Job ID = 10223838 SRX = ERX4439593 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-10-15T23:21:32 prefetch.2.10.7: 1) Downloading 'ERR4501522'... 2020-10-15T23:21:32 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:22:09 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:22:10 prefetch.2.10.7: 'ERR4501522' is valid 2020-10-15T23:22:10 prefetch.2.10.7: 1) 'ERR4501522' was downloaded successfully 2020-10-15T23:22:37 prefetch.2.10.7: 'ERR4501522' has 5 unresolved dependencies 2020-10-15T23:22:37 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001136.8?vdb-ctx=refseq'... 2020-10-15T23:22:37 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:22:49 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:22:49 prefetch.2.10.7: 2) 'ncbi-acc:NC_001136.8?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:22:49 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001139.7?vdb-ctx=refseq'... 2020-10-15T23:22:49 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:23:01 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:23:01 prefetch.2.10.7: 3) 'ncbi-acc:NC_001139.7?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:23:01 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001144.4?vdb-ctx=refseq'... 2020-10-15T23:23:01 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:23:13 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:23:13 prefetch.2.10.7: 4) 'ncbi-acc:NC_001144.4?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:23:13 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001147.5?vdb-ctx=refseq'... 2020-10-15T23:23:13 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:23:25 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:23:25 prefetch.2.10.7: 5) 'ncbi-acc:NC_001147.5?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:23:25 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-10-15T23:23:25 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:23:31 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:23:31 prefetch.2.10.7: 6) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 3537948 spots for ERR4501522/ERR4501522.sra Written 3537948 spots for ERR4501522/ERR4501522.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: 00:02:34 3537948 reads; of these: 3537948 (100.00%) were paired; of these: 1044852 (29.53%) aligned concordantly 0 times 2235955 (63.20%) aligned concordantly exactly 1 time 257141 (7.27%) aligned concordantly >1 times ---- 1044852 pairs aligned concordantly 0 times; of these: 443534 (42.45%) aligned discordantly 1 time ---- 601318 pairs aligned 0 times concordantly or discordantly; of these: 1202636 mates make up the pairs; of these: 1037825 (86.30%) aligned 0 times 61670 (5.13%) aligned exactly 1 time 103141 (8.58%) aligned >1 times 85.33% overall alignment rate Time searching: 00:02:34 Overall time: 00:02:34 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] 38116 / 2907414 = 0.0131 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 08:29:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.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 @ Fri, 16 Oct 2020 08:29:44: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:29:44: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:29:49: 1000000 INFO @ Fri, 16 Oct 2020 08:29:54: 2000000 INFO @ Fri, 16 Oct 2020 08:30:00: 3000000 INFO @ Fri, 16 Oct 2020 08:30:05: 4000000 INFO @ Fri, 16 Oct 2020 08:30:11: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 08:30:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.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 @ Fri, 16 Oct 2020 08:30:14: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:30:14: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:30:16: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:30:16: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:30:16: #1 total tags in treatment: 2462298 INFO @ Fri, 16 Oct 2020 08:30:16: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:30:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:30:16: #1 tags after filtering in treatment: 2224753 INFO @ Fri, 16 Oct 2020 08:30:16: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 16 Oct 2020 08:30:16: #1 finished! INFO @ Fri, 16 Oct 2020 08:30:16: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:30:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:30:16: #2 number of paired peaks: 172 WARNING @ Fri, 16 Oct 2020 08:30:16: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Fri, 16 Oct 2020 08:30:16: start model_add_line... INFO @ Fri, 16 Oct 2020 08:30:16: start X-correlation... INFO @ Fri, 16 Oct 2020 08:30:16: end of X-cor INFO @ Fri, 16 Oct 2020 08:30:16: #2 finished! INFO @ Fri, 16 Oct 2020 08:30:16: #2 predicted fragment length is 159 bps INFO @ Fri, 16 Oct 2020 08:30:16: #2 alternative fragment length(s) may be 1,138,159,186,565,597 bps INFO @ Fri, 16 Oct 2020 08:30:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.05_model.r WARNING @ Fri, 16 Oct 2020 08:30:16: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:30:16: #2 You may need to consider one of the other alternative d(s): 1,138,159,186,565,597 WARNING @ Fri, 16 Oct 2020 08:30:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Oct 2020 