Job ID = 5791007 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,583,214 reads read : 3,166,428 reads written : 3,166,428 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:00:51 1583214 reads; of these: 1583214 (100.00%) were paired; of these: 809097 (51.10%) aligned concordantly 0 times 593315 (37.48%) aligned concordantly exactly 1 time 180802 (11.42%) aligned concordantly >1 times ---- 809097 pairs aligned concordantly 0 times; of these: 1404 (0.17%) aligned discordantly 1 time ---- 807693 pairs aligned 0 times concordantly or discordantly; of these: 1615386 mates make up the pairs; of these: 1606499 (99.45%) aligned 0 times 5703 (0.35%) aligned exactly 1 time 3184 (0.20%) aligned >1 times 49.26% overall alignment rate Time searching: 00:00:51 Overall time: 00:00:51 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] 21863 / 772922 = 0.0283 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 Apr 2020 08:15:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.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 Apr 2020 08:15:38: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:15:38: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:15:47: 1000000 INFO @ Wed, 22 Apr 2020 08:15:51: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:15:51: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:15:51: #1 total tags in treatment: 752272 INFO @ Wed, 22 Apr 2020 08:15:51: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:15:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:15:51: #1 tags after filtering in treatment: 690202 INFO @ Wed, 22 Apr 2020 08:15:51: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 22 Apr 2020 08:15:51: #1 finished! INFO @ Wed, 22 Apr 2020 08:15:51: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:15:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:15:51: #2 number of paired peaks: 338 WARNING @ Wed, 22 Apr 2020 08:15:51: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Wed, 22 Apr 2020 08:15:51: start model_add_line... INFO @ Wed, 22 Apr 2020 08:15:51: start X-correlation... INFO @ Wed, 22 Apr 2020 08:15:51: end of X-cor INFO @ Wed, 22 Apr 2020 08:15:51: #2 finished! INFO @ Wed, 22 Apr 2020 08:15:51: #2 predicted fragment length is 150 bps INFO @ Wed, 22 Apr 2020 08:15:51: #2 alternative fragment length(s) may be 4,150 bps INFO @ Wed, 22 Apr 2020 08:15:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.05_model.r INFO @ Wed, 22 Apr 2020 08:15:51: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:15:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:15:54: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:15:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:15:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:15:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.05_summits.bed INFO @ Wed, 22 Apr 2020 08:15:55: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (184 records, 4 fields): 1 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 Apr 2020 08:16:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.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 Apr 2020 08:16:08: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:16:08: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:16:16: 1000000 INFO @ Wed, 22 Apr 2020 08:16:21: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:16:21: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:16:21: #1 total tags in treatment: 752272 INFO @ Wed, 22 Apr 2020 08:16:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:16:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:16:21: #1 tags after filtering in treatment: 690202 INFO @ Wed, 22 Apr 2020 08:16:21: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 22 Apr 2020 08:16:21: #1 finished! INFO @ Wed, 22 Apr 2020 08:16:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:16:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:16:21: #2 number of paired peaks: 338 WARNING @ Wed, 22 Apr 2020 08:16:21: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Wed, 22 Apr 2020 08:16:21: start model_add_line... INFO @ Wed, 22 Apr 2020 08:16:21: start X-correlation... INFO @ Wed, 22 Apr 2020 08:16:21: end of X-cor INFO @ Wed, 22 Apr 2020 08:16:21: #2 finished! INFO @ Wed, 22 Apr 2020 08:16:21: #2 predicted fragment length is 150 bps INFO @ Wed, 22 Apr 2020 08:16:21: #2 alternative fragment length(s) may be 4,150 bps INFO @ Wed, 22 Apr 2020 08:16:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.10_model.r INFO @ Wed, 22 Apr 2020 08:16:21: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:16:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:16:23: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:16:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:16:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:16:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.10_summits.bed INFO @ Wed, 22 Apr 2020 08:16:24: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (113 records, 4 fields): 3 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 Apr 2020 08:16:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.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 Apr 2020 08:16:38: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:16:38: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:16:46: 1000000 INFO @ Wed, 22 Apr 2020 08:16:51: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:16:51: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:16:51: #1 total tags in treatment: 752272 INFO @ Wed, 22 Apr 2020 08:16:51: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:16:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:16:51: #1 tags after filtering in treatment: 690202 INFO @ Wed, 22 Apr 2020 08:16:51: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 22 Apr 2020 08:16:51: #1 finished! INFO @ Wed, 22 Apr 2020 08:16:51: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:16:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:16:51: #2 number of paired peaks: 338 WARNING @ Wed, 22 Apr 2020 08:16:51: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Wed, 22 Apr 2020 08:16:51: start model_add_line... INFO @ Wed, 22 Apr 2020 08:16:51: start X-correlation... INFO @ Wed, 22 Apr 2020 08:16:51: end of X-cor INFO @ Wed, 22 Apr 2020 08:16:51: #2 finished! INFO @ Wed, 22 Apr 2020 08:16:51: #2 predicted fragment length is 150 bps INFO @ Wed, 22 Apr 2020 08:16:51: #2 alternative fragment length(s) may be 4,150 bps INFO @ Wed, 22 Apr 2020 08:16:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.20_model.r INFO @ Wed, 22 Apr 2020 08:16:51: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:16:51: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 08:16:53: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:16:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:16:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:16:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874504/SRX5874504.20_summits.bed INFO @ Wed, 22 Apr 2020 08:16:54: Done! BigWig に変換しました。 pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (68 records, 4 fields): 1 millis CompletedMACS2peakCalling