Job ID = 14519999 SRX = SRX10341717 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T09:10:55 prefetch.2.10.7: 1) Downloading 'SRR13963725'... 2022-01-15T09:10:55 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T09:11:05 prefetch.2.10.7: HTTPS download succeed 2022-01-15T09:11:05 prefetch.2.10.7: 'SRR13963725' is valid 2022-01-15T09:11:05 prefetch.2.10.7: 1) 'SRR13963725' was downloaded successfully 2022-01-15T09:12:12 prefetch.2.10.7: 'SRR13963725' has 7 unresolved dependencies 2022-01-15T09:12:12 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001133.9?vdb-ctx=refseq'... 2022-01-15T09:12:12 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T09:12:13 prefetch.2.10.7: HTTPS download succeed 2022-01-15T09:12:13 prefetch.2.10.7: 2) 'ncbi-acc:NC_001133.9?vdb-ctx=refseq' was downloaded successfully 2022-01-15T09:12:13 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001134.8?vdb-ctx=refseq'... 2022-01-15T09:12:13 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T09:12:15 prefetch.2.10.7: HTTPS download succeed 2022-01-15T09:12:15 prefetch.2.10.7: 3) 'ncbi-acc:NC_001134.8?vdb-ctx=refseq' was downloaded successfully 2022-01-15T09:12:15 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001135.5?vdb-ctx=refseq'... 2022-01-15T09:12:15 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T09:12:16 prefetch.2.10.7: HTTPS download succeed 2022-01-15T09:12:16 prefetch.2.10.7: 4) 'ncbi-acc:NC_001135.5?vdb-ctx=refseq' was downloaded successfully 2022-01-15T09:12:16 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001136.10?vdb-ctx=refseq'... 2022-01-15T09:12:16 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T09:12:17 prefetch.2.10.7: HTTPS download succeed 2022-01-15T09:12:17 prefetch.2.10.7: 5) 'ncbi-acc:NC_001136.10?vdb-ctx=refseq' was downloaded successfully 2022-01-15T09:12:17 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001139.9?vdb-ctx=refseq'... 2022-01-15T09:12:17 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T09:12:19 prefetch.2.10.7: HTTPS download succeed 2022-01-15T09:12:19 prefetch.2.10.7: 6) 'ncbi-acc:NC_001139.9?vdb-ctx=refseq' was downloaded successfully 2022-01-15T09:12:19 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NC_001144.5?vdb-ctx=refseq'... 2022-01-15T09:12:19 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T09:12:20 prefetch.2.10.7: HTTPS download succeed 2022-01-15T09:12:20 prefetch.2.10.7: 7) 'ncbi-acc:NC_001144.5?vdb-ctx=refseq' was downloaded successfully 2022-01-15T09:12:20 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NC_001147.6?vdb-ctx=refseq'... 2022-01-15T09:12:20 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T09:12:22 prefetch.2.10.7: HTTPS download succeed 2022-01-15T09:12:22 prefetch.2.10.7: 8) 'ncbi-acc:NC_001147.6?vdb-ctx=refseq' was downloaded successfully Read 1450662 spots for SRR13963725/SRR13963725.sra Written 1450662 spots for SRR13963725/SRR13963725.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: 00:02:01 1450662 reads; of these: 1450662 (100.00%) were paired; of these: 5 (0.00%) aligned concordantly 0 times 1426028 (98.30%) aligned concordantly exactly 1 time 24629 (1.70%) aligned concordantly >1 times ---- 5 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 5 pairs aligned 0 times concordantly or discordantly; of these: 10 mates make up the pairs; of these: 5 (50.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 5 (50.00%) aligned >1 times 100.00% overall alignment rate Time searching: 00:02:01 Overall time: 00:02:01 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 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] 0 / 1076830 = 0.0000 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 18:17:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.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 18:17:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:17:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:17:27: 1000000 INFO @ Sat, 15 Jan 2022 18:17:36: 2000000 INFO @ Sat, 15 Jan 2022 18:17:44: #1 tag size is determined as 140 bps INFO @ Sat, 15 Jan 2022 18:17:44: #1 tag size = 140 INFO @ Sat, 15 Jan 2022 18:17:44: #1 total tags in treatment: 1450657 INFO @ Sat, 15 Jan 2022 18:17:44: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:17:44: #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 18:17:44: #1 tags after filtering in treatment: 1043853 INFO @ Sat, 15 Jan 2022 18:17:44: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 18:17:44: #1 finished! INFO @ Sat, 15 Jan 2022 18:17:44: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:17:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:17:44: #2 number of paired peaks: 250 WARNING @ Sat, 15 Jan 2022 18:17:44: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Sat, 15 Jan 2022 18:17:44: start model_add_line... INFO @ Sat, 15 Jan 2022 18:17:44: start X-correlation... INFO @ Sat, 15 Jan 2022 18:17:44: end of X-cor INFO @ Sat, 15 Jan 2022 18:17:44: #2 finished! INFO @ Sat, 15 Jan 2022 18:17:44: #2 predicted fragment length is 133 bps INFO @ Sat, 15 Jan 2022 18:17:44: #2 alternative fragment length(s) may be 133 bps INFO @ Sat, 15 Jan 2022 18:17:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.05_model.r WARNING @ Sat, 15 Jan 2022 18:17:45: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:17:45: #2 You may need to consider one of the other alternative d(s): 133 WARNING @ Sat, 15 Jan 2022 18:17:45: #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 18:17:45: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:17:45: #3 Pre-compute pvalue-qvalue table... 