Job ID = 12531518 SRX = SRX2997372 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6867115 spots for SRR5819447/SRR5819447.sra Written 6867115 spots for SRR5819447/SRR5819447.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: 00:05:06 6867115 reads; of these: 6867115 (100.00%) were paired; of these: 3511941 (51.14%) aligned concordantly 0 times 2062796 (30.04%) aligned concordantly exactly 1 time 1292378 (18.82%) aligned concordantly >1 times ---- 3511941 pairs aligned concordantly 0 times; of these: 510608 (14.54%) aligned discordantly 1 time ---- 3001333 pairs aligned 0 times concordantly or discordantly; of these: 6002666 mates make up the pairs; of these: 5156649 (85.91%) aligned 0 times 122760 (2.05%) aligned exactly 1 time 723257 (12.05%) aligned >1 times 62.45% overall alignment rate Time searching: 00:05:06 Overall time: 00:05:06 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_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] 1021592 / 3819735 = 0.2675 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 08:08:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.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 08:08:00: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:08:00: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:08:07: 1000000 INFO @ Sat, 17 Apr 2021 08:08:14: 2000000 INFO @ Sat, 17 Apr 2021 08:08:20: 3000000 INFO @ Sat, 17 Apr 2021 08:08:27: 4000000 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 08:08:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.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 08:08:30: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:08:30: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:08:35: 5000000 INFO @ Sat, 17 Apr 2021 08:08:39: 1000000 INFO @ Sat, 17 Apr 2021 08:08:43: 6000000 INFO @ Sat, 17 Apr 2021 08:08:48: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 08:08:48: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 08:08:48: #1 total tags in treatment: 2425613 INFO @ Sat, 17 Apr 2021 08:08:48: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:08:48: #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 08:08:48: #1 tags after filtering in treatment: 1332248 INFO @ Sat, 17 Apr 2021 08:08:48: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 17 Apr 2021 08:08:48: #1 finished! INFO @ Sat, 17 Apr 2021 08:08:48: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:08:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:08:48: #2 number of paired peaks: 236 WARNING @ Sat, 17 Apr 2021 08:08:48: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Sat, 17 Apr 2021 08:08:48: start model_add_line... INFO @ Sat, 17 Apr 2021 08:08:48: start X-correlation... INFO @ Sat, 17 Apr 2021 08:08:48: end of X-cor INFO @ Sat, 17 Apr 2021 08:08:48: #2 finished! INFO @ Sat, 17 Apr 2021 08:08:48: #2 predicted fragment length is 95 bps INFO @ Sat, 17 Apr 2021 08:08:48: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 17 Apr 2021 08:08:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.05_model.r WARNING @ Sat, 17 Apr 2021 08:08:48: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:08:48: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 17 Apr 2021 08:08:48: #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 08:08:48: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:08:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:08:49: 2000000 INFO @ Sat, 17 Apr 2021 08:08:52: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:08:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.05_peaks.xls INFO @ Sat, 17 Apr 2021 08:08:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:08:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.05_summits.bed INFO @ Sat, 17 Apr 2021 08:08:53: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1752 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:08:56: 3000000 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 08:09:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.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 08:09:00: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:09:00: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:09:04: 4000000 INFO @ Sat, 17 Apr 2021 08:09:08: 1000000 INFO @ Sat, 17 Apr 2021 08:09:12: 5000000 INFO @ Sat, 17 Apr 2021 08:09:17: 2000000 INFO @ Sat, 17 Apr 2021 08:09:20: 6000000 INFO @ Sat, 17 Apr 2021 08:09:25: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 08:09:25: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 08:09:25: #1 total tags in treatment: 2425613 INFO @ Sat, 17 Apr 2021 08:09:25: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:09:25: #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 08:09:25: #1 tags after filtering in treatment: 1332248 INFO @ Sat, 17 Apr 2021 08:09:25: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 17 Apr 2021 08:09:25: #1 finished! INFO @ Sat, 17 Apr 2021 08:09:25: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:09:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:09:25: 3000000 INFO @ Sat, 17 Apr 2021 08:09:25: #2 number of paired peaks: 236 WARNING @ Sat, 17 Apr 2021 08:09:25: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Sat, 17 Apr 2021 08:09:25: start model_add_line... INFO @ Sat, 17 Apr 2021 08:09:25: start X-correlation... INFO @ Sat, 17 Apr 2021 08:09:25: end of X-cor INFO @ Sat, 17 Apr 2021 08:09:25: #2 finished! INFO @ Sat, 17 Apr 2021 08:09:25: #2 predicted fragment length is 95 bps INFO @ Sat, 17 Apr 2021 08:09:25: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 17 Apr 2021 08:09:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.10_model.r WARNING @ Sat, 17 Apr 2021 08:09:25: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:09:25: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 17 Apr 2021 08:09:25: #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 08:09:25: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:09:25: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 08:09:29: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:09:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.10_peaks.xls INFO @ Sat, 17 Apr 2021 08:09:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:09:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.10_summits.bed INFO @ Sat, 17 Apr 2021 08:09:30: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (1130 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:09:32: 4000000 BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 08:09:39: 5000000 INFO @ Sat, 17 Apr 2021 08:09:46: 6000000 INFO @ Sat, 17 Apr 2021 08:09:49: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 08:09:49: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 08:09:49: #1 total tags in treatment: 2425613 INFO @ Sat, 17 Apr 2021 08:09:49: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:09:49: #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 08:09:49: #1 tags after filtering in treatment: 1332248 INFO @ Sat, 17 Apr 2021 08:09:49: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 17 Apr 2021 08:09:49: #1 finished! INFO @ Sat, 17 Apr 2021 08:09:49: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:09:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:09:49: #2 number of paired peaks: 236 WARNING @ Sat, 17 Apr 2021 08:09:49: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Sat, 17 Apr 2021 08:09:49: start model_add_line... INFO @ Sat, 17 Apr 2021 08:09:49: start X-correlation... INFO @ Sat, 17 Apr 2021 08:09:49: end of X-cor INFO @ Sat, 17 Apr 2021 08:09:49: #2 finished! INFO @ Sat, 17 Apr 2021 08:09:49: #2 predicted fragment length is 95 bps INFO @ Sat, 17 Apr 2021 08:09:49: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 17 Apr 2021 08:09:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.20_model.r WARNING @ Sat, 17 Apr 2021 08:09:49: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:09:49: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 17 Apr 2021 08:09:49: #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 08:09:49: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:09:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:09:53: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:09:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.20_peaks.xls INFO @ Sat, 17 Apr 2021 08:09:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:09:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2997372/SRX2997372.20_summits.bed INFO @ Sat, 17 Apr 2021 08:09:54: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (528 records, 4 fields): 2 millis CompletedMACS2peakCalling