Job ID = 14521869 SRX = ERX4439560 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3441521 spots for ERR4501489/ERR4501489.sra Written 3441521 spots for ERR4501489/ERR4501489.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: 00:02:44 3441521 reads; of these: 3441521 (100.00%) were paired; of these: 843387 (24.51%) aligned concordantly 0 times 2096368 (60.91%) aligned concordantly exactly 1 time 501766 (14.58%) aligned concordantly >1 times ---- 843387 pairs aligned concordantly 0 times; of these: 345384 (40.95%) aligned discordantly 1 time ---- 498003 pairs aligned 0 times concordantly or discordantly; of these: 996006 mates make up the pairs; of these: 773628 (77.67%) aligned 0 times 50173 (5.04%) aligned exactly 1 time 172205 (17.29%) aligned >1 times 88.76% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:44 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] 123138 / 2917671 = 0.0422 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 21:52:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.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 21:52:47: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:52:47: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:52:55: 1000000 INFO @ Sat, 15 Jan 2022 21:53:03: 2000000 INFO @ Sat, 15 Jan 2022 21:53:12: 3000000 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 21:53:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.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 21:53:17: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:53:17: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:53:19: 4000000 INFO @ Sat, 15 Jan 2022 21:53:25: 1000000 INFO @ Sat, 15 Jan 2022 21:53:28: 5000000 INFO @ Sat, 15 Jan 2022 21:53:33: 2000000 INFO @ Sat, 15 Jan 2022 21:53:35: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:53:35: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:53:35: #1 total tags in treatment: 2493392 INFO @ Sat, 15 Jan 2022 21:53:35: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:53:35: #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 21:53:35: #1 tags after filtering in treatment: 1825912 INFO @ Sat, 15 Jan 2022 21:53:35: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:53:35: #1 finished! INFO @ Sat, 15 Jan 2022 21:53:35: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:53:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:53:35: #2 number of paired peaks: 256 WARNING @ Sat, 15 Jan 2022 21:53:35: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Sat, 15 Jan 2022 21:53:35: start model_add_line... INFO @ Sat, 15 Jan 2022 21:53:35: start X-correlation... INFO @ Sat, 15 Jan 2022 21:53:35: end of X-cor INFO @ Sat, 15 Jan 2022 21:53:35: #2 finished! INFO @ Sat, 15 Jan 2022 21:53:35: #2 predicted fragment length is 172 bps INFO @ Sat, 15 Jan 2022 21:53:35: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 15 Jan 2022 21:53:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.05_model.r WARNING @ Sat, 15 Jan 2022 21:53:35: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:53:35: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Sat, 15 Jan 2022 21:53:35: #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 21:53:35: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:53:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:53:40: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:53:41: 3000000 INFO @ Sat, 15 Jan 2022 21:53:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:53:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:53:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.05_summits.bed INFO @ Sat, 15 Jan 2022 21:53:41: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (1445 records, 4 fields): 4 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 21:53:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.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 21:53:47: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:53:47: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:53:48: 4000000 INFO @ Sat, 15 Jan 2022 21:53:55: 1000000 INFO @ Sat, 15 Jan 2022 21:53:57: 5000000 INFO @ Sat, 15 Jan 2022 21:54:03: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:54:03: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:54:03: #1 total tags in treatment: 2493392 INFO @ Sat, 15 Jan 2022 21:54:03: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:54:03: #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 21:54:03: #1 tags after filtering in treatment: 1825912 INFO @ Sat, 15 Jan 2022 21:54:03: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:54:03: #1 finished! INFO @ Sat, 15 Jan 2022 21:54:03: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:54:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:54:04: 2000000 INFO @ Sat, 15 Jan 2022 21:54:04: #2 number of paired peaks: 256 WARNING @ Sat, 15 Jan 2022 21:54:04: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Sat, 15 Jan 2022 21:54:04: start model_add_line... INFO @ Sat, 15 Jan 2022 21:54:04: start X-correlation... INFO @ Sat, 15 Jan 2022 21:54:04: end of X-cor INFO @ Sat, 15 Jan 2022 21:54:04: #2 finished! INFO @ Sat, 15 Jan 2022 21:54:04: #2 predicted fragment length is 172 bps INFO @ Sat, 15 Jan 2022 21:54:04: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 15 Jan 2022 21:54:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.10_model.r WARNING @ Sat, 15 Jan 2022 21:54:04: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:54:04: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Sat, 15 Jan 2022 21:54:04: #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 21:54:04: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:54:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:54:08: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:54:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:54:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:54:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.10_summits.bed INFO @ Sat, 15 Jan 2022 21:54:10: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1047 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:54:11: 3000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:54:18: 4000000 INFO @ Sat, 15 Jan 2022 21:54:25: 5000000 INFO @ Sat, 15 Jan 2022 21:54:31: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:54:31: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:54:31: #1 total tags in treatment: 2493392 INFO @ Sat, 15 Jan 2022 21:54:31: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:54:31: #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 21:54:31: #1 tags after filtering in treatment: 1825912 INFO @ Sat, 15 Jan 2022 21:54:31: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:54:31: #1 finished! INFO @ Sat, 15 Jan 2022 21:54:31: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:54:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:54:31: #2 number of paired peaks: 256 WARNING @ Sat, 15 Jan 2022 21:54:31: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Sat, 15 Jan 2022 21:54:31: start model_add_line... INFO @ Sat, 15 Jan 2022 21:54:31: start X-correlation... INFO @ Sat, 15 Jan 2022 21:54:31: end of X-cor INFO @ Sat, 15 Jan 2022 21:54:31: #2 finished! INFO @ Sat, 15 Jan 2022 21:54:31: #2 predicted fragment length is 172 bps INFO @ Sat, 15 Jan 2022 21:54:31: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 15 Jan 2022 21:54:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.20_model.r WARNING @ Sat, 15 Jan 2022 21:54:31: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:54:31: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Sat, 15 Jan 2022 21:54:31: #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 21:54:31: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:54:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:54:36: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:54:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:54:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:54:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439560/ERX4439560.20_summits.bed INFO @ Sat, 15 Jan 2022 21:54:37: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (698 records, 4 fields): 14 millis CompletedMACS2peakCalling