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 18:17:47: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:17:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.05_peaks.xls INFO @ Sat, 15 Jan 2022 18:17:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:17:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.05_summits.bed INFO @ Sat, 15 Jan 2022 18:17:49: Done! INFO @ Sat, 15 Jan 2022 18:17:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.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 18:17:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:17:49: #1 read treatment tags... pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (1513 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 18:17:57: 1000000 INFO @ Sat, 15 Jan 2022 18:18:06: 2000000 INFO @ Sat, 15 Jan 2022 18:18:14: #1 tag size is determined as 140 bps INFO @ Sat, 15 Jan 2022 18:18:14: #1 tag size = 140 INFO @ Sat, 15 Jan 2022 18:18:14: #1 total tags in treatment: 1450657 INFO @ Sat, 15 Jan 2022 18:18:14: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:18:14: #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 18:18:14: #1 tags after filtering in treatment: 1043853 INFO @ Sat, 15 Jan 2022 18:18:14: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 18:18:14: #1 finished! INFO @ Sat, 15 Jan 2022 18:18:14: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:18:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:18:14: #2 number of paired peaks: 250 WARNING @ Sat, 15 Jan 2022 18:18:14: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Sat, 15 Jan 2022 18:18:14: start model_add_line... INFO @ Sat, 15 Jan 2022 18:18:14: start X-correlation... INFO @ Sat, 15 Jan 2022 18:18:14: end of X-cor INFO @ Sat, 15 Jan 2022 18:18:14: #2 finished! INFO @ Sat, 15 Jan 2022 18:18:14: #2 predicted fragment length is 133 bps INFO @ Sat, 15 Jan 2022 18:18:14: #2 alternative fragment length(s) may be 133 bps INFO @ Sat, 15 Jan 2022 18:18:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.10_model.r WARNING @ Sat, 15 Jan 2022 18:18:14: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:18:14: #2 You may need to consider one of the other alternative d(s): 133 WARNING @ Sat, 15 Jan 2022 18:18:14: #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 18:18:14: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:18:14: #3 Pre-compute pvalue-qvalue table... 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 18:18:17: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:18:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.10_peaks.xls INFO @ Sat, 15 Jan 2022 18:18:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:18:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.10_summits.bed INFO @ Sat, 15 Jan 2022 18:18:18: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (951 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 18:18:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.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 18:18:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:18:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:18:28: 1000000 INFO @ Sat, 15 Jan 2022 18:18:36: 2000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 18:18:44: #1 tag size is determined as 140 bps INFO @ Sat, 15 Jan 2022 18:18:44: #1 tag size = 140 INFO @ Sat, 15 Jan 2022 18:18:44: #1 total tags in treatment: 1450657 INFO @ Sat, 15 Jan 2022 18:18:44: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:18:44: #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 18:18:44: #1 tags after filtering in treatment: 1043853 INFO @ Sat, 15 Jan 2022 18:18:44: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 18:18:44: #1 finished! INFO @ Sat, 15 Jan 2022 18:18:44: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:18:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:18:45: #2 number of paired peaks: 250 WARNING @ Sat, 15 Jan 2022 18:18:45: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Sat, 15 Jan 2022 18:18:45: start model_add_line... INFO @ Sat, 15 Jan 2022 18:18:45: start X-correlation... INFO @ Sat, 15 Jan 2022 18:18:45: end of X-cor INFO @ Sat, 15 Jan 2022 18:18:45: #2 finished! INFO @ Sat, 15 Jan 2022 18:18:45: #2 predicted fragment length is 133 bps INFO @ Sat, 15 Jan 2022 18:18:45: #2 alternative fragment length(s) may be 133 bps INFO @ Sat, 15 Jan 2022 18:18:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.20_model.r WARNING @ Sat, 15 Jan 2022 18:18:45: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:18:45: #2 You may need to consider one of the other alternative d(s): 133 WARNING @ Sat, 15 Jan 2022 18:18:45: #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 18:18:45: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:18:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:18:47: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:18:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.20_peaks.xls INFO @ Sat, 15 Jan 2022 18:18:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:18:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10341717/SRX10341717.20_summits.bed INFO @ Sat, 15 Jan 2022 18:18:48: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (510 records, 4 fields): 3 millis CompletedMACS2peakCalling