Job ID = 5791038 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,193,456 reads read : 10,386,912 reads written : 10,386,912 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: 00:01:49 5193456 reads; of these: 5193456 (100.00%) were paired; of these: 1604015 (30.89%) aligned concordantly 0 times 3173332 (61.10%) aligned concordantly exactly 1 time 416109 (8.01%) aligned concordantly >1 times ---- 1604015 pairs aligned concordantly 0 times; of these: 203813 (12.71%) aligned discordantly 1 time ---- 1400202 pairs aligned 0 times concordantly or discordantly; of these: 2800404 mates make up the pairs; of these: 2304233 (82.28%) aligned 0 times 396290 (14.15%) aligned exactly 1 time 99881 (3.57%) aligned >1 times 77.82% overall alignment rate Time searching: 00:01:49 Overall time: 00:01:49 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] 65927 / 3760611 = 0.0175 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 08:25:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.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 08:25:50: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:25:50: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:25:54: 1000000 INFO @ Wed, 22 Apr 2020 08:25:58: 2000000 INFO @ Wed, 22 Apr 2020 08:26:03: 3000000 INFO @ Wed, 22 Apr 2020 08:26:07: 4000000 INFO @ Wed, 22 Apr 2020 08:26:11: 5000000 INFO @ Wed, 22 Apr 2020 08:26:15: 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 08:26:19: 7000000 INFO @ Wed, 22 Apr 2020 08:26:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.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 08:26:19: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:26:19: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:26:23: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 08:26:23: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 08:26:23: #1 total tags in treatment: 3527659 INFO @ Wed, 22 Apr 2020 08:26:23: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:26:23: #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 08:26:23: #1 tags after filtering in treatment: 2936098 INFO @ Wed, 22 Apr 2020 08:26:23: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 22 Apr 2020 08:26:23: #1 finished! INFO @ Wed, 22 Apr 2020 08:26:23: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:26:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:26:23: #2 number of paired peaks: 33 WARNING @ Wed, 22 Apr 2020 08:26:23: Too few paired peaks (33) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Apr 2020 08:26:23: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 08:26:23: 1000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:26:27: 2000000 INFO @ Wed, 22 Apr 2020 08:26:31: 3000000 INFO @ Wed, 22 Apr 2020 08:26:35: 4000000 INFO @ Wed, 22 Apr 2020 08:26:40: 5000000 INFO @ Wed, 22 Apr 2020 08:26:44: 6000000 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 08:26:48: 7000000 INFO @ Wed, 22 Apr 2020 08:26:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.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 08:26:49: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:26:49: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:26:52: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 08:26:52: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 08:26:52: #1 total tags in treatment: 3527659 INFO @ Wed, 22 Apr 2020 08:26:52: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:26:52: #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 08:26:52: #1 tags after filtering in treatment: 2936098 INFO @ Wed, 22 Apr 2020 08:26:52: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 22 Apr 2020 08:26:52: #1 finished! INFO @ Wed, 22 Apr 2020 08:26:52: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:26:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:26:52: #2 number of paired peaks: 33 WARNING @ Wed, 22 Apr 2020 08:26:52: Too few paired peaks (33) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Apr 2020 08:26:52: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 08:26:53: 1000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:26:57: 2000000 INFO @ Wed, 22 Apr 2020 08:27:01: 3000000 INFO @ Wed, 22 Apr 2020 08:27:06: 4000000 INFO @ Wed, 22 Apr 2020 08:27:10: 5000000 INFO @ Wed, 22 Apr 2020 08:27:14: 6000000 INFO @ Wed, 22 Apr 2020 08:27:18: 7000000 INFO @ Wed, 22 Apr 2020 08:27:22: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 08:27:22: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 08:27:22: #1 total tags in treatment: 3527659 INFO @ Wed, 22 Apr 2020 08:27:22: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:27:22: #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 08:27:22: #1 tags after filtering in treatment: 2936098 INFO @ Wed, 22 Apr 2020 08:27:22: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 22 Apr 2020 08:27:22: #1 finished! INFO @ Wed, 22 Apr 2020 08:27:22: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:27:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:27:22: #2 number of paired peaks: 33 WARNING @ Wed, 22 Apr 2020 08:27:22: Too few paired peaks (33) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Apr 2020 08:27:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883262/SRX5883262.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。