Job ID = 7118913 SRX = SRX8641883 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-22T07:26:19 prefetch.2.10.7: 1) Downloading 'SRR12120416'... 2020-07-22T07:26:19 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T07:27:42 prefetch.2.10.7: HTTPS download succeed 2020-07-22T07:27:43 prefetch.2.10.7: 'SRR12120416' is valid 2020-07-22T07:27:43 prefetch.2.10.7: 1) 'SRR12120416' was downloaded successfully 2020-07-22T07:27:43 prefetch.2.10.7: 'SRR12120416' has 0 unresolved dependencies Read 14067372 spots for SRR12120416/SRR12120416.sra Written 14067372 spots for SRR12120416/SRR12120416.sra 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: 00:03:48 14067372 reads; of these: 14067372 (100.00%) were unpaired; of these: 3187626 (22.66%) aligned 0 times 9709880 (69.02%) aligned exactly 1 time 1169866 (8.32%) aligned >1 times 77.34% overall alignment rate Time searching: 00:03:48 Overall time: 00:03:48 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_sort_core] merging from 8 files... [bam_rmdupse_core] 6176794 / 10879746 = 0.5677 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 Jul 2020 16:35:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8641883/SRX8641883.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8641883/SRX8641883.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8641883/SRX8641883.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8641883/SRX8641883.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 Jul 2020 16:35:15: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:35:15: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:35:21: 1000000 INFO @ Wed, 22 Jul 2020 16:35:27: 2000000 INFO @ Wed, 22 Jul 2020 16:35:33: 3000000 INFO @ Wed, 22 Jul 2020 16:35:39: 4000000 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 Jul 2020 16:35:43: #1 tag size is determined as 74 bps INFO @ Wed, 22 Jul 2020 16:35:43: #1 tag size = 74 INFO @ Wed, 22 Jul 2020 16:35:43: #1 total tags in treatment: 4702952 INFO @ Wed, 22 Jul 2020 16:35:43: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:35:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 16:35:43: #1 tags after filtering in treatment: 4702952 INFO @ Wed, 22 Jul 2020 16:35:43: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 16:35:43: #1 finished! INFO @ Wed, 22 Jul 2020 16:35:43: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:35:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:35:43: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:35:43: Too few paired peaks (0) 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 Jul 2020 16:35:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8641883/SRX8641883.05_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/SRX8641883/SRX8641883.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8641883/SRX8641883.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8641883/SRX8641883.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:35:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8641883/SRX8641883.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8641883/SRX8641883.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8641883/SRX8641883.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8641883/SRX8641883.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 Jul 2020 16:35:45: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:35:45: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:35:52: 1000000 INFO @ Wed, 22 Jul 2020 16:35:58: 2000000 INFO @ Wed, 22 Jul 2020 16:36:05: 3000000 INFO @ Wed, 22 Jul 2020 16:36:12: 4000000 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 Jul 2020 16:36:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8641883/SRX8641883.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8641883/SRX8641883.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8641883/SRX8641883.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8641883/SRX8641883.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 Jul 2020 16:36:15: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:36:15: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:36:16: #1 tag size is determined as 74 bps INFO @ Wed, 22 Jul 2020 16:36:16: #1 tag size = 74 INFO @ Wed, 22 Jul 2020 16:36:16: #1 total tags in treatment: 4702952 INFO @ Wed, 22 Jul 2020 16:36:16: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:36:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 16:36:16: #1 tags after filtering in treatment: 4702952 INFO @ Wed, 22 Jul 2020 16:36:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 16:36:16: #1 finished! INFO @ Wed, 22 Jul 2020 16:36:16: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:36:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:36:16: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:36:16: Too few paired peaks (0) 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 Jul 2020 16:36:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8641883/SRX8641883.10_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/SRX8641883/SRX8641883.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8641883/SRX8641883.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8641883/SRX8641883.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:36:22: 1000000 INFO @ Wed, 22 Jul 2020 16:36:29: 2000000 INFO @ Wed, 22 Jul 2020 16:36:36: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:36:42: 4000000 INFO @ Wed, 22 Jul 2020 16:36:47: #1 tag size is determined as 74 bps INFO @ Wed, 22 Jul 2020 16:36:47: #1 tag size = 74 INFO @ Wed, 22 Jul 2020 16:36:47: #1 total tags in treatment: 4702952 INFO @ Wed, 22 Jul 2020 16:36:47: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:36:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 16:36:47: #1 tags after filtering in treatment: 4702952 INFO @ Wed, 22 Jul 2020 16:36:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 16:36:47: #1 finished! INFO @ Wed, 22 Jul 2020 16:36:47: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:36:47: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:36:47: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:36:47: Too few paired peaks (0) 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 Jul 2020 16:36:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8641883/SRX8641883.20_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/SRX8641883/SRX8641883.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8641883/SRX8641883.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8641883/SRX8641883.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling