Job ID = 5791043 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,733,910 reads read : 7,467,820 reads written : 7,467,820 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: 00:01:32 3733910 reads; of these: 3733910 (100.00%) were paired; of these: 846894 (22.68%) aligned concordantly 0 times 2391804 (64.06%) aligned concordantly exactly 1 time 495212 (13.26%) aligned concordantly >1 times ---- 846894 pairs aligned concordantly 0 times; of these: 164077 (19.37%) aligned discordantly 1 time ---- 682817 pairs aligned 0 times concordantly or discordantly; of these: 1365634 mates make up the pairs; of these: 1060289 (77.64%) aligned 0 times 211346 (15.48%) aligned exactly 1 time 93999 (6.88%) aligned >1 times 85.80% overall alignment rate Time searching: 00:01:32 Overall time: 00:01:32 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] 92541 / 3022056 = 0.0306 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 08:23:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883267/SRX5883267.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883267/SRX5883267.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883267/SRX5883267.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883267/SRX5883267.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 08:23:41: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:23:41: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:23:47: 1000000 INFO @ Wed, 22 Apr 2020 08:23:52: 2000000 INFO @ Wed, 22 Apr 2020 08:23:57: 3000000 INFO @ Wed, 22 Apr 2020 08:24:03: 4000000 INFO @ Wed, 22 Apr 2020 08:24:08: 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 08:24:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883267/SRX5883267.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883267/SRX5883267.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883267/SRX5883267.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883267/SRX5883267.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 08:24:11: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:24:11: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:24:13: 6000000 INFO @ Wed, 22 Apr 2020 08:24:14: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 08:24:14: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 08:24:14: #1 total tags in treatment: 2798751 INFO @ Wed, 22 Apr 2020 08:24:14: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:24:14: #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 08:24:14: #1 tags after filtering in treatment: 2132920 INFO @ Wed, 22 Apr 2020 08:24:14: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Apr 2020 08:24:14: #1 finished! INFO @ Wed, 22 Apr 2020 08:24:14: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:24:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:24:15: #2 number of paired peaks: 28 WARNING @ Wed, 22 Apr 2020 08:24:15: Too few paired peaks (28) 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 08:24:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5883267/SRX5883267.05_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/SRX5883267/SRX5883267.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883267/SRX5883267.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883267/SRX5883267.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:24:17: 1000000 INFO @ Wed, 22 Apr 2020 08:24:22: 2000000 INFO @ Wed, 22 Apr 2020 08:24:27: 3000000 INFO @ Wed, 22 Apr 2020 08:24:33: 4000000 INFO @ Wed, 22 Apr 2020 08:24:39: 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 08:24:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883267/SRX5883267.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883267/SRX5883267.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883267/SRX5883267.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883267/SRX5883267.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 08:24:41: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:24:41: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:24:44: 6000000 INFO @ Wed, 22 Apr 2020 08:24:45: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 08:24:45: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 08:24:45: #1 total tags in treatment: 2798751 INFO @ Wed, 22 Apr 2020 08:24:45: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:24:45: #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 08:24:46: #1 tags after filtering in treatment: 2132920 INFO @ Wed, 22 Apr 2020 08:24:46: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Apr 2020 08:24:46: #1 finished! INFO @ Wed, 22 Apr 2020 08:24:46: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:24:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:24:46: #2 number of paired peaks: 28 WARNING @ Wed, 22 Apr 2020 08:24:46: Too few paired peaks (28) 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 08:24:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5883267/SRX5883267.10_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/SRX5883267/SRX5883267.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883267/SRX5883267.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883267/SRX5883267.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:24:47: 1000000 INFO @ Wed, 22 Apr 2020 08:24:52: 2000000 INFO @ Wed, 22 Apr 2020 08:24:57: 3000000 INFO @ Wed, 22 Apr 2020 08:25:03: 4000000 INFO @ Wed, 22 Apr 2020 08:25:08: 5000000 INFO @ Wed, 22 Apr 2020 08:25:14: 6000000 INFO @ Wed, 22 Apr 2020 08:25:15: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 08:25:15: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 08:25:15: #1 total tags in treatment: 2798751 INFO @ Wed, 22 Apr 2020 08:25:15: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:25:15: #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 08:25:15: #1 tags after filtering in treatment: 2132920 INFO @ Wed, 22 Apr 2020 08:25:15: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Apr 2020 08:25:15: #1 finished! INFO @ Wed, 22 Apr 2020 08:25:15: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:25:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:25:15: #2 number of paired peaks: 28 WARNING @ Wed, 22 Apr 2020 08:25:15: Too few paired peaks (28) 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 08:25:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5883267/SRX5883267.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883267/SRX5883267.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883267/SRX5883267.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883267/SRX5883267.20_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。