Job ID = 14521680 SRX = ERX4439610 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3570001 spots for ERR4501539/ERR4501539.sra Written 3570001 spots for ERR4501539/ERR4501539.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: 00:03:04 3570001 reads; of these: 3570001 (100.00%) were paired; of these: 747918 (20.95%) aligned concordantly 0 times 2254693 (63.16%) aligned concordantly exactly 1 time 567390 (15.89%) aligned concordantly >1 times ---- 747918 pairs aligned concordantly 0 times; of these: 318111 (42.53%) aligned discordantly 1 time ---- 429807 pairs aligned 0 times concordantly or discordantly; of these: 859614 mates make up the pairs; of these: 616619 (71.73%) aligned 0 times 54730 (6.37%) aligned exactly 1 time 188265 (21.90%) aligned >1 times 91.36% overall alignment rate Time searching: 00:03:04 Overall time: 00:03:04 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] 138006 / 3112567 = 0.0443 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 21:31:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.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 21:31:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:31:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:31:19: 1000000 INFO @ Sat, 15 Jan 2022 21:31:24: 2000000 INFO @ Sat, 15 Jan 2022 21:31:30: 3000000 INFO @ Sat, 15 Jan 2022 21:31:36: 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 21:31:42: 5000000 INFO @ Sat, 15 Jan 2022 21:31:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.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 21:31:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:31:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:31:49: 6000000 INFO @ Sat, 15 Jan 2022 21:31:49: 1000000 INFO @ Sat, 15 Jan 2022 21:31:50: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:31:50: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:31:50: #1 total tags in treatment: 2701561 INFO @ Sat, 15 Jan 2022 21:31:50: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:31:50: #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 21:31:51: #1 tags after filtering in treatment: 2029886 INFO @ Sat, 15 Jan 2022 21:31:51: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 21:31:51: #1 finished! INFO @ Sat, 15 Jan 2022 21:31:51: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:31:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:31:51: #2 number of paired peaks: 165 WARNING @ Sat, 15 Jan 2022 21:31:51: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Sat, 15 Jan 2022 21:31:51: start model_add_line... INFO @ Sat, 15 Jan 2022 21:31:51: start X-correlation... INFO @ Sat, 15 Jan 2022 21:31:51: end of X-cor INFO @ Sat, 15 Jan 2022 21:31:51: #2 finished! INFO @ Sat, 15 Jan 2022 21:31:51: #2 predicted fragment length is 171 bps INFO @ Sat, 15 Jan 2022 21:31:51: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 15 Jan 2022 21:31:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.05_model.r WARNING @ Sat, 15 Jan 2022 21:31:51: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:31:51: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Sat, 15 Jan 2022 21:31:51: #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 21:31:51: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:31:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:31:55: 2000000 INFO @ Sat, 15 Jan 2022 21:31:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:31:57: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:31:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:31:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.05_summits.bed INFO @ Sat, 15 Jan 2022 21:31:58: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1304 records, 4 fields): 118 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:32:01: 3000000 INFO @ Sat, 15 Jan 2022 21:32:07: 4000000 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 21:32:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.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 21:32:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:32:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:32:13: 5000000 INFO @ Sat, 15 Jan 2022 21:32:20: 6000000 INFO @ Sat, 15 Jan 2022 21:32:20: 1000000 INFO @ Sat, 15 Jan 2022 21:32:22: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:32:22: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:32:22: #1 total tags in treatment: 2701561 INFO @ Sat, 15 Jan 2022 21:32:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:32:22: #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 21:32:22: #1 tags after filtering in treatment: 2029886 INFO @ Sat, 15 Jan 2022 21:32:22: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 21:32:22: #1 finished! INFO @ Sat, 15 Jan 2022 21:32:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:32:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:32:22: #2 number of paired peaks: 165 WARNING @ Sat, 15 Jan 2022 21:32:22: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Sat, 15 Jan 2022 21:32:22: start model_add_line... INFO @ Sat, 15 Jan 2022 21:32:22: start X-correlation... INFO @ Sat, 15 Jan 2022 21:32:22: end of X-cor INFO @ Sat, 15 Jan 2022 21:32:22: #2 finished! INFO @ Sat, 15 Jan 2022 21:32:22: #2 predicted fragment length is 171 bps INFO @ Sat, 15 Jan 2022 21:32:22: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 15 Jan 2022 21:32:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.10_model.r WARNING @ Sat, 15 Jan 2022 21:32:22: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:32:22: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Sat, 15 Jan 2022 21:32:22: #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 21:32:22: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:32:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:32:27: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:32:28: 2000000 INFO @ Sat, 15 Jan 2022 21:32:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:32:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:32:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.10_summits.bed INFO @ Sat, 15 Jan 2022 21:32:29: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (915 records, 4 fields): 143 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:32:36: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:32:43: 4000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:32:51: 5000000 INFO @ Sat, 15 Jan 2022 21:32:58: 6000000 INFO @ Sat, 15 Jan 2022 21:33:00: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:33:00: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:33:00: #1 total tags in treatment: 2701561 INFO @ Sat, 15 Jan 2022 21:33:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:33:00: #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 21:33:00: #1 tags after filtering in treatment: 2029886 INFO @ Sat, 15 Jan 2022 21:33:00: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 21:33:00: #1 finished! INFO @ Sat, 15 Jan 2022 21:33:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:33:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:33:01: #2 number of paired peaks: 165 WARNING @ Sat, 15 Jan 2022 21:33:01: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Sat, 15 Jan 2022 21:33:01: start model_add_line... INFO @ Sat, 15 Jan 2022 21:33:01: start X-correlation... INFO @ Sat, 15 Jan 2022 21:33:01: end of X-cor INFO @ Sat, 15 Jan 2022 21:33:01: #2 finished! INFO @ Sat, 15 Jan 2022 21:33:01: #2 predicted fragment length is 171 bps INFO @ Sat, 15 Jan 2022 21:33:01: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 15 Jan 2022 21:33:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.20_model.r WARNING @ Sat, 15 Jan 2022 21:33:01: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:33:01: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Sat, 15 Jan 2022 21:33:01: #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 21:33:01: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:33:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:33:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:33:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:33:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:33:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439610/ERX4439610.20_summits.bed INFO @ Sat, 15 Jan 2022 21:33:07: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (548 records, 4 fields): 2 millis CompletedMACS2peakCalling