Job ID = 14521844 SRX = ERX4439557 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2676227 spots for ERR4501486/ERR4501486.sra Written 2676227 spots for ERR4501486/ERR4501486.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: 00:02:13 2676227 reads; of these: 2676227 (100.00%) were paired; of these: 685362 (25.61%) aligned concordantly 0 times 1682665 (62.87%) aligned concordantly exactly 1 time 308200 (11.52%) aligned concordantly >1 times ---- 685362 pairs aligned concordantly 0 times; of these: 312651 (45.62%) aligned discordantly 1 time ---- 372711 pairs aligned 0 times concordantly or discordantly; of these: 745422 mates make up the pairs; of these: 584290 (78.38%) aligned 0 times 42244 (5.67%) aligned exactly 1 time 118888 (15.95%) aligned >1 times 89.08% overall alignment rate Time searching: 00:02:13 Overall time: 00:02:13 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] 37943 / 2281113 = 0.0166 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 21:48:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.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 21:48:16: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:48:16: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:48:22: 1000000 INFO @ Sat, 15 Jan 2022 21:48:28: 2000000 INFO @ Sat, 15 Jan 2022 21:48:34: 3000000 INFO @ Sat, 15 Jan 2022 21:48:40: 4000000 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 21:48:45: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:48:45: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:48:45: #1 total tags in treatment: 1958379 INFO @ Sat, 15 Jan 2022 21:48:45: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:48:45: #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 21:48:45: #1 tags after filtering in treatment: 1686416 INFO @ Sat, 15 Jan 2022 21:48:45: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Jan 2022 21:48:45: #1 finished! INFO @ Sat, 15 Jan 2022 21:48:45: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:48:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:48:45: #2 number of paired peaks: 108 WARNING @ Sat, 15 Jan 2022 21:48:45: 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 21:48:45: start model_add_line... INFO @ Sat, 15 Jan 2022 21:48:45: start X-correlation... INFO @ Sat, 15 Jan 2022 21:48:45: end of X-cor INFO @ Sat, 15 Jan 2022 21:48:45: #2 finished! INFO @ Sat, 15 Jan 2022 21:48:45: #2 predicted fragment length is 185 bps INFO @ Sat, 15 Jan 2022 21:48:45: #2 alternative fragment length(s) may be 4,167,185 bps INFO @ Sat, 15 Jan 2022 21:48:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.05_model.r WARNING @ Sat, 15 Jan 2022 21:48:45: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:48:45: #2 You may need to consider one of the other alternative d(s): 4,167,185 WARNING @ Sat, 15 Jan 2022 21:48:45: #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 21:48:45: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:48:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:48:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.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 21:48:46: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:48:46: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:48:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:48:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:48:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:48:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.05_summits.bed INFO @ Sat, 15 Jan 2022 21:48:51: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (416 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:48:52: 1000000 INFO @ Sat, 15 Jan 2022 21:48:58: 2000000 INFO @ Sat, 15 Jan 2022 21:49:04: 3000000 INFO @ Sat, 15 Jan 2022 21:49:10: 4000000 INFO @ Sat, 15 Jan 2022 21:49:14: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:49:14: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:49:14: #1 total tags in treatment: 1958379 INFO @ Sat, 15 Jan 2022 21:49:14: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:49:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換中... INFO @ Sat, 15 Jan 2022 21:49:14: #1 tags after filtering in treatment: 1686416 INFO @ Sat, 15 Jan 2022 21:49:14: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Jan 2022 21:49:14: #1 finished! INFO @ Sat, 15 Jan 2022 21:49:14: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:49:14: #2 looking for paired plus/minus strand peaks... 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 21:49:14: #2 number of paired peaks: 108 WARNING @ Sat, 15 Jan 2022 21:49:14: 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 21:49:14: start model_add_line... INFO @ Sat, 15 Jan 2022 21:49:14: start X-correlation... INFO @ Sat, 15 Jan 2022 21:49:14: end of X-cor INFO @ Sat, 15 Jan 2022 21:49:14: #2 finished! INFO @ Sat, 15 Jan 2022 21:49:14: #2 predicted fragment length is 185 bps INFO @ Sat, 15 Jan 2022 21:49:14: #2 alternative fragment length(s) may be 4,167,185 bps INFO @ Sat, 15 Jan 2022 21:49:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.10_model.r WARNING @ Sat, 15 Jan 2022 21:49:15: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:49:15: #2 You may need to consider one of the other alternative d(s): 4,167,185 WARNING @ Sat, 15 Jan 2022 21:49:15: #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 21:49:15: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:49:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:49:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.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 21:49:16: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:49:16: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:49:18: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:49:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:49:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:49:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.10_summits.bed INFO @ Sat, 15 Jan 2022 21:49:20: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (214 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:49:24: 1000000 INFO @ Sat, 15 Jan 2022 21:49:31: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:49:37: 3000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:49:44: 4000000 INFO @ Sat, 15 Jan 2022 21:49:48: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:49:48: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:49:48: #1 total tags in treatment: 1958379 INFO @ Sat, 15 Jan 2022 21:49:48: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:49:48: #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 21:49:48: #1 tags after filtering in treatment: 1686416 INFO @ Sat, 15 Jan 2022 21:49:48: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Jan 2022 21:49:48: #1 finished! INFO @ Sat, 15 Jan 2022 21:49:48: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:49:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:49:48: #2 number of paired peaks: 108 WARNING @ Sat, 15 Jan 2022 21:49:48: 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 21:49:48: start model_add_line... INFO @ Sat, 15 Jan 2022 21:49:48: start X-correlation... INFO @ Sat, 15 Jan 2022 21:49:48: end of X-cor INFO @ Sat, 15 Jan 2022 21:49:48: #2 finished! INFO @ Sat, 15 Jan 2022 21:49:48: #2 predicted fragment length is 185 bps INFO @ Sat, 15 Jan 2022 21:49:48: #2 alternative fragment length(s) may be 4,167,185 bps INFO @ Sat, 15 Jan 2022 21:49:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.20_model.r WARNING @ Sat, 15 Jan 2022 21:49:48: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:49:48: #2 You may need to consider one of the other alternative d(s): 4,167,185 WARNING @ Sat, 15 Jan 2022 21:49:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 21:49:48: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:49:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:49:52: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:49:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:49:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:49:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439557/ERX4439557.20_summits.bed INFO @ Sat, 15 Jan 2022 21:49:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (114 records, 4 fields): 1 millis CompletedMACS2peakCalling