Job ID = 14521892 SRX = ERX4439576 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3354100 spots for ERR4501505/ERR4501505.sra Written 3354100 spots for ERR4501505/ERR4501505.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: 00:02:36 3354100 reads; of these: 3354100 (100.00%) were paired; of these: 1001664 (29.86%) aligned concordantly 0 times 2050806 (61.14%) aligned concordantly exactly 1 time 301630 (8.99%) aligned concordantly >1 times ---- 1001664 pairs aligned concordantly 0 times; of these: 461742 (46.10%) aligned discordantly 1 time ---- 539922 pairs aligned 0 times concordantly or discordantly; of these: 1079844 mates make up the pairs; of these: 868398 (80.42%) aligned 0 times 65012 (6.02%) aligned exactly 1 time 146434 (13.56%) aligned >1 times 87.05% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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] 51076 / 2784012 = 0.0183 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 21:55:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.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 21:55:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:55:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:55:13: 1000000 INFO @ Sat, 15 Jan 2022 21:55:19: 2000000 INFO @ Sat, 15 Jan 2022 21:55:25: 3000000 INFO @ Sat, 15 Jan 2022 21:55:32: 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 21:55:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.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 21:55:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:55:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:55:38: 5000000 INFO @ Sat, 15 Jan 2022 21:55:43: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:55:43: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:55:43: #1 total tags in treatment: 2314627 INFO @ Sat, 15 Jan 2022 21:55:43: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:55:43: #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 21:55:43: #1 tags after filtering in treatment: 1874061 INFO @ Sat, 15 Jan 2022 21:55:43: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 21:55:43: #1 finished! INFO @ Sat, 15 Jan 2022 21:55:43: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:55:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:55:43: #2 number of paired peaks: 154 WARNING @ Sat, 15 Jan 2022 21:55:43: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Sat, 15 Jan 2022 21:55:43: start model_add_line... INFO @ Sat, 15 Jan 2022 21:55:43: start X-correlation... INFO @ Sat, 15 Jan 2022 21:55:43: end of X-cor INFO @ Sat, 15 Jan 2022 21:55:43: #2 finished! INFO @ Sat, 15 Jan 2022 21:55:43: #2 predicted fragment length is 177 bps INFO @ Sat, 15 Jan 2022 21:55:43: #2 alternative fragment length(s) may be 177 bps INFO @ Sat, 15 Jan 2022 21:55:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.05_model.r WARNING @ Sat, 15 Jan 2022 21:55:43: #2 Since the d (177) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:55:43: #2 You may need to consider one of the other alternative d(s): 177 WARNING @ Sat, 15 Jan 2022 21:55:43: #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 21:55:43: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:55:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:55:43: 1000000 INFO @ Sat, 15 Jan 2022 21:55:47: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:55:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:55:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:55:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.05_summits.bed INFO @ Sat, 15 Jan 2022 21:55:49: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1214 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:55:49: 2000000 INFO @ Sat, 15 Jan 2022 21:55:56: 3000000 INFO @ Sat, 15 Jan 2022 21:56:02: 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 21:56:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.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 21:56:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:56:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:56:08: 5000000 INFO @ Sat, 15 Jan 2022 21:56:13: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:56:13: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:56:13: #1 total tags in treatment: 2314627 INFO @ Sat, 15 Jan 2022 21:56:13: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:56:13: #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 21:56:13: #1 tags after filtering in treatment: 1874061 INFO @ Sat, 15 Jan 2022 21:56:13: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 21:56:13: #1 finished! INFO @ Sat, 15 Jan 2022 21:56:13: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:56:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:56:13: #2 number of paired peaks: 154 WARNING @ Sat, 15 Jan 2022 21:56:13: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Sat, 15 Jan 2022 21:56:13: start model_add_line... INFO @ Sat, 15 Jan 2022 21:56:13: start X-correlation... INFO @ Sat, 15 Jan 2022 21:56:13: end of X-cor INFO @ Sat, 15 Jan 2022 21:56:13: #2 finished! INFO @ Sat, 15 Jan 2022 21:56:13: #2 predicted fragment length is 177 bps INFO @ Sat, 15 Jan 2022 21:56:13: #2 alternative fragment length(s) may be 177 bps INFO @ Sat, 15 Jan 2022 21:56:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.10_model.r WARNING @ Sat, 15 Jan 2022 21:56:13: #2 Since the d (177) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:56:13: #2 You may need to consider one of the other alternative d(s): 177 WARNING @ Sat, 15 Jan 2022 21:56:13: #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 21:56:13: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:56:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:56:13: 1000000 INFO @ Sat, 15 Jan 2022 21:56:18: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:56:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:56:20: 2000000 INFO @ Sat, 15 Jan 2022 21:56:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:56:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.10_summits.bed INFO @ Sat, 15 Jan 2022 21:56:20: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (948 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:56:26: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:56:32: 4000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:56:39: 5000000 INFO @ Sat, 15 Jan 2022 21:56:43: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:56:43: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:56:43: #1 total tags in treatment: 2314627 INFO @ Sat, 15 Jan 2022 21:56:43: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:56:43: #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 21:56:43: #1 tags after filtering in treatment: 1874061 INFO @ Sat, 15 Jan 2022 21:56:43: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 21:56:43: #1 finished! INFO @ Sat, 15 Jan 2022 21:56:43: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:56:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:56:43: #2 number of paired peaks: 154 WARNING @ Sat, 15 Jan 2022 21:56:43: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Sat, 15 Jan 2022 21:56:43: start model_add_line... INFO @ Sat, 15 Jan 2022 21:56:43: start X-correlation... INFO @ Sat, 15 Jan 2022 21:56:43: end of X-cor INFO @ Sat, 15 Jan 2022 21:56:43: #2 finished! INFO @ Sat, 15 Jan 2022 21:56:43: #2 predicted fragment length is 177 bps INFO @ Sat, 15 Jan 2022 21:56:43: #2 alternative fragment length(s) may be 177 bps INFO @ Sat, 15 Jan 2022 21:56:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.20_model.r WARNING @ Sat, 15 Jan 2022 21:56:43: #2 Since the d (177) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:56:43: #2 You may need to consider one of the other alternative d(s): 177 WARNING @ Sat, 15 Jan 2022 21:56:43: #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 21:56:43: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:56:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:56:48: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:56:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:56:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:56:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439576/ERX4439576.20_summits.bed INFO @ Sat, 15 Jan 2022 21:56:50: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (731 records, 4 fields): 4 millis CompletedMACS2peakCalling