Job ID = 5791050 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,261,958 reads read : 12,523,916 reads written : 12,523,916 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: 00:02:14 6261958 reads; of these: 6261958 (100.00%) were paired; of these: 2176300 (34.75%) aligned concordantly 0 times 3616495 (57.75%) aligned concordantly exactly 1 time 469163 (7.49%) aligned concordantly >1 times ---- 2176300 pairs aligned concordantly 0 times; of these: 340739 (15.66%) aligned discordantly 1 time ---- 1835561 pairs aligned 0 times concordantly or discordantly; of these: 3671122 mates make up the pairs; of these: 2919353 (79.52%) aligned 0 times 596232 (16.24%) aligned exactly 1 time 155537 (4.24%) aligned >1 times 76.69% overall alignment rate Time searching: 00:02:14 Overall time: 00:02:14 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] 141148 / 4372469 = 0.0323 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 08:27:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883274/SRX5883274.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883274/SRX5883274.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883274/SRX5883274.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883274/SRX5883274.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 08:27:41: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:27:41: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:27:45: 1000000 INFO @ Wed, 22 Apr 2020 08:27:50: 2000000 INFO @ Wed, 22 Apr 2020 08:27:54: 3000000 INFO @ Wed, 22 Apr 2020 08:27:59: 4000000 INFO @ Wed, 22 Apr 2020 08:28:03: 5000000 INFO @ Wed, 22 Apr 2020 08:28:07: 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 08:28:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883274/SRX5883274.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883274/SRX5883274.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883274/SRX5883274.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883274/SRX5883274.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 08:28:11: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:28:11: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:28:12: 7000000 INFO @ Wed, 22 Apr 2020 08:28:16: 1000000 INFO @ Wed, 22 Apr 2020 08:28:17: 8000000 INFO @ Wed, 22 Apr 2020 08:28:22: 2000000 INFO @ Wed, 22 Apr 2020 08:28:23: 9000000 INFO @ Wed, 22 Apr 2020 08:28:24: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 08:28:24: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 08:28:24: #1 total tags in treatment: 3957738 INFO @ Wed, 22 Apr 2020 08:28:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:28:24: #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 08:28:24: #1 tags after filtering in treatment: 3276163 INFO @ Wed, 22 Apr 2020 08:28:24: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 22 Apr 2020 08:28:24: #1 finished! INFO @ Wed, 22 Apr 2020 08:28:24: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:28:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:28:24: #2 number of paired peaks: 30 WARNING @ Wed, 22 Apr 2020 08:28:24: Too few paired peaks (30) 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 08:28:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5883274/SRX5883274.05_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/SRX5883274/SRX5883274.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883274/SRX5883274.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883274/SRX5883274.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:28:28: 3000000 INFO @ Wed, 22 Apr 2020 08:28:33: 4000000 INFO @ Wed, 22 Apr 2020 08:28:38: 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 08:28:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883274/SRX5883274.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883274/SRX5883274.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883274/SRX5883274.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883274/SRX5883274.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 08:28:41: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:28:41: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:28:44: 6000000 INFO @ Wed, 22 Apr 2020 08:28:46: 1000000 INFO @ Wed, 22 Apr 2020 08:28:50: 7000000 INFO @ Wed, 22 Apr 2020 08:28:52: 2000000 INFO @ Wed, 22 Apr 2020 08:28:56: 8000000 INFO @ Wed, 22 Apr 2020 08:28:58: 3000000 INFO @ Wed, 22 Apr 2020 08:29:02: 9000000 INFO @ Wed, 22 Apr 2020 08:29:03: 4000000 INFO @ Wed, 22 Apr 2020 08:29:04: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 08:29:04: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 08:29:04: #1 total tags in treatment: 3957738 INFO @ Wed, 22 Apr 2020 08:29:04: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:29:04: #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 08:29:04: #1 tags after filtering in treatment: 3276163 INFO @ Wed, 22 Apr 2020 08:29:04: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 22 Apr 2020 08:29:04: #1 finished! INFO @ Wed, 22 Apr 2020 08:29:04: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:29:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:29:04: #2 number of paired peaks: 30 WARNING @ Wed, 22 Apr 2020 08:29:04: Too few paired peaks (30) 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 08:29:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5883274/SRX5883274.10_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/SRX5883274/SRX5883274.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883274/SRX5883274.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883274/SRX5883274.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:29:09: 5000000 INFO @ Wed, 22 Apr 2020 08:29:14: 6000000 INFO @ Wed, 22 Apr 2020 08:29:19: 7000000 INFO @ Wed, 22 Apr 2020 08:29:25: 8000000 INFO @ Wed, 22 Apr 2020 08:29:30: 9000000 INFO @ Wed, 22 Apr 2020 08:29:32: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 08:29:32: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 08:29:32: #1 total tags in treatment: 3957738 INFO @ Wed, 22 Apr 2020 08:29:32: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:29:32: #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 08:29:32: #1 tags after filtering in treatment: 3276163 INFO @ Wed, 22 Apr 2020 08:29:32: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 22 Apr 2020 08:29:32: #1 finished! INFO @ Wed, 22 Apr 2020 08:29:32: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:29:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:29:32: #2 number of paired peaks: 30 WARNING @ Wed, 22 Apr 2020 08:29:32: Too few paired peaks (30) 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 08:29:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5883274/SRX5883274.20_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/SRX5883274/SRX5883274.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883274/SRX5883274.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883274/SRX5883274.20_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。