Job ID = 5791277 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,214,014 reads read : 26,428,028 reads written : 26,428,028 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: 00:03:12 13214014 reads; of these: 13214014 (100.00%) were paired; of these: 8746686 (66.19%) aligned concordantly 0 times 3497746 (26.47%) aligned concordantly exactly 1 time 969582 (7.34%) aligned concordantly >1 times ---- 8746686 pairs aligned concordantly 0 times; of these: 301889 (3.45%) aligned discordantly 1 time ---- 8444797 pairs aligned 0 times concordantly or discordantly; of these: 16889594 mates make up the pairs; of these: 16106153 (95.36%) aligned 0 times 544554 (3.22%) aligned exactly 1 time 238887 (1.41%) aligned >1 times 39.06% overall alignment rate Time searching: 00:03:12 Overall time: 00:03:12 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] 1092369 / 4720890 = 0.2314 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 09:32:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7399908/SRX7399908.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7399908/SRX7399908.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7399908/SRX7399908.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7399908/SRX7399908.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 09:32:01: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:32:01: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:32:07: 1000000 INFO @ Wed, 22 Apr 2020 09:32:12: 2000000 INFO @ Wed, 22 Apr 2020 09:32:17: 3000000 INFO @ Wed, 22 Apr 2020 09:32:22: 4000000 INFO @ Wed, 22 Apr 2020 09:32:27: 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 09:32:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7399908/SRX7399908.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7399908/SRX7399908.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7399908/SRX7399908.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7399908/SRX7399908.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 09:32:31: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:32:31: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:32:32: 6000000 INFO @ Wed, 22 Apr 2020 09:32:37: 1000000 INFO @ Wed, 22 Apr 2020 09:32:38: 7000000 INFO @ Wed, 22 Apr 2020 09:32:42: 2000000 INFO @ Wed, 22 Apr 2020 09:32:43: 8000000 INFO @ Wed, 22 Apr 2020 09:32:44: #1 tag size is determined as 41 bps INFO @ Wed, 22 Apr 2020 09:32:44: #1 tag size = 41 INFO @ Wed, 22 Apr 2020 09:32:44: #1 total tags in treatment: 3447294 INFO @ Wed, 22 Apr 2020 09:32:44: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:32:44: #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 09:32:44: #1 tags after filtering in treatment: 2433944 INFO @ Wed, 22 Apr 2020 09:32:44: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 22 Apr 2020 09:32:44: #1 finished! INFO @ Wed, 22 Apr 2020 09:32:44: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:32:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:32:44: #2 number of paired peaks: 38 WARNING @ Wed, 22 Apr 2020 09:32:44: Too few paired peaks (38) 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 09:32:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7399908/SRX7399908.05_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/SRX7399908/SRX7399908.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399908/SRX7399908.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399908/SRX7399908.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:32:47: 3000000 INFO @ Wed, 22 Apr 2020 09:32:52: 4000000 INFO @ Wed, 22 Apr 2020 09:32:57: 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 09:33:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7399908/SRX7399908.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7399908/SRX7399908.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7399908/SRX7399908.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7399908/SRX7399908.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 09:33:01: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:33:01: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:33:02: 6000000 INFO @ Wed, 22 Apr 2020 09:33:07: 1000000 INFO @ Wed, 22 Apr 2020 09:33:08: 7000000 INFO @ Wed, 22 Apr 2020 09:33:12: 2000000 INFO @ Wed, 22 Apr 2020 09:33:13: 8000000 INFO @ Wed, 22 Apr 2020 09:33:14: #1 tag size is determined as 41 bps INFO @ Wed, 22 Apr 2020 09:33:14: #1 tag size = 41 INFO @ Wed, 22 Apr 2020 09:33:14: #1 total tags in treatment: 3447294 INFO @ Wed, 22 Apr 2020 09:33:14: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:33:14: #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 09:33:14: #1 tags after filtering in treatment: 2433944 INFO @ Wed, 22 Apr 2020 09:33:14: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 22 Apr 2020 09:33:14: #1 finished! INFO @ Wed, 22 Apr 2020 09:33:14: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:33:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:33:14: #2 number of paired peaks: 38 WARNING @ Wed, 22 Apr 2020 09:33:14: Too few paired peaks (38) 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 09:33:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7399908/SRX7399908.10_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/SRX7399908/SRX7399908.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399908/SRX7399908.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399908/SRX7399908.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:33:18: 3000000 INFO @ Wed, 22 Apr 2020 09:33:23: 4000000 INFO @ Wed, 22 Apr 2020 09:33:28: 5000000 INFO @ Wed, 22 Apr 2020 09:33:34: 6000000 INFO @ Wed, 22 Apr 2020 09:33:39: 7000000 INFO @ Wed, 22 Apr 2020 09:33:44: 8000000 INFO @ Wed, 22 Apr 2020 09:33:45: #1 tag size is determined as 41 bps INFO @ Wed, 22 Apr 2020 09:33:45: #1 tag size = 41 INFO @ Wed, 22 Apr 2020 09:33:45: #1 total tags in treatment: 3447294 INFO @ Wed, 22 Apr 2020 09:33:45: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:33:45: #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 09:33:45: #1 tags after filtering in treatment: 2433944 INFO @ Wed, 22 Apr 2020 09:33:45: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 22 Apr 2020 09:33:45: #1 finished! INFO @ Wed, 22 Apr 2020 09:33:45: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:33:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:33:45: #2 number of paired peaks: 38 WARNING @ Wed, 22 Apr 2020 09:33:45: Too few paired peaks (38) 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 09:33:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7399908/SRX7399908.20_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/SRX7399908/SRX7399908.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399908/SRX7399908.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399908/SRX7399908.20_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。