Job ID = 7111283 SRX = SRX8189511 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-22T05:04:59 prefetch.2.10.7: 1) Downloading 'SRR11625407'... 2020-07-22T05:04:59 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:05:18 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:05:18 prefetch.2.10.7: 'SRR11625407' is valid 2020-07-22T05:05:18 prefetch.2.10.7: 1) 'SRR11625407' was downloaded successfully 2020-07-22T05:06:00 prefetch.2.10.7: 'SRR11625407' has 8 unresolved dependencies 2020-07-22T05:06:00 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001133.9?vdb-ctx=refseq'... 2020-07-22T05:06:00 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:06:07 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:06:07 prefetch.2.10.7: 2) 'ncbi-acc:NC_001133.9?vdb-ctx=refseq' was downloaded successfully 2020-07-22T05:06:07 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001134.8?vdb-ctx=refseq'... 2020-07-22T05:06:07 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:06:15 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:06:15 prefetch.2.10.7: 3) 'ncbi-acc:NC_001134.8?vdb-ctx=refseq' was downloaded successfully 2020-07-22T05:06:15 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001135.5?vdb-ctx=refseq'... 2020-07-22T05:06:15 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:06:22 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:06:22 prefetch.2.10.7: 4) 'ncbi-acc:NC_001135.5?vdb-ctx=refseq' was downloaded successfully 2020-07-22T05:06:22 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001136.10?vdb-ctx=refseq'... 2020-07-22T05:06:22 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:06:30 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:06:30 prefetch.2.10.7: 5) 'ncbi-acc:NC_001136.10?vdb-ctx=refseq' was downloaded successfully 2020-07-22T05:06:30 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001139.9?vdb-ctx=refseq'... 2020-07-22T05:06:30 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:06:38 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:06:38 prefetch.2.10.7: 6) 'ncbi-acc:NC_001139.9?vdb-ctx=refseq' was downloaded successfully 2020-07-22T05:06:38 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NC_001144.5?vdb-ctx=refseq'... 2020-07-22T05:06:38 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:06:50 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:06:50 prefetch.2.10.7: 7) 'ncbi-acc:NC_001144.5?vdb-ctx=refseq' was downloaded successfully 2020-07-22T05:06:50 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NC_001147.6?vdb-ctx=refseq'... 2020-07-22T05:06:50 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:06:59 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:06:59 prefetch.2.10.7: 8) 'ncbi-acc:NC_001147.6?vdb-ctx=refseq' was downloaded successfully 2020-07-22T05:06:59 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-07-22T05:06:59 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:07:05 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:07:05 prefetch.2.10.7: 9) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 2962173 spots for SRR11625407/SRR11625407.sra Written 2962173 spots for SRR11625407/SRR11625407.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: 00:00:01 Multiseed full-index search: 00:00:22 2962173 reads; of these: 2962173 (100.00%) were unpaired; of these: 164826 (5.56%) aligned 0 times 1313526 (44.34%) aligned exactly 1 time 1483821 (50.09%) aligned >1 times 94.44% overall alignment rate Time searching: 00:00:23 Overall time: 00:00:23 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_rmdupse_core] 1874945 / 2797347 = 0.6703 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 @ Wed, 22 Jul 2020 14:08:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.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 @ Wed, 22 Jul 2020 14:08:42: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:08:42: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:08:47: #1 tag size is determined as 64 bps INFO @ Wed, 22 Jul 2020 14:08:47: #1 tag size = 64 INFO @ Wed, 22 Jul 2020 14:08:47: #1 total tags in treatment: 922402 INFO @ Wed, 22 Jul 2020 14:08:47: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:08:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 14:08:47: #1 tags after filtering in treatment: 922402 INFO @ Wed, 22 Jul 2020 14:08:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 14:08:47: #1 finished! INFO @ Wed, 22 Jul 2020 14:08:47: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:08:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:08:47: #2 number of paired peaks: 196 WARNING @ Wed, 22 Jul 2020 14:08:47: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Wed, 22 Jul 2020 14:08:47: start model_add_line... INFO @ Wed, 22 Jul 2020 14:08:47: start X-correlation... INFO @ Wed, 22 Jul 2020 14:08:47: end of X-cor INFO @ Wed, 22 Jul 2020 14:08:47: #2 finished! INFO @ Wed, 22 Jul 2020 14:08:47: #2 predicted fragment length is 258 bps INFO @ Wed, 22 Jul 2020 14:08:47: #2 alternative fragment length(s) may be 258 bps INFO @ Wed, 22 Jul 2020 14:08:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.05_model.r INFO @ Wed, 22 Jul 2020 14:08:47: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:08:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 14:08:49: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:08:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.05_peaks.xls INFO @ Wed, 22 Jul 2020 14:08:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:08:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.05_summits.bed INFO @ Wed, 22 Jul 2020 14:08:50: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (570 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 @ Wed, 22 Jul 2020 14:09:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.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 @ Wed, 22 Jul 2020 14:09:12: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:09:12: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:09:16: #1 tag size is determined as 64 bps INFO @ Wed, 22 Jul 2020 14:09:16: #1 tag size = 64 INFO @ Wed, 22 Jul 2020 14:09:16: #1 total tags in treatment: 922402 INFO @ Wed, 22 Jul 2020 14:09:16: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:09:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 14:09:16: #1 tags after filtering in treatment: 922402 INFO @ Wed, 22 Jul 2020 14:09:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 14:09:16: #1 finished! INFO @ Wed, 22 Jul 2020 14:09:16: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:09:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:09:16: #2 number of paired peaks: 196 WARNING @ Wed, 22 Jul 2020 14:09:16: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Wed, 22 Jul 2020 14:09:16: start model_add_line... INFO @ Wed, 22 Jul 2020 14:09:16: start X-correlation... INFO @ Wed, 22 Jul 2020 14:09:16: end of X-cor INFO @ Wed, 22 Jul 2020 14:09:16: #2 finished! INFO @ Wed, 22 Jul 2020 14:09:16: #2 predicted fragment length is 258 bps INFO @ Wed, 22 Jul 2020 14:09:16: #2 alternative fragment length(s) may be 258 bps INFO @ Wed, 22 Jul 2020 14:09:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.10_model.r INFO @ Wed, 22 Jul 2020 14:09:16: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:09:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 14:09:19: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:09:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.10_peaks.xls INFO @ Wed, 22 Jul 2020 14:09:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:09:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.10_summits.bed INFO @ Wed, 22 Jul 2020 14:09:20: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (391 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 @ Wed, 22 Jul 2020 14:09:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.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 @ Wed, 22 Jul 2020 14:09:42: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:09:42: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 14:09:47: #1 tag size is determined as 64 bps INFO @ Wed, 22 Jul 2020 14:09:47: #1 tag size = 64 INFO @ Wed, 22 Jul 2020 14:09:47: #1 total tags in treatment: 922402 INFO @ Wed, 22 Jul 2020 14:09:47: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:09:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 14:09:47: #1 tags after filtering in treatment: 922402 INFO @ Wed, 22 Jul 2020 14:09:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 14:09:47: #1 finished! INFO @ Wed, 22 Jul 2020 14:09:47: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:09:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:09:47: #2 number of paired peaks: 196 WARNING @ Wed, 22 Jul 2020 14:09:47: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Wed, 22 Jul 2020 14:09:47: start model_add_line... INFO @ Wed, 22 Jul 2020 14:09:47: start X-correlation... INFO @ Wed, 22 Jul 2020 14:09:47: end of X-cor INFO @ Wed, 22 Jul 2020 14:09:47: #2 finished! INFO @ Wed, 22 Jul 2020 14:09:47: #2 predicted fragment length is 258 bps INFO @ Wed, 22 Jul 2020 14:09:47: #2 alternative fragment length(s) may be 258 bps INFO @ Wed, 22 Jul 2020 14:09:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.20_model.r INFO @ Wed, 22 Jul 2020 14:09:47: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:09:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 14:09:49: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:09:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.20_peaks.xls INFO @ Wed, 22 Jul 2020 14:09:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:09:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8189511/SRX8189511.20_summits.bed INFO @ Wed, 22 Jul 2020 14:09:50: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (247 records, 4 fields): 1 millis CompletedMACS2peakCalling