Job ID = 14520328 SRX = SRX8398384 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1058700 spots for SRR11848080/SRR11848080.sra Written 1058700 spots for SRR11848080/SRR11848080.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: 00:00:46 1058700 reads; of these: 1058700 (100.00%) were paired; of these: 152991 (14.45%) aligned concordantly 0 times 760313 (71.82%) aligned concordantly exactly 1 time 145396 (13.73%) aligned concordantly >1 times ---- 152991 pairs aligned concordantly 0 times; of these: 4177 (2.73%) aligned discordantly 1 time ---- 148814 pairs aligned 0 times concordantly or discordantly; of these: 297628 mates make up the pairs; of these: 294428 (98.92%) aligned 0 times 1637 (0.55%) aligned exactly 1 time 1563 (0.53%) aligned >1 times 86.09% overall alignment rate Time searching: 00:00:46 Overall time: 00:00:46 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] 183180 / 900608 = 0.2034 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 18:58:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.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 18:58:52: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:58:52: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:58:59: 1000000 INFO @ Sat, 15 Jan 2022 18:59:02: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:59:02: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:59:02: #1 total tags in treatment: 722852 INFO @ Sat, 15 Jan 2022 18:59:02: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:59:02: #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 18:59:02: #1 tags after filtering in treatment: 617303 INFO @ Sat, 15 Jan 2022 18:59:02: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 15 Jan 2022 18:59:02: #1 finished! INFO @ Sat, 15 Jan 2022 18:59:02: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:59:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:59:02: #2 number of paired peaks: 142 WARNING @ Sat, 15 Jan 2022 18:59:02: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Sat, 15 Jan 2022 18:59:02: start model_add_line... INFO @ Sat, 15 Jan 2022 18:59:02: start X-correlation... INFO @ Sat, 15 Jan 2022 18:59:02: end of X-cor INFO @ Sat, 15 Jan 2022 18:59:02: #2 finished! INFO @ Sat, 15 Jan 2022 18:59:02: #2 predicted fragment length is 79 bps INFO @ Sat, 15 Jan 2022 18:59:02: #2 alternative fragment length(s) may be 79,93,551,592 bps INFO @ Sat, 15 Jan 2022 18:59:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.05_model.r WARNING @ Sat, 15 Jan 2022 18:59:02: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:59:02: #2 You may need to consider one of the other alternative d(s): 79,93,551,592 WARNING @ Sat, 15 Jan 2022 18:59:02: #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 18:59:02: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:59:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:59:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:59:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.05_peaks.xls INFO @ Sat, 15 Jan 2022 18:59:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:59:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.05_summits.bed INFO @ Sat, 15 Jan 2022 18:59:04: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (139 records, 4 fields): 159 millis CompletedMACS2peakCalling 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 18:59:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.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 18:59:22: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:59:22: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:59:29: 1000000 INFO @ Sat, 15 Jan 2022 18:59:32: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:59:32: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:59:32: #1 total tags in treatment: 722852 INFO @ Sat, 15 Jan 2022 18:59:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:59:32: #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 18:59:32: #1 tags after filtering in treatment: 617303 INFO @ Sat, 15 Jan 2022 18:59:32: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 15 Jan 2022 18:59:32: #1 finished! INFO @ Sat, 15 Jan 2022 18:59:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:59:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:59:32: #2 number of paired peaks: 142 WARNING @ Sat, 15 Jan 2022 18:59:32: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Sat, 15 Jan 2022 18:59:32: start model_add_line... INFO @ Sat, 15 Jan 2022 18:59:32: start X-correlation... INFO @ Sat, 15 Jan 2022 18:59:32: end of X-cor INFO @ Sat, 15 Jan 2022 18:59:32: #2 finished! INFO @ Sat, 15 Jan 2022 18:59:32: #2 predicted fragment length is 79 bps INFO @ Sat, 15 Jan 2022 18:59:32: #2 alternative fragment length(s) may be 79,93,551,592 bps INFO @ Sat, 15 Jan 2022 18:59:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.10_model.r WARNING @ Sat, 15 Jan 2022 18:59:32: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:59:32: #2 You may need to consider one of the other alternative d(s): 79,93,551,592 WARNING @ Sat, 15 Jan 2022 18:59:32: #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 18:59:32: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:59:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:59:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:59:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.10_peaks.xls INFO @ Sat, 15 Jan 2022 18:59:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:59:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.10_summits.bed INFO @ Sat, 15 Jan 2022 18:59:35: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (105 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換中... 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 18:59:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.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 18:59:52: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:59:52: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 18:59:59: 1000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:00:02: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:00:02: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:00:02: #1 total tags in treatment: 722852 INFO @ Sat, 15 Jan 2022 19:00:02: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:00:02: #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 19:00:02: #1 tags after filtering in treatment: 617303 INFO @ Sat, 15 Jan 2022 19:00:02: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 15 Jan 2022 19:00:02: #1 finished! INFO @ Sat, 15 Jan 2022 19:00:02: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:00:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:00:02: #2 number of paired peaks: 142 WARNING @ Sat, 15 Jan 2022 19:00:02: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Sat, 15 Jan 2022 19:00:02: start model_add_line... INFO @ Sat, 15 Jan 2022 19:00:02: start X-correlation... INFO @ Sat, 15 Jan 2022 19:00:02: end of X-cor INFO @ Sat, 15 Jan 2022 19:00:02: #2 finished! INFO @ Sat, 15 Jan 2022 19:00:02: #2 predicted fragment length is 79 bps INFO @ Sat, 15 Jan 2022 19:00:02: #2 alternative fragment length(s) may be 79,93,551,592 bps INFO @ Sat, 15 Jan 2022 19:00:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.20_model.r WARNING @ Sat, 15 Jan 2022 19:00:02: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:00:02: #2 You may need to consider one of the other alternative d(s): 79,93,551,592 WARNING @ Sat, 15 Jan 2022 19:00:02: #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 19:00:02: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:00:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:00:04: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:00:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:00:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:00:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8398384/SRX8398384.20_summits.bed INFO @ Sat, 15 Jan 2022 19:00:05: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (27 records, 4 fields): 2 millis CompletedMACS2peakCalling