08:30:16: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:30:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:30:19: 1000000 INFO @ Fri, 16 Oct 2020 08:30:20: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:30:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.05_peaks.xls INFO @ Fri, 16 Oct 2020 08:30:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:30:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.05_summits.bed INFO @ Fri, 16 Oct 2020 08:30:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (24 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:30:25: 2000000 INFO @ Fri, 16 Oct 2020 08:30:30: 3000000 INFO @ Fri, 16 Oct 2020 08:30:35: 4000000 INFO @ Fri, 16 Oct 2020 08:30:41: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 08:30:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.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 @ Fri, 16 Oct 2020 08:30:44: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:30:44: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:30:46: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:30:46: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:30:46: #1 total tags in treatment: 2462298 INFO @ Fri, 16 Oct 2020 08:30:46: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:30:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:30:46: #1 tags after filtering in treatment: 2224753 INFO @ Fri, 16 Oct 2020 08:30:46: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 16 Oct 2020 08:30:46: #1 finished! INFO @ Fri, 16 Oct 2020 08:30:46: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:30:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:30:46: #2 number of paired peaks: 172 WARNING @ Fri, 16 Oct 2020 08:30:46: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Fri, 16 Oct 2020 08:30:46: start model_add_line... INFO @ Fri, 16 Oct 2020 08:30:46: start X-correlation... INFO @ Fri, 16 Oct 2020 08:30:46: end of X-cor INFO @ Fri, 16 Oct 2020 08:30:46: #2 finished! INFO @ Fri, 16 Oct 2020 08:30:46: #2 predicted fragment length is 159 bps INFO @ Fri, 16 Oct 2020 08:30:46: #2 alternative fragment length(s) may be 1,138,159,186,565,597 bps INFO @ Fri, 16 Oct 2020 08:30:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.10_model.r WARNING @ Fri, 16 Oct 2020 08:30:46: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:30:46: #2 You may need to consider one of the other alternative d(s): 1,138,159,186,565,597 WARNING @ Fri, 16 Oct 2020 08:30:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Oct 2020 08:30:46: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:30:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:30:49: 1000000 INFO @ Fri, 16 Oct 2020 08:30:51: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:30:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.10_peaks.xls INFO @ Fri, 16 Oct 2020 08:30:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:30:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.10_summits.bed INFO @ Fri, 16 Oct 2020 08:30:52: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:30:54: 2000000 INFO @ Fri, 16 Oct 2020 08:31:00: 3000000 INFO @ Fri, 16 Oct 2020 08:31:05: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:31:11: 5000000 INFO @ Fri, 16 Oct 2020 08:31:16: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:31:16: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:31:16: #1 total tags in treatment: 2462298 INFO @ Fri, 16 Oct 2020 08:31:16: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:31:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:31:16: #1 tags after filtering in treatment: 2224753 INFO @ Fri, 16 Oct 2020 08:31:16: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 16 Oct 2020 08:31:16: #1 finished! INFO @ Fri, 16 Oct 2020 08:31:16: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:31:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:31:16: #2 number of paired peaks: 172 WARNING @ Fri, 16 Oct 2020 08:31:16: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Fri, 16 Oct 2020 08:31:16: start model_add_line... INFO @ Fri, 16 Oct 2020 08:31:16: start X-correlation... INFO @ Fri, 16 Oct 2020 08:31:16: end of X-cor INFO @ Fri, 16 Oct 2020 08:31:16: #2 finished! INFO @ Fri, 16 Oct 2020 08:31:16: #2 predicted fragment length is 159 bps INFO @ Fri, 16 Oct 2020 08:31:16: #2 alternative fragment length(s) may be 1,138,159,186,565,597 bps INFO @ Fri, 16 Oct 2020 08:31:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.20_model.r WARNING @ Fri, 16 Oct 2020 08:31:16: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 08:31:16: #2 You may need to consider one of the other alternative d(s): 1,138,159,186,565,597 WARNING @ Fri, 16 Oct 2020 08:31:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Oct 2020 08:31:16: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:31:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:31:20: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:31:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.20_peaks.xls INFO @ Fri, 16 Oct 2020 08:31:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:31:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439593/ERX4439593.20_summits.bed INFO @ Fri, 16 Oct 2020 08:31:22: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling