Job ID = 14521741 SRX = ERX4439631 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3622482 spots for ERR4501560/ERR4501560.sra Written 3622482 spots for ERR4501560/ERR4501560.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: 00:03:25 3622482 reads; of these: 3622482 (100.00%) were paired; of these: 795263 (21.95%) aligned concordantly 0 times 2506862 (69.20%) aligned concordantly exactly 1 time 320357 (8.84%) aligned concordantly >1 times ---- 795263 pairs aligned concordantly 0 times; of these: 385440 (48.47%) aligned discordantly 1 time ---- 409823 pairs aligned 0 times concordantly or discordantly; of these: 819646 mates make up the pairs; of these: 652024 (79.55%) aligned 0 times 55935 (6.82%) aligned exactly 1 time 111687 (13.63%) aligned >1 times 91.00% overall alignment rate Time searching: 00:03:25 Overall time: 00:03:25 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] 68171 / 3185847 = 0.0214 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 21:40:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.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 21:40:31: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:40:31: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:40:37: 1000000 INFO @ Sat, 15 Jan 2022 21:40:43: 2000000 INFO @ Sat, 15 Jan 2022 21:40:49: 3000000 INFO @ Sat, 15 Jan 2022 21:40:55: 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 21:41:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.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 21:41:01: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:41:01: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:41:01: 5000000 INFO @ Sat, 15 Jan 2022 21:41:08: 6000000 INFO @ Sat, 15 Jan 2022 21:41:09: 1000000 INFO @ Sat, 15 Jan 2022 21:41:11: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:41:11: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:41:11: #1 total tags in treatment: 2771631 INFO @ Sat, 15 Jan 2022 21:41:11: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:41:11: #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 21:41:11: #1 tags after filtering in treatment: 2240875 INFO @ Sat, 15 Jan 2022 21:41:11: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 21:41:11: #1 finished! INFO @ Sat, 15 Jan 2022 21:41:11: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:41:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:41:11: #2 number of paired peaks: 136 WARNING @ Sat, 15 Jan 2022 21:41:11: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Sat, 15 Jan 2022 21:41:11: start model_add_line... INFO @ Sat, 15 Jan 2022 21:41:11: start X-correlation... INFO @ Sat, 15 Jan 2022 21:41:11: end of X-cor INFO @ Sat, 15 Jan 2022 21:41:11: #2 finished! INFO @ Sat, 15 Jan 2022 21:41:11: #2 predicted fragment length is 187 bps INFO @ Sat, 15 Jan 2022 21:41:11: #2 alternative fragment length(s) may be 187 bps INFO @ Sat, 15 Jan 2022 21:41:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.05_model.r WARNING @ Sat, 15 Jan 2022 21:41:11: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:41:11: #2 You may need to consider one of the other alternative d(s): 187 WARNING @ Sat, 15 Jan 2022 21:41:11: #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 21:41:11: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:41:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:41:17: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:41:17: 2000000 INFO @ Sat, 15 Jan 2022 21:41:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:41:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:41:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.05_summits.bed INFO @ Sat, 15 Jan 2022 21:41:20: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (1126 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:41:24: 3000000 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 21:41:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.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 21:41:31: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:41:31: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:41:31: 4000000 INFO @ Sat, 15 Jan 2022 21:41:38: 5000000 INFO @ Sat, 15 Jan 2022 21:41:39: 1000000 INFO @ Sat, 15 Jan 2022 21:41:46: 6000000 INFO @ Sat, 15 Jan 2022 21:41:48: 2000000 INFO @ Sat, 15 Jan 2022 21:41:49: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:41:49: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:41:49: #1 total tags in treatment: 2771631 INFO @ Sat, 15 Jan 2022 21:41:49: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:41:49: #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 21:41:49: #1 tags after filtering in treatment: 2240875 INFO @ Sat, 15 Jan 2022 21:41:49: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 21:41:49: #1 finished! INFO @ Sat, 15 Jan 2022 21:41:49: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:41:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:41:49: #2 number of paired peaks: 136 WARNING @ Sat, 15 Jan 2022 21:41:49: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Sat, 15 Jan 2022 21:41:49: start model_add_line... INFO @ Sat, 15 Jan 2022 21:41:49: start X-correlation... INFO @ Sat, 15 Jan 2022 21:41:49: end of X-cor INFO @ Sat, 15 Jan 2022 21:41:49: #2 finished! INFO @ Sat, 15 Jan 2022 21:41:49: #2 predicted fragment length is 187 bps INFO @ Sat, 15 Jan 2022 21:41:49: #2 alternative fragment length(s) may be 187 bps INFO @ Sat, 15 Jan 2022 21:41:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.10_model.r WARNING @ Sat, 15 Jan 2022 21:41:49: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:41:49: #2 You may need to consider one of the other alternative d(s): 187 WARNING @ Sat, 15 Jan 2022 21:41:49: #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 21:41:49: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:41:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:41:55: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:41:56: 3000000 INFO @ Sat, 15 Jan 2022 21:41:57: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:41:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:41:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.10_summits.bed INFO @ Sat, 15 Jan 2022 21:41:57: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (824 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:42:04: 4000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:42:12: 5000000 INFO @ Sat, 15 Jan 2022 21:42:20: 6000000 INFO @ Sat, 15 Jan 2022 21:42:24: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:42:24: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:42:24: #1 total tags in treatment: 2771631 INFO @ Sat, 15 Jan 2022 21:42:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:42:24: #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 21:42:24: #1 tags after filtering in treatment: 2240875 INFO @ Sat, 15 Jan 2022 21:42:24: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 21:42:24: #1 finished! INFO @ Sat, 15 Jan 2022 21:42:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:42:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:42:24: #2 number of paired peaks: 136 WARNING @ Sat, 15 Jan 2022 21:42:24: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Sat, 15 Jan 2022 21:42:24: start model_add_line... INFO @ Sat, 15 Jan 2022 21:42:24: start X-correlation... INFO @ Sat, 15 Jan 2022 21:42:24: end of X-cor INFO @ Sat, 15 Jan 2022 21:42:24: #2 finished! INFO @ Sat, 15 Jan 2022 21:42:24: #2 predicted fragment length is 187 bps INFO @ Sat, 15 Jan 2022 21:42:24: #2 alternative fragment length(s) may be 187 bps INFO @ Sat, 15 Jan 2022 21:42:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.20_model.r WARNING @ Sat, 15 Jan 2022 21:42:24: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:42:24: #2 You may need to consider one of the other alternative d(s): 187 WARNING @ Sat, 15 Jan 2022 21:42:24: #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 21:42:24: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:42:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:42:29: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:42:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:42:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:42:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439631/ERX4439631.20_summits.bed INFO @ Sat, 15 Jan 2022 21:42:31: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (555 records, 4 fields): 2 millis CompletedMACS2peakCalling