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:15:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:15:21: 6000000 INFO @ Sat, 17 Apr 2021 08:15:22: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:15:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.10_peaks.xls INFO @ Sat, 17 Apr 2021 08:15:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:15:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.10_summits.bed INFO @ Sat, 17 Apr 2021 08:15:23: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1479 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:15:30: 7000000 INFO @ Sat, 17 Apr 2021 08:15:38: 8000000 INFO @ Sat, 17 Apr 2021 08:15:40: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 08:15:40: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 08:15:40: #1 total tags in treatment: 3125425 INFO @ Sat, 17 Apr 2021 08:15:40: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:15:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 08:15:40: #1 tags after filtering in treatment: 1548008 INFO @ Sat, 17 Apr 2021 08:15:40: #1 Redundant rate of treatment: 0.50 INFO @ Sat, 17 Apr 2021 08:15:40: #1 finished! INFO @ Sat, 17 Apr 2021 08:15:40: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:15:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:15:40: #2 number of paired peaks: 288 WARNING @ Sat, 17 Apr 2021 08:15:40: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Sat, 17 Apr 2021 08:15:40: start model_add_line... INFO @ Sat, 17 Apr 2021 08:15:40: start X-correlation... INFO @ Sat, 17 Apr 2021 08:15:40: end of X-cor INFO @ Sat, 17 Apr 2021 08:15:40: #2 finished! INFO @ Sat, 17 Apr 2021 08:15:40: #2 predicted fragment length is 84 bps INFO @ Sat, 17 Apr 2021 08:15:40: #2 alternative fragment length(s) may be 4,63,84 bps INFO @ Sat, 17 Apr 2021 08:15:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.20_model.r WARNING @ Sat, 17 Apr 2021 08:15:40: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:15:40: #2 You may need to consider one of the other alternative d(s): 4,63,84 WARNING @ Sat, 17 Apr 2021 08:15:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:15:40: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:15:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:15:43: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:15:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.20_peaks.xls INFO @ Sat, 17 Apr 2021 08:15:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:15:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2997374/SRX2997374.20_summits.bed INFO @ Sat, 17 Apr 2021 08:15:45: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (619 records, 4 fields): 20 millis CompletedMACS2peakCalling