Job ID = 12531540 SRX = SRX2997388 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5737031 spots for SRR5819463/SRR5819463.sra Written 5737031 spots for SRR5819463/SRR5819463.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: 00:06:41 5737031 reads; of these: 5737031 (100.00%) were paired; of these: 2052823 (35.78%) aligned concordantly 0 times 2403373 (41.89%) aligned concordantly exactly 1 time 1280835 (22.33%) aligned concordantly >1 times ---- 2052823 pairs aligned concordantly 0 times; of these: 435569 (21.22%) aligned discordantly 1 time ---- 1617254 pairs aligned 0 times concordantly or discordantly; of these: 3234508 mates make up the pairs; of these: 2671676 (82.60%) aligned 0 times 108288 (3.35%) aligned exactly 1 time 454544 (14.05%) aligned >1 times 76.72% overall alignment rate Time searching: 00:06:41 Overall time: 00:06:41 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] 1007976 / 4078240 = 0.2472 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 08:19:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.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 08:19:32: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:19:32: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:19:43: 1000000 INFO @ Sat, 17 Apr 2021 08:19:54: 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 08:20:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.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 08:20:01: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:20:01: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:20:03: 3000000 INFO @ Sat, 17 Apr 2021 08:20:10: 1000000 INFO @ Sat, 17 Apr 2021 08:20:13: 4000000 INFO @ Sat, 17 Apr 2021 08:20:19: 2000000 INFO @ Sat, 17 Apr 2021 08:20:22: 5000000 INFO @ Sat, 17 Apr 2021 08:20:28: 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 08:20:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.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 08:20:32: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:20:32: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:20:32: 6000000 INFO @ Sat, 17 Apr 2021 08:20:37: 4000000 INFO @ Sat, 17 Apr 2021 08:20:40: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 08:20:40: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 08:20:40: #1 total tags in treatment: 2753207 INFO @ Sat, 17 Apr 2021 08:20:40: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:20:40: #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 08:20:40: #1 tags after filtering in treatment: 1419189 INFO @ Sat, 17 Apr 2021 08:20:40: #1 Redundant rate of treatment: 0.48 INFO @ Sat, 17 Apr 2021 08:20:40: #1 finished! INFO @ Sat, 17 Apr 2021 08:20:40: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:20:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:20:40: #2 number of paired peaks: 309 WARNING @ Sat, 17 Apr 2021 08:20:40: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sat, 17 Apr 2021 08:20:40: start model_add_line... INFO @ Sat, 17 Apr 2021 08:20:40: start X-correlation... INFO @ Sat, 17 Apr 2021 08:20:40: end of X-cor INFO @ Sat, 17 Apr 2021 08:20:40: #2 finished! INFO @ Sat, 17 Apr 2021 08:20:40: #2 predicted fragment length is 96 bps INFO @ Sat, 17 Apr 2021 08:20:40: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 17 Apr 2021 08:20:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.05_model.r WARNING @ Sat, 17 Apr 2021 08:20:40: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:20:40: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 17 Apr 2021 08:20:40: #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 08:20:40: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:20:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:20:41: 1000000 INFO @ Sat, 17 Apr 2021 08:20:45: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:20:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.05_peaks.xls INFO @ Sat, 17 Apr 2021 08:20:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:20:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.05_summits.bed INFO @ Sat, 17 Apr 2021 08:20:47: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (2229 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:20:48: 5000000 INFO @ Sat, 17 Apr 2021 08:20:51: 2000000 INFO @ Sat, 17 Apr 2021 08:21:00: 3000000 INFO @ Sat, 17 Apr 2021 08:21:00: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 08:21:09: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 08:21:09: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 08:21:09: #1 total tags in treatment: 2753207 INFO @ Sat, 17 Apr 2021 08:21:09: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:21:09: #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 08:21:09: #1 tags after filtering in treatment: 1419189 INFO @ Sat, 17 Apr 2021 08:21:09: #1 Redundant rate of treatment: 0.48 INFO @ Sat, 17 Apr 2021 08:21:09: #1 finished! INFO @ Sat, 17 Apr 2021 08:21:09: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:21:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:21:09: #2 number of paired peaks: 309 WARNING @ Sat, 17 Apr 2021 08:21:09: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sat, 17 Apr 2021 08:21:09: start model_add_line... INFO @ Sat, 17 Apr 2021 08:21:09: start X-correlation... INFO @ Sat, 17 Apr 2021 08:21:09: end of X-cor INFO @ Sat, 17 Apr 2021 08:21:09: #2 finished! INFO @ Sat, 17 Apr 2021 08:21:09: #2 predicted fragment length is 96 bps INFO @ Sat, 17 Apr 2021 08:21:09: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 17 Apr 2021 08:21:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.10_model.r WARNING @ Sat, 17 Apr 2021 08:21:09: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:21:09: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 17 Apr 2021 08:21:09: #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 08:21:09: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:21:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:21:09: 4000000 BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 08:21:14: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:21:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.10_peaks.xls INFO @ Sat, 17 Apr 2021 08:21:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:21:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.10_summits.bed INFO @ Sat, 17 Apr 2021 08:21:16: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1530 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:21:20: 5000000 INFO @ Sat, 17 Apr 2021 08:21:31: 6000000 INFO @ Sat, 17 Apr 2021 08:21:39: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 08:21:39: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 08:21:39: #1 total tags in treatment: 2753207 INFO @ Sat, 17 Apr 2021 08:21:39: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:21:39: #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 08:21:39: #1 tags after filtering in treatment: 1419189 INFO @ Sat, 17 Apr 2021 08:21:39: #1 Redundant rate of treatment: 0.48 INFO @ Sat, 17 Apr 2021 08:21:39: #1 finished! INFO @ Sat, 17 Apr 2021 08:21:39: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:21:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:21:40: #2 number of paired peaks: 309 WARNING @ Sat, 17 Apr 2021 08:21:40: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sat, 17 Apr 2021 08:21:40: start model_add_line... INFO @ Sat, 17 Apr 2021 08:21:40: start X-correlation... INFO @ Sat, 17 Apr 2021 08:21:40: end of X-cor INFO @ Sat, 17 Apr 2021 08:21:40: #2 finished! INFO @ Sat, 17 Apr 2021 08:21:40: #2 predicted fragment length is 96 bps INFO @ Sat, 17 Apr 2021 08:21:40: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 17 Apr 2021 08:21:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.20_model.r WARNING @ Sat, 17 Apr 2021 08:21:40: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:21:40: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 17 Apr 2021 08:21:40: #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 08:21:40: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:21:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:21:44: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:21:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.20_peaks.xls INFO @ Sat, 17 Apr 2021 08:21:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:21:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2997388/SRX2997388.20_summits.bed INFO @ Sat, 17 Apr 2021 08:21:46: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (863 records, 4 fields): 24 millis CompletedMACS2peakCalling