Job ID = 7113409 SRX = SRX8462166 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T05:35:59 prefetch.2.10.7: 1) Downloading 'SRR11915625'... 2020-07-22T05:35:59 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:37:37 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:37:38 prefetch.2.10.7: 'SRR11915625' is valid 2020-07-22T05:37:38 prefetch.2.10.7: 1) 'SRR11915625' was downloaded successfully 2020-07-22T05:37:38 prefetch.2.10.7: 'SRR11915625' has 0 unresolved dependencies Read 7555285 spots for SRR11915625/SRR11915625.sra Written 7555285 spots for SRR11915625/SRR11915625.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: 00:03:25 7555285 reads; of these: 7555285 (100.00%) were paired; of these: 4414653 (58.43%) aligned concordantly 0 times 2597740 (34.38%) aligned concordantly exactly 1 time 542892 (7.19%) aligned concordantly >1 times ---- 4414653 pairs aligned concordantly 0 times; of these: 13416 (0.30%) aligned discordantly 1 time ---- 4401237 pairs aligned 0 times concordantly or discordantly; of these: 8802474 mates make up the pairs; of these: 8734827 (99.23%) aligned 0 times 49206 (0.56%) aligned exactly 1 time 18441 (0.21%) aligned >1 times 42.19% overall alignment rate Time searching: 00:03:25 Overall time: 00:03:26 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] 2789062 / 3153768 = 0.8844 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 14:43:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.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 14:43:28: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:43:28: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:43:33: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 14:43:33: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 14:43:33: #1 total tags in treatment: 360323 INFO @ Wed, 22 Jul 2020 14:43:33: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:43:33: #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 14:43:33: #1 tags after filtering in treatment: 275522 INFO @ Wed, 22 Jul 2020 14:43:33: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Jul 2020 14:43:33: #1 finished! INFO @ Wed, 22 Jul 2020 14:43:33: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:43:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:43:33: #2 number of paired peaks: 187 WARNING @ Wed, 22 Jul 2020 14:43:33: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Wed, 22 Jul 2020 14:43:33: start model_add_line... INFO @ Wed, 22 Jul 2020 14:43:33: start X-correlation... INFO @ Wed, 22 Jul 2020 14:43:33: end of X-cor INFO @ Wed, 22 Jul 2020 14:43:33: #2 finished! INFO @ Wed, 22 Jul 2020 14:43:33: #2 predicted fragment length is 250 bps INFO @ Wed, 22 Jul 2020 14:43:33: #2 alternative fragment length(s) may be 12,115,164,183,196,212,250,297,483,486,532 bps INFO @ Wed, 22 Jul 2020 14:43:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.05_model.r INFO @ Wed, 22 Jul 2020 14:43:33: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:43:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 14:43:34: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:43:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.05_peaks.xls INFO @ Wed, 22 Jul 2020 14:43:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:43:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.05_summits.bed INFO @ Wed, 22 Jul 2020 14:43:34: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (60 records, 4 fields): 3 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 14:43:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.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 14:43:58: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:43:58: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:44:02: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 14:44:02: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 14:44:02: #1 total tags in treatment: 360323 INFO @ Wed, 22 Jul 2020 14:44:02: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:44:02: #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 14:44:02: #1 tags after filtering in treatment: 275522 INFO @ Wed, 22 Jul 2020 14:44:02: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Jul 2020 14:44:02: #1 finished! INFO @ Wed, 22 Jul 2020 14:44:02: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:44:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:44:02: #2 number of paired peaks: 187 WARNING @ Wed, 22 Jul 2020 14:44:02: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Wed, 22 Jul 2020 14:44:02: start model_add_line... INFO @ Wed, 22 Jul 2020 14:44:02: start X-correlation... INFO @ Wed, 22 Jul 2020 14:44:02: end of X-cor INFO @ Wed, 22 Jul 2020 14:44:02: #2 finished! INFO @ Wed, 22 Jul 2020 14:44:02: #2 predicted fragment length is 250 bps INFO @ Wed, 22 Jul 2020 14:44:02: #2 alternative fragment length(s) may be 12,115,164,183,196,212,250,297,483,486,532 bps INFO @ Wed, 22 Jul 2020 14:44:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.10_model.r INFO @ Wed, 22 Jul 2020 14:44:02: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:44:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 14:44:03: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:44:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.10_peaks.xls INFO @ Wed, 22 Jul 2020 14:44:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:44:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.10_summits.bed INFO @ Wed, 22 Jul 2020 14:44:04: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 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 14:44:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.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 14:44:28: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:44:28: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 14:44:33: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 14:44:33: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 14:44:33: #1 total tags in treatment: 360323 INFO @ Wed, 22 Jul 2020 14:44:33: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:44:33: #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 14:44:33: #1 tags after filtering in treatment: 275522 INFO @ Wed, 22 Jul 2020 14:44:33: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Jul 2020 14:44:33: #1 finished! INFO @ Wed, 22 Jul 2020 14:44:33: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:44:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:44:33: #2 number of paired peaks: 187 WARNING @ Wed, 22 Jul 2020 14:44:33: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Wed, 22 Jul 2020 14:44:33: start model_add_line... INFO @ Wed, 22 Jul 2020 14:44:33: start X-correlation... INFO @ Wed, 22 Jul 2020 14:44:33: end of X-cor INFO @ Wed, 22 Jul 2020 14:44:33: #2 finished! INFO @ Wed, 22 Jul 2020 14:44:33: #2 predicted fragment length is 250 bps INFO @ Wed, 22 Jul 2020 14:44:33: #2 alternative fragment length(s) may be 12,115,164,183,196,212,250,297,483,486,532 bps INFO @ Wed, 22 Jul 2020 14:44:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.20_model.r INFO @ Wed, 22 Jul 2020 14:44:33: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:44:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 14:44:34: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:44:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.20_peaks.xls INFO @ Wed, 22 Jul 2020 14:44:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:44:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8462166/SRX8462166.20_summits.bed INFO @ Wed, 22 Jul 2020 14:44:34: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 14 millis CompletedMACS2peakCalling