Job ID = 5791249 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,386,570 reads read : 12,773,140 reads written : 12,773,140 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: 00:03:11 6386570 reads; of these: 6386570 (100.00%) were paired; of these: 3589258 (56.20%) aligned concordantly 0 times 2249801 (35.23%) aligned concordantly exactly 1 time 547511 (8.57%) aligned concordantly >1 times ---- 3589258 pairs aligned concordantly 0 times; of these: 2149019 (59.87%) aligned discordantly 1 time ---- 1440239 pairs aligned 0 times concordantly or discordantly; of these: 2880478 mates make up the pairs; of these: 630212 (21.88%) aligned 0 times 1138898 (39.54%) aligned exactly 1 time 1111368 (38.58%) aligned >1 times 95.07% overall alignment rate Time searching: 00:03:11 Overall time: 00:03:11 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] 1214157 / 2965002 = 0.4095 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 09:19:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.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 09:19:05: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:19:05: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:19:09: 1000000 INFO @ Wed, 22 Apr 2020 09:19:14: 2000000 INFO @ Wed, 22 Apr 2020 09:19:19: 3000000 INFO @ Wed, 22 Apr 2020 09:19:24: 4000000 INFO @ Wed, 22 Apr 2020 09:19:29: 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 09:19:33: 6000000 INFO @ Wed, 22 Apr 2020 09:19:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.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 09:19:35: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:19:35: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:19:39: 7000000 INFO @ Wed, 22 Apr 2020 09:19:40: 1000000 INFO @ Wed, 22 Apr 2020 09:19:44: 8000000 INFO @ Wed, 22 Apr 2020 09:19:45: 2000000 INFO @ Wed, 22 Apr 2020 09:19:49: 9000000 INFO @ Wed, 22 Apr 2020 09:19:51: 3000000 INFO @ Wed, 22 Apr 2020 09:19:53: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:19:53: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:19:53: #1 total tags in treatment: 1586888 INFO @ Wed, 22 Apr 2020 09:19:53: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:19:53: #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 09:19:53: #1 tags after filtering in treatment: 773315 INFO @ Wed, 22 Apr 2020 09:19:53: #1 Redundant rate of treatment: 0.51 INFO @ Wed, 22 Apr 2020 09:19:53: #1 finished! INFO @ Wed, 22 Apr 2020 09:19:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:19:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:19:53: #2 number of paired peaks: 549 WARNING @ Wed, 22 Apr 2020 09:19:53: Fewer paired peaks (549) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 549 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 71 bps INFO @ Wed, 22 Apr 2020 09:19:53: #2 alternative fragment length(s) may be 71 bps INFO @ Wed, 22 Apr 2020 09:19:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.05_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 09:19:55: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:19:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:19:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:19:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.05_summits.bed INFO @ Wed, 22 Apr 2020 09:19:55: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (3916 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:19:56: 4000000 INFO @ Wed, 22 Apr 2020 09:20:01: 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 09:20:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.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 09:20:05: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:20:05: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:20:07: 6000000 INFO @ Wed, 22 Apr 2020 09:20:10: 1000000 INFO @ Wed, 22 Apr 2020 09:20:12: 7000000 INFO @ Wed, 22 Apr 2020 09:20:15: 2000000 INFO @ Wed, 22 Apr 2020 09:20:17: 8000000 INFO @ Wed, 22 Apr 2020 09:20:20: 3000000 INFO @ Wed, 22 Apr 2020 09:20:22: 9000000 INFO @ Wed, 22 Apr 2020 09:20:26: 4000000 INFO @ Wed, 22 Apr 2020 09:20:26: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:20:26: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:20:26: #1 total tags in treatment: 1586888 INFO @ Wed, 22 Apr 2020 09:20:26: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:20:26: #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 09:20:26: #1 tags after filtering in treatment: 773315 INFO @ Wed, 22 Apr 2020 09:20:26: #1 Redundant rate of treatment: 0.51 INFO @ Wed, 22 Apr 2020 09:20:26: #1 finished! INFO @ Wed, 22 Apr 2020 09:20:26: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:20:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:20:26: #2 number of paired peaks: 549 WARNING @ Wed, 22 Apr 2020 09:20:26: Fewer paired peaks (549) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 549 pairs to build model! INFO @ Wed, 22 Apr 2020 09:20:26: start model_add_line... INFO @ Wed, 22 Apr 2020 09:20:26: start X-correlation... INFO @ Wed, 22 Apr 2020 09:20:26: end of X-cor INFO @ Wed, 22 Apr 2020 09:20:26: #2 finished! INFO @ Wed, 22 Apr 2020 09:20:26: #2 predicted fragment length is 71 bps INFO @ Wed, 22 Apr 2020 09:20:26: #2 alternative fragment length(s) may be 71 bps INFO @ Wed, 22 Apr 2020 09:20:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.10_model.r INFO @ Wed, 22 Apr 2020 09:20:26: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:20:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:20:28: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:20:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:20:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:20:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.10_summits.bed INFO @ Wed, 22 Apr 2020 09:20:28: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (2729 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:20:31: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:20:35: 6000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:20:40: 7000000 INFO @ Wed, 22 Apr 2020 09:20:45: 8000000 INFO @ Wed, 22 Apr 2020 09:20:50: 9000000 INFO @ Wed, 22 Apr 2020 09:20:54: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:20:54: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:20:54: #1 total tags in treatment: 1586888 INFO @ Wed, 22 Apr 2020 09:20:54: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:20:54: #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 09:20:54: #1 tags after filtering in treatment: 773315 INFO @ Wed, 22 Apr 2020 09:20:54: #1 Redundant rate of treatment: 0.51 INFO @ Wed, 22 Apr 2020 09:20:54: #1 finished! INFO @ Wed, 22 Apr 2020 09:20:54: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:20:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:20:54: #2 number of paired peaks: 549 WARNING @ Wed, 22 Apr 2020 09:20:54: Fewer paired peaks (549) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 549 pairs to build model! INFO @ Wed, 22 Apr 2020 09:20:54: start model_add_line... INFO @ Wed, 22 Apr 2020 09:20:54: start X-correlation... INFO @ Wed, 22 Apr 2020 09:20:54: end of X-cor INFO @ Wed, 22 Apr 2020 09:20:54: #2 finished! INFO @ Wed, 22 Apr 2020 09:20:54: #2 predicted fragment length is 71 bps INFO @ Wed, 22 Apr 2020 09:20:54: #2 alternative fragment length(s) may be 71 bps INFO @ Wed, 22 Apr 2020 09:20:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.20_model.r INFO @ Wed, 22 Apr 2020 09:20:54: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:20:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:20:55: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:20:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:20:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:20:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388391/SRX7388391.20_summits.bed INFO @ Wed, 22 Apr 2020 09:20:56: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1267 records, 4 fields): 3 millis CompletedMACS2peakCalling