Job ID = 5791001 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,021,469 reads read : 20,042,938 reads written : 20,042,938 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: 00:03:50 10021469 reads; of these: 10021469 (100.00%) were paired; of these: 3775268 (37.67%) aligned concordantly 0 times 4636987 (46.27%) aligned concordantly exactly 1 time 1609214 (16.06%) aligned concordantly >1 times ---- 3775268 pairs aligned concordantly 0 times; of these: 2896 (0.08%) aligned discordantly 1 time ---- 3772372 pairs aligned 0 times concordantly or discordantly; of these: 7544744 mates make up the pairs; of these: 7472928 (99.05%) aligned 0 times 46411 (0.62%) aligned exactly 1 time 25405 (0.34%) aligned >1 times 62.72% overall alignment rate Time searching: 00:03:50 Overall time: 00:03:50 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] 1925219 / 6247906 = 0.3081 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 08:19:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.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 08:19:48: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:19:48: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:19:53: 1000000 INFO @ Wed, 22 Apr 2020 08:19:57: 2000000 INFO @ Wed, 22 Apr 2020 08:20:02: 3000000 INFO @ Wed, 22 Apr 2020 08:20:06: 4000000 INFO @ Wed, 22 Apr 2020 08:20:11: 5000000 INFO @ Wed, 22 Apr 2020 08:20:16: 6000000 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 08:20:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.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 08:20:18: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:20:18: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:20:21: 7000000 INFO @ Wed, 22 Apr 2020 08:20:23: 1000000 INFO @ Wed, 22 Apr 2020 08:20:26: 8000000 INFO @ Wed, 22 Apr 2020 08:20:28: 2000000 INFO @ Wed, 22 Apr 2020 08:20:29: #1 tag size is determined as 42 bps INFO @ Wed, 22 Apr 2020 08:20:29: #1 tag size = 42 INFO @ Wed, 22 Apr 2020 08:20:29: #1 total tags in treatment: 4321862 INFO @ Wed, 22 Apr 2020 08:20:29: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:20:29: #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 08:20:29: #1 tags after filtering in treatment: 3264098 INFO @ Wed, 22 Apr 2020 08:20:29: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Apr 2020 08:20:29: #1 finished! INFO @ Wed, 22 Apr 2020 08:20:29: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:20:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:20:30: #2 number of paired peaks: 257 WARNING @ Wed, 22 Apr 2020 08:20:30: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Wed, 22 Apr 2020 08:20:30: start model_add_line... INFO @ Wed, 22 Apr 2020 08:20:30: start X-correlation... INFO @ Wed, 22 Apr 2020 08:20:30: end of X-cor INFO @ Wed, 22 Apr 2020 08:20:30: #2 finished! INFO @ Wed, 22 Apr 2020 08:20:30: #2 predicted fragment length is 124 bps INFO @ Wed, 22 Apr 2020 08:20:30: #2 alternative fragment length(s) may be 1,91,116,124 bps INFO @ Wed, 22 Apr 2020 08:20:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.05_model.r INFO @ Wed, 22 Apr 2020 08:20:30: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:20:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:20:33: 3000000 INFO @ Wed, 22 Apr 2020 08:20:37: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:20:38: 4000000 INFO @ Wed, 22 Apr 2020 08:20:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:20:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:20:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.05_summits.bed INFO @ Wed, 22 Apr 2020 08:20:39: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (512 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:20:43: 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 @ Wed, 22 Apr 2020 08:20:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.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 08:20:48: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:20:48: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:20:48: 6000000 INFO @ Wed, 22 Apr 2020 08:20:53: 1000000 INFO @ Wed, 22 Apr 2020 08:20:53: 7000000 INFO @ Wed, 22 Apr 2020 08:20:59: 2000000 INFO @ Wed, 22 Apr 2020 08:20:59: 8000000 INFO @ Wed, 22 Apr 2020 08:21:02: #1 tag size is determined as 42 bps INFO @ Wed, 22 Apr 2020 08:21:02: #1 tag size = 42 INFO @ Wed, 22 Apr 2020 08:21:02: #1 total tags in treatment: 4321862 INFO @ Wed, 22 Apr 2020 08:21:02: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:21:02: #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 08:21:02: #1 tags after filtering in treatment: 3264098 INFO @ Wed, 22 Apr 2020 08:21:02: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Apr 2020 08:21:02: #1 finished! INFO @ Wed, 22 Apr 2020 08:21:02: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:21:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:21:03: #2 number of paired peaks: 257 WARNING @ Wed, 22 Apr 2020 08:21:03: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Wed, 22 Apr 2020 08:21:03: start model_add_line... INFO @ Wed, 22 Apr 2020 08:21:03: start X-correlation... INFO @ Wed, 22 Apr 2020 08:21:03: end of X-cor INFO @ Wed, 22 Apr 2020 08:21:03: #2 finished! INFO @ Wed, 22 Apr 2020 08:21:03: #2 predicted fragment length is 124 bps INFO @ Wed, 22 Apr 2020 08:21:03: #2 alternative fragment length(s) may be 1,91,116,124 bps INFO @ Wed, 22 Apr 2020 08:21:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.10_model.r INFO @ Wed, 22 Apr 2020 08:21:03: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:21:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:21:04: 3000000 INFO @ Wed, 22 Apr 2020 08:21:09: 4000000 INFO @ Wed, 22 Apr 2020 08:21:10: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:21:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:21:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:21:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.10_summits.bed INFO @ Wed, 22 Apr 2020 08:21:12: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (326 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:21:14: 5000000 INFO @ Wed, 22 Apr 2020 08:21:19: 6000000 INFO @ Wed, 22 Apr 2020 08:21:24: 7000000 INFO @ Wed, 22 Apr 2020 08:21:29: 8000000 INFO @ Wed, 22 Apr 2020 08:21:33: #1 tag size is determined as 42 bps INFO @ Wed, 22 Apr 2020 08:21:33: #1 tag size = 42 INFO @ Wed, 22 Apr 2020 08:21:33: #1 total tags in treatment: 4321862 INFO @ Wed, 22 Apr 2020 08:21:33: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:21:33: #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 08:21:33: #1 tags after filtering in treatment: 3264098 INFO @ Wed, 22 Apr 2020 08:21:33: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Apr 2020 08:21:33: #1 finished! INFO @ Wed, 22 Apr 2020 08:21:33: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:21:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:21:33: #2 number of paired peaks: 257 WARNING @ Wed, 22 Apr 2020 08:21:33: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Wed, 22 Apr 2020 08:21:33: start model_add_line... INFO @ Wed, 22 Apr 2020 08:21:33: start X-correlation... INFO @ Wed, 22 Apr 2020 08:21:33: end of X-cor INFO @ Wed, 22 Apr 2020 08:21:33: #2 finished! INFO @ Wed, 22 Apr 2020 08:21:33: #2 predicted fragment length is 124 bps INFO @ Wed, 22 Apr 2020 08:21:33: #2 alternative fragment length(s) may be 1,91,116,124 bps INFO @ Wed, 22 Apr 2020 08:21:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.20_model.r INFO @ Wed, 22 Apr 2020 08:21:33: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:21:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:21:40: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 08:21:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:21:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:21:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874500/SRX5874500.20_summits.bed INFO @ Wed, 22 Apr 2020 08:21:43: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (141 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。