Job ID = 14520220 SRX = SRX8398410 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2223534 spots for SRR11848054/SRR11848054.sra Written 2223534 spots for SRR11848054/SRR11848054.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: 00:01:47 2223534 reads; of these: 2223534 (100.00%) were paired; of these: 445805 (20.05%) aligned concordantly 0 times 1573113 (70.75%) aligned concordantly exactly 1 time 204616 (9.20%) aligned concordantly >1 times ---- 445805 pairs aligned concordantly 0 times; of these: 51705 (11.60%) aligned discordantly 1 time ---- 394100 pairs aligned 0 times concordantly or discordantly; of these: 788200 mates make up the pairs; of these: 756786 (96.01%) aligned 0 times 19130 (2.43%) aligned exactly 1 time 12284 (1.56%) aligned >1 times 82.98% overall alignment rate Time searching: 00:01:47 Overall time: 00:01:47 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] 134032 / 1802204 = 0.0744 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 18:44:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.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 18:44:41: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:44:41: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:44:48: 1000000 INFO @ Sat, 15 Jan 2022 18:44:55: 2000000 INFO @ Sat, 15 Jan 2022 18:45:03: 3000000 INFO @ Sat, 15 Jan 2022 18:45:05: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:45:05: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:45:05: #1 total tags in treatment: 1644979 INFO @ Sat, 15 Jan 2022 18:45:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:45:05: #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 18:45:06: #1 tags after filtering in treatment: 1228552 INFO @ Sat, 15 Jan 2022 18:45:06: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 18:45:06: #1 finished! INFO @ Sat, 15 Jan 2022 18:45:06: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:45:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:45:06: #2 number of paired peaks: 311 WARNING @ Sat, 15 Jan 2022 18:45:06: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Sat, 15 Jan 2022 18:45:06: start model_add_line... INFO @ Sat, 15 Jan 2022 18:45:06: start X-correlation... INFO @ Sat, 15 Jan 2022 18:45:06: end of X-cor INFO @ Sat, 15 Jan 2022 18:45:06: #2 finished! INFO @ Sat, 15 Jan 2022 18:45:06: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 18:45:06: #2 alternative fragment length(s) may be 3,89,132,175,182,217,269,298,337,390,472,479,488,491,524,567 bps INFO @ Sat, 15 Jan 2022 18:45:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.05_model.r WARNING @ Sat, 15 Jan 2022 18:45:06: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:45:06: #2 You may need to consider one of the other alternative d(s): 3,89,132,175,182,217,269,298,337,390,472,479,488,491,524,567 WARNING @ Sat, 15 Jan 2022 18:45:06: #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 18:45:06: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:45:06: #3 Pre-compute pvalue-qvalue table... 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 18:45:08: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:45:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.05_peaks.xls INFO @ Sat, 15 Jan 2022 18:45:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:45:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.05_summits.bed INFO @ Sat, 15 Jan 2022 18:45:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 18:45:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.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 18:45:10: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:45:10: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:45:18: 1000000 INFO @ Sat, 15 Jan 2022 18:45:25: 2000000 INFO @ Sat, 15 Jan 2022 18:45:33: 3000000 INFO @ Sat, 15 Jan 2022 18:45:36: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:45:36: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:45:36: #1 total tags in treatment: 1644979 INFO @ Sat, 15 Jan 2022 18:45:36: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:45:36: #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 18:45:36: #1 tags after filtering in treatment: 1228552 INFO @ Sat, 15 Jan 2022 18:45:36: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 18:45:36: #1 finished! INFO @ Sat, 15 Jan 2022 18:45:36: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:45:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:45:36: #2 number of paired peaks: 311 WARNING @ Sat, 15 Jan 2022 18:45:36: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Sat, 15 Jan 2022 18:45:36: start model_add_line... INFO @ Sat, 15 Jan 2022 18:45:36: start X-correlation... INFO @ Sat, 15 Jan 2022 18:45:36: end of X-cor INFO @ Sat, 15 Jan 2022 18:45:36: #2 finished! INFO @ Sat, 15 Jan 2022 18:45:36: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 18:45:36: #2 alternative fragment length(s) may be 3,89,132,175,182,217,269,298,337,390,472,479,488,491,524,567 bps INFO @ Sat, 15 Jan 2022 18:45:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.10_model.r WARNING @ Sat, 15 Jan 2022 18:45:36: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:45:36: #2 You may need to consider one of the other alternative d(s): 3,89,132,175,182,217,269,298,337,390,472,479,488,491,524,567 WARNING @ Sat, 15 Jan 2022 18:45:36: #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 18:45:36: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:45:36: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... INFO @ Sat, 15 Jan 2022 18:45:38: #3 Call peaks for each chromosome... 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 18:45:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.10_peaks.xls INFO @ Sat, 15 Jan 2022 18:45:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:45:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.10_summits.bed INFO @ Sat, 15 Jan 2022 18:45:39: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 18:45:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.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 18:45:40: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:45:40: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:45:48: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 18:45:55: 2000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 18:46:03: 3000000 INFO @ Sat, 15 Jan 2022 18:46:05: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:46:05: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:46:05: #1 total tags in treatment: 1644979 INFO @ Sat, 15 Jan 2022 18:46:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:46:05: #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 18:46:05: #1 tags after filtering in treatment: 1228552 INFO @ Sat, 15 Jan 2022 18:46:05: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 18:46:05: #1 finished! INFO @ Sat, 15 Jan 2022 18:46:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:46:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:46:06: #2 number of paired peaks: 311 WARNING @ Sat, 15 Jan 2022 18:46:06: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Sat, 15 Jan 2022 18:46:06: start model_add_line... INFO @ Sat, 15 Jan 2022 18:46:06: start X-correlation... INFO @ Sat, 15 Jan 2022 18:46:06: end of X-cor INFO @ Sat, 15 Jan 2022 18:46:06: #2 finished! INFO @ Sat, 15 Jan 2022 18:46:06: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 18:46:06: #2 alternative fragment length(s) may be 3,89,132,175,182,217,269,298,337,390,472,479,488,491,524,567 bps INFO @ Sat, 15 Jan 2022 18:46:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.20_model.r WARNING @ Sat, 15 Jan 2022 18:46:06: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:46:06: #2 You may need to consider one of the other alternative d(s): 3,89,132,175,182,217,269,298,337,390,472,479,488,491,524,567 WARNING @ Sat, 15 Jan 2022 18:46:06: #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 18:46:06: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:46:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:46:08: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:46:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.20_peaks.xls INFO @ Sat, 15 Jan 2022 18:46:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:46:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8398410/SRX8398410.20_summits.bed INFO @ Sat, 15 Jan 2022 18:46:09: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling