Job ID = 5791250 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,359,565 reads read : 12,719,130 reads written : 12,719,130 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: 00:02:42 6359565 reads; of these: 6359565 (100.00%) were paired; of these: 1337171 (21.03%) aligned concordantly 0 times 4130908 (64.96%) aligned concordantly exactly 1 time 891486 (14.02%) aligned concordantly >1 times ---- 1337171 pairs aligned concordantly 0 times; of these: 708178 (52.96%) aligned discordantly 1 time ---- 628993 pairs aligned 0 times concordantly or discordantly; of these: 1257986 mates make up the pairs; of these: 512840 (40.77%) aligned 0 times 377952 (30.04%) aligned exactly 1 time 367194 (29.19%) aligned >1 times 95.97% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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] 2091722 / 5080293 = 0.4117 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 09:18:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.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 09:18:43: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:18:43: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:18:48: 1000000 INFO @ Wed, 22 Apr 2020 09:18:52: 2000000 INFO @ Wed, 22 Apr 2020 09:18:57: 3000000 INFO @ Wed, 22 Apr 2020 09:19:01: 4000000 INFO @ Wed, 22 Apr 2020 09:19:05: 5000000 INFO @ Wed, 22 Apr 2020 09:19:10: 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 09:19:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.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 09:19:13: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:19:13: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:19:14: 7000000 INFO @ Wed, 22 Apr 2020 09:19:18: 1000000 INFO @ Wed, 22 Apr 2020 09:19:19: 8000000 INFO @ Wed, 22 Apr 2020 09:19:19: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:19:19: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:19:19: #1 total tags in treatment: 2937594 INFO @ Wed, 22 Apr 2020 09:19:19: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:19:19: #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 09:19:19: #1 tags after filtering in treatment: 1844434 INFO @ Wed, 22 Apr 2020 09:19:19: #1 Redundant rate of treatment: 0.37 INFO @ Wed, 22 Apr 2020 09:19:19: #1 finished! INFO @ Wed, 22 Apr 2020 09:19:19: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:19:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:19:20: #2 number of paired peaks: 177 WARNING @ Wed, 22 Apr 2020 09:19:20: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Wed, 22 Apr 2020 09:19:20: start model_add_line... INFO @ Wed, 22 Apr 2020 09:19:20: start X-correlation... INFO @ Wed, 22 Apr 2020 09:19:20: end of X-cor INFO @ Wed, 22 Apr 2020 09:19:20: #2 finished! INFO @ Wed, 22 Apr 2020 09:19:20: #2 predicted fragment length is 78 bps INFO @ Wed, 22 Apr 2020 09:19:20: #2 alternative fragment length(s) may be 0,78,210,251,277,298,468,523,535 bps INFO @ Wed, 22 Apr 2020 09:19:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.05_model.r INFO @ Wed, 22 Apr 2020 09:19:20: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:19:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:19:23: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:19:23: 2000000 INFO @ Wed, 22 Apr 2020 09:19:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:19:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:19:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.05_summits.bed INFO @ Wed, 22 Apr 2020 09:19:25: Done! INFO @ Wed, 22 Apr 2020 09:19:28: 3000000 pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (1686 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:19:33: 4000000 INFO @ Wed, 22 Apr 2020 09:19:37: 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 09:19:42: 6000000 INFO @ Wed, 22 Apr 2020 09:19:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.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 09:19:44: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:19:44: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:19:47: 7000000 INFO @ Wed, 22 Apr 2020 09:19:49: 1000000 INFO @ Wed, 22 Apr 2020 09:19:52: 8000000 INFO @ Wed, 22 Apr 2020 09:19:52: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:19:52: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:19:52: #1 total tags in treatment: 2937594 INFO @ Wed, 22 Apr 2020 09:19:52: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:19:52: #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 09:19:52: #1 tags after filtering in treatment: 1844434 INFO @ Wed, 22 Apr 2020 09:19:52: #1 Redundant rate of treatment: 0.37 INFO @ Wed, 22 Apr 2020 09:19:52: #1 finished! INFO @ Wed, 22 Apr 2020 09:19:52: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:19:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:19:53: #2 number of paired peaks: 177 WARNING @ Wed, 22 Apr 2020 09:19:53: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Wed, 22 Apr 2020 09:19:53: start model_add_line... INFO @ Wed, 22 Apr 2020 09:19:53: start X-correlation... INFO @ Wed, 22 Apr 2020 09:19:53: end of X-cor INFO @ Wed, 22 Apr 2020 09:19:53: #2 finished! INFO @ Wed, 22 Apr 2020 09:19:53: #2 predicted fragment length is 78 bps INFO @ Wed, 22 Apr 2020 09:19:53: #2 alternative fragment length(s) may be 0,78,210,251,277,298,468,523,535 bps INFO @ Wed, 22 Apr 2020 09:19:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.10_model.r INFO @ Wed, 22 Apr 2020 09:19:53: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:19:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:19:54: 2000000 INFO @ Wed, 22 Apr 2020 09:19:56: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:19:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:19:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:19:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.10_summits.bed INFO @ Wed, 22 Apr 2020 09:19:58: Done! INFO @ Wed, 22 Apr 2020 09:19:59: 3000000 pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1045 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:20:04: 4000000 INFO @ Wed, 22 Apr 2020 09:20:08: 5000000 INFO @ Wed, 22 Apr 2020 09:20:13: 6000000 INFO @ Wed, 22 Apr 2020 09:20:18: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:20:22: 8000000 INFO @ Wed, 22 Apr 2020 09:20:22: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:20:22: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:20:22: #1 total tags in treatment: 2937594 INFO @ Wed, 22 Apr 2020 09:20:22: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:20:22: #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 09:20:22: #1 tags after filtering in treatment: 1844434 INFO @ Wed, 22 Apr 2020 09:20:22: #1 Redundant rate of treatment: 0.37 INFO @ Wed, 22 Apr 2020 09:20:22: #1 finished! INFO @ Wed, 22 Apr 2020 09:20:22: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:20:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:20:23: #2 number of paired peaks: 177 WARNING @ Wed, 22 Apr 2020 09:20:23: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Wed, 22 Apr 2020 09:20:23: start model_add_line... INFO @ Wed, 22 Apr 2020 09:20:23: start X-correlation... INFO @ Wed, 22 Apr 2020 09:20:23: end of X-cor INFO @ Wed, 22 Apr 2020 09:20:23: #2 finished! INFO @ Wed, 22 Apr 2020 09:20:23: #2 predicted fragment length is 78 bps INFO @ Wed, 22 Apr 2020 09:20:23: #2 alternative fragment length(s) may be 0,78,210,251,277,298,468,523,535 bps INFO @ Wed, 22 Apr 2020 09:20:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.20_model.r INFO @ Wed, 22 Apr 2020 09:20:23: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:20:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:20:26: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:20:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:20:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:20:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388393/SRX7388393.20_summits.bed INFO @ Wed, 22 Apr 2020 09:20:27: Done! BigWig に変換しました。 pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (322 records, 4 fields): 1 millis CompletedMACS2peakCalling