Job ID = 5791048 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,139,695 reads read : 10,279,390 reads written : 10,279,390 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 5139695 reads; of these: 5139695 (100.00%) were paired; of these: 1679916 (32.69%) aligned concordantly 0 times 3007521 (58.52%) aligned concordantly exactly 1 time 452258 (8.80%) aligned concordantly >1 times ---- 1679916 pairs aligned concordantly 0 times; of these: 186393 (11.10%) aligned discordantly 1 time ---- 1493523 pairs aligned 0 times concordantly or discordantly; of these: 2987046 mates make up the pairs; of these: 2386301 (79.89%) aligned 0 times 476634 (15.96%) aligned exactly 1 time 124111 (4.15%) aligned >1 times 76.79% 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] 90395 / 3615128 = 0.0250 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 08:26:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883272/SRX5883272.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883272/SRX5883272.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883272/SRX5883272.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883272/SRX5883272.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 08:26:13: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:26:13: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:26:18: 1000000 INFO @ Wed, 22 Apr 2020 08:26:22: 2000000 INFO @ Wed, 22 Apr 2020 08:26:27: 3000000 INFO @ Wed, 22 Apr 2020 08:26:31: 4000000 INFO @ Wed, 22 Apr 2020 08:26:36: 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 08:26:40: 6000000 INFO @ Wed, 22 Apr 2020 08:26:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883272/SRX5883272.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883272/SRX5883272.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883272/SRX5883272.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883272/SRX5883272.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 08:26:43: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:26:43: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:26:45: 7000000 INFO @ Wed, 22 Apr 2020 08:26:48: 1000000 INFO @ Wed, 22 Apr 2020 08:26:49: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 08:26:49: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 08:26:49: #1 total tags in treatment: 3373180 INFO @ Wed, 22 Apr 2020 08:26:49: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:26:49: #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 08:26:49: #1 tags after filtering in treatment: 2845714 INFO @ Wed, 22 Apr 2020 08:26:49: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 22 Apr 2020 08:26:49: #1 finished! INFO @ Wed, 22 Apr 2020 08:26:49: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:26:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:26:49: #2 number of paired peaks: 26 WARNING @ Wed, 22 Apr 2020 08:26:49: Too few paired peaks (26) 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 08:26:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5883272/SRX5883272.05_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/SRX5883272/SRX5883272.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883272/SRX5883272.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883272/SRX5883272.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:26:53: 2000000 INFO @ Wed, 22 Apr 2020 08:26:58: 3000000 INFO @ Wed, 22 Apr 2020 08:27:03: 4000000 INFO @ Wed, 22 Apr 2020 08:27:08: 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 08:27:13: 6000000 INFO @ Wed, 22 Apr 2020 08:27:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883272/SRX5883272.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883272/SRX5883272.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883272/SRX5883272.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883272/SRX5883272.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 08:27:13: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:27:13: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:27:18: 7000000 INFO @ Wed, 22 Apr 2020 08:27:18: 1000000 INFO @ Wed, 22 Apr 2020 08:27:21: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 08:27:21: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 08:27:21: #1 total tags in treatment: 3373180 INFO @ Wed, 22 Apr 2020 08:27:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:27:21: #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 08:27:21: #1 tags after filtering in treatment: 2845714 INFO @ Wed, 22 Apr 2020 08:27:21: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 22 Apr 2020 08:27:21: #1 finished! INFO @ Wed, 22 Apr 2020 08:27:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:27:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:27:22: #2 number of paired peaks: 26 WARNING @ Wed, 22 Apr 2020 08:27:22: Too few paired peaks (26) 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! INFO @ Wed, 22 Apr 2020 08:27:23: 2000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX5883272/SRX5883272.10_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/SRX5883272/SRX5883272.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883272/SRX5883272.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883272/SRX5883272.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:27:28: 3000000 INFO @ Wed, 22 Apr 2020 08:27:33: 4000000 INFO @ Wed, 22 Apr 2020 08:27:37: 5000000 INFO @ Wed, 22 Apr 2020 08:27:42: 6000000 INFO @ Wed, 22 Apr 2020 08:27:47: 7000000 INFO @ Wed, 22 Apr 2020 08:27:50: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 08:27:50: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 08:27:50: #1 total tags in treatment: 3373180 INFO @ Wed, 22 Apr 2020 08:27:50: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:27:50: #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 08:27:50: #1 tags after filtering in treatment: 2845714 INFO @ Wed, 22 Apr 2020 08:27:50: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 22 Apr 2020 08:27:50: #1 finished! INFO @ Wed, 22 Apr 2020 08:27:50: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:27:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:27:51: #2 number of paired peaks: 26 WARNING @ Wed, 22 Apr 2020 08:27:51: Too few paired peaks (26) 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 08:27:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5883272/SRX5883272.20_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/SRX5883272/SRX5883272.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883272/SRX5883272.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883272/SRX5883272.20_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。