Job ID = 5791263 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,384,561 reads read : 6,769,122 reads written : 6,769,122 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: 00:00:47 3384561 reads; of these: 3384561 (100.00%) were paired; of these: 1196795 (35.36%) aligned concordantly 0 times 2031450 (60.02%) aligned concordantly exactly 1 time 156316 (4.62%) aligned concordantly >1 times ---- 1196795 pairs aligned concordantly 0 times; of these: 46488 (3.88%) aligned discordantly 1 time ---- 1150307 pairs aligned 0 times concordantly or discordantly; of these: 2300614 mates make up the pairs; of these: 2253870 (97.97%) aligned 0 times 30308 (1.32%) aligned exactly 1 time 16436 (0.71%) aligned >1 times 66.70% overall alignment rate Time searching: 00:00:47 Overall time: 00:00:47 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] 723934 / 2228357 = 0.3249 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 09:17:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.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 09:17:41: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:17:41: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:17:47: 1000000 INFO @ Wed, 22 Apr 2020 09:17:53: 2000000 INFO @ Wed, 22 Apr 2020 09:17:59: 3000000 INFO @ Wed, 22 Apr 2020 09:17:59: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:17:59: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:17:59: #1 total tags in treatment: 1470185 INFO @ Wed, 22 Apr 2020 09:17:59: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:17:59: #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 09:17:59: #1 tags after filtering in treatment: 1049975 INFO @ Wed, 22 Apr 2020 09:17:59: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 22 Apr 2020 09:17:59: #1 finished! INFO @ Wed, 22 Apr 2020 09:17:59: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:17:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:17:59: #2 number of paired peaks: 127 WARNING @ Wed, 22 Apr 2020 09:17:59: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Wed, 22 Apr 2020 09:17:59: start model_add_line... INFO @ Wed, 22 Apr 2020 09:17:59: start X-correlation... INFO @ Wed, 22 Apr 2020 09:17:59: end of X-cor INFO @ Wed, 22 Apr 2020 09:17:59: #2 finished! INFO @ Wed, 22 Apr 2020 09:17:59: #2 predicted fragment length is 144 bps INFO @ Wed, 22 Apr 2020 09:17:59: #2 alternative fragment length(s) may be 1,67,108,144,158,216,244,264,286,330,447,525,569,595 bps INFO @ Wed, 22 Apr 2020 09:17:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.05_model.r INFO @ Wed, 22 Apr 2020 09:17:59: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:17:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:18:02: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:18:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:18:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:18:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.05_summits.bed INFO @ Wed, 22 Apr 2020 09:18:03: Done! 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 pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (1429 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:18:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.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 09:18:11: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:18:11: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:18:16: 1000000 INFO @ Wed, 22 Apr 2020 09:18:21: 2000000 INFO @ Wed, 22 Apr 2020 09:18:26: 3000000 INFO @ Wed, 22 Apr 2020 09:18:26: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:18:26: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:18:26: #1 total tags in treatment: 1470185 INFO @ Wed, 22 Apr 2020 09:18:26: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:18:26: #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 09:18:26: #1 tags after filtering in treatment: 1049975 INFO @ Wed, 22 Apr 2020 09:18:26: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 22 Apr 2020 09:18:26: #1 finished! INFO @ Wed, 22 Apr 2020 09:18:26: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:18:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:18:26: #2 number of paired peaks: 127 WARNING @ Wed, 22 Apr 2020 09:18:26: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Wed, 22 Apr 2020 09:18:26: start model_add_line... INFO @ Wed, 22 Apr 2020 09:18:26: start X-correlation... INFO @ Wed, 22 Apr 2020 09:18:26: end of X-cor INFO @ Wed, 22 Apr 2020 09:18:26: #2 finished! INFO @ Wed, 22 Apr 2020 09:18:26: #2 predicted fragment length is 144 bps INFO @ Wed, 22 Apr 2020 09:18:26: #2 alternative fragment length(s) may be 1,67,108,144,158,216,244,264,286,330,447,525,569,595 bps INFO @ Wed, 22 Apr 2020 09:18:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.10_model.r INFO @ Wed, 22 Apr 2020 09:18:26: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:18:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:18:29: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:18:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:18:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:18:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.10_summits.bed INFO @ Wed, 22 Apr 2020 09:18:30: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (493 records, 4 fields): 4 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 09:18:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.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 09:18:40: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:18:40: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:18:45: 1000000 INFO @ Wed, 22 Apr 2020 09:18:50: 2000000 INFO @ Wed, 22 Apr 2020 09:18:55: 3000000 INFO @ Wed, 22 Apr 2020 09:18:55: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:18:55: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:18:55: #1 total tags in treatment: 1470185 INFO @ Wed, 22 Apr 2020 09:18:55: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:18:55: #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 09:18:55: #1 tags after filtering in treatment: 1049975 INFO @ Wed, 22 Apr 2020 09:18:55: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 22 Apr 2020 09:18:55: #1 finished! INFO @ Wed, 22 Apr 2020 09:18:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:18:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:18:55: #2 number of paired peaks: 127 WARNING @ Wed, 22 Apr 2020 09:18:55: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Wed, 22 Apr 2020 09:18:55: start model_add_line... INFO @ Wed, 22 Apr 2020 09:18:55: start X-correlation... INFO @ Wed, 22 Apr 2020 09:18:55: end of X-cor INFO @ Wed, 22 Apr 2020 09:18:55: #2 finished! INFO @ Wed, 22 Apr 2020 09:18:55: #2 predicted fragment length is 144 bps INFO @ Wed, 22 Apr 2020 09:18:55: #2 alternative fragment length(s) may be 1,67,108,144,158,216,244,264,286,330,447,525,569,595 bps INFO @ Wed, 22 Apr 2020 09:18:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.20_model.r INFO @ Wed, 22 Apr 2020 09:18:55: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:18:55: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:18:57: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:18:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:18:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:18:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388404/SRX7388404.20_summits.bed INFO @ Wed, 22 Apr 2020 09:18:59: Done! BigWig に変換しました。 pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (64 records, 4 fields): 3 millis CompletedMACS2peakCalling