Job ID = 5791245 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,284,689 reads read : 10,569,378 reads written : 10,569,378 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: 00:01:43 5284689 reads; of these: 5284689 (100.00%) were paired; of these: 426913 (8.08%) aligned concordantly 0 times 4240381 (80.24%) aligned concordantly exactly 1 time 617395 (11.68%) aligned concordantly >1 times ---- 426913 pairs aligned concordantly 0 times; of these: 107450 (25.17%) aligned discordantly 1 time ---- 319463 pairs aligned 0 times concordantly or discordantly; of these: 638926 mates make up the pairs; of these: 506066 (79.21%) aligned 0 times 85312 (13.35%) aligned exactly 1 time 47548 (7.44%) aligned >1 times 95.21% overall alignment rate Time searching: 00:01:43 Overall time: 00:01:43 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] 1742220 / 4872369 = 0.3576 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 09:15:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.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 09:15:45: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:15:45: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:15:50: 1000000 INFO @ Wed, 22 Apr 2020 09:15:54: 2000000 INFO @ Wed, 22 Apr 2020 09:15:59: 3000000 INFO @ Wed, 22 Apr 2020 09:16:04: 4000000 INFO @ Wed, 22 Apr 2020 09:16:09: 5000000 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 09:16:13: 6000000 INFO @ Wed, 22 Apr 2020 09:16:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.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 09:16:15: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:16:15: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:16:16: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:16:16: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:16:16: #1 total tags in treatment: 3117146 INFO @ Wed, 22 Apr 2020 09:16:16: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:16:16: #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 09:16:16: #1 tags after filtering in treatment: 1581405 INFO @ Wed, 22 Apr 2020 09:16:16: #1 Redundant rate of treatment: 0.49 INFO @ Wed, 22 Apr 2020 09:16:16: #1 finished! INFO @ Wed, 22 Apr 2020 09:16:16: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:16:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:16:16: #2 number of paired peaks: 184 WARNING @ Wed, 22 Apr 2020 09:16:16: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Wed, 22 Apr 2020 09:16:16: start model_add_line... INFO @ Wed, 22 Apr 2020 09:16:16: start X-correlation... INFO @ Wed, 22 Apr 2020 09:16:16: end of X-cor INFO @ Wed, 22 Apr 2020 09:16:16: #2 finished! INFO @ Wed, 22 Apr 2020 09:16:16: #2 predicted fragment length is 81 bps INFO @ Wed, 22 Apr 2020 09:16:16: #2 alternative fragment length(s) may be 0,66,81,284,509,538 bps INFO @ Wed, 22 Apr 2020 09:16:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.05_model.r INFO @ Wed, 22 Apr 2020 09:16:16: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:16:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:16:19: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:16:20: 1000000 INFO @ Wed, 22 Apr 2020 09:16:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:16:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:16:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.05_summits.bed INFO @ Wed, 22 Apr 2020 09:16:21: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (3535 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:16:25: 2000000 INFO @ Wed, 22 Apr 2020 09:16:29: 3000000 INFO @ Wed, 22 Apr 2020 09:16:34: 4000000 INFO @ Wed, 22 Apr 2020 09:16:39: 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 09:16:43: 6000000 INFO @ Wed, 22 Apr 2020 09:16:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.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 09:16:45: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:16:45: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:16:46: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:16:46: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:16:46: #1 total tags in treatment: 3117146 INFO @ Wed, 22 Apr 2020 09:16:46: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:16:46: #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 09:16:46: #1 tags after filtering in treatment: 1581405 INFO @ Wed, 22 Apr 2020 09:16:46: #1 Redundant rate of treatment: 0.49 INFO @ Wed, 22 Apr 2020 09:16:46: #1 finished! INFO @ Wed, 22 Apr 2020 09:16:46: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:16:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:16:46: #2 number of paired peaks: 184 WARNING @ Wed, 22 Apr 2020 09:16:46: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Wed, 22 Apr 2020 09:16:46: start model_add_line... INFO @ Wed, 22 Apr 2020 09:16:46: start X-correlation... INFO @ Wed, 22 Apr 2020 09:16:46: end of X-cor INFO @ Wed, 22 Apr 2020 09:16:46: #2 finished! INFO @ Wed, 22 Apr 2020 09:16:46: #2 predicted fragment length is 81 bps INFO @ Wed, 22 Apr 2020 09:16:46: #2 alternative fragment length(s) may be 0,66,81,284,509,538 bps INFO @ Wed, 22 Apr 2020 09:16:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.10_model.r INFO @ Wed, 22 Apr 2020 09:16:46: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:16:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:16:50: 1000000 INFO @ Wed, 22 Apr 2020 09:16:50: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:16:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:16:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:16:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.10_summits.bed INFO @ Wed, 22 Apr 2020 09:16:51: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (2336 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:16:54: 2000000 INFO @ Wed, 22 Apr 2020 09:16:59: 3000000 INFO @ Wed, 22 Apr 2020 09:17:04: 4000000 INFO @ Wed, 22 Apr 2020 09:17:09: 5000000 INFO @ Wed, 22 Apr 2020 09:17:13: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:17:16: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:17:16: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:17:16: #1 total tags in treatment: 3117146 INFO @ Wed, 22 Apr 2020 09:17:16: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:17:16: #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 09:17:16: #1 tags after filtering in treatment: 1581405 INFO @ Wed, 22 Apr 2020 09:17:16: #1 Redundant rate of treatment: 0.49 INFO @ Wed, 22 Apr 2020 09:17:16: #1 finished! INFO @ Wed, 22 Apr 2020 09:17:16: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:17:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:17:16: #2 number of paired peaks: 184 WARNING @ Wed, 22 Apr 2020 09:17:16: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Wed, 22 Apr 2020 09:17:16: start model_add_line... INFO @ Wed, 22 Apr 2020 09:17:16: start X-correlation... INFO @ Wed, 22 Apr 2020 09:17:16: end of X-cor INFO @ Wed, 22 Apr 2020 09:17:16: #2 finished! INFO @ Wed, 22 Apr 2020 09:17:16: #2 predicted fragment length is 81 bps INFO @ Wed, 22 Apr 2020 09:17:16: #2 alternative fragment length(s) may be 0,66,81,284,509,538 bps INFO @ Wed, 22 Apr 2020 09:17:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.20_model.r INFO @ Wed, 22 Apr 2020 09:17:16: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:17:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:17:19: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:17:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:17:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:17:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388388/SRX7388388.20_summits.bed INFO @ Wed, 22 Apr 2020 09:17:21: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (799 records, 4 fields): 3 millis CompletedMACS2peakCalling