Job ID = 14521832 SRX = SRX9399085 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4529070 spots for SRR12935366/SRR12935366.sra Written 4529070 spots for SRR12935366/SRR12935366.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: 00:02:45 4529070 reads; of these: 4529070 (100.00%) were paired; of these: 466252 (10.29%) aligned concordantly 0 times 3753750 (82.88%) aligned concordantly exactly 1 time 309068 (6.82%) aligned concordantly >1 times ---- 466252 pairs aligned concordantly 0 times; of these: 122141 (26.20%) aligned discordantly 1 time ---- 344111 pairs aligned 0 times concordantly or discordantly; of these: 688222 mates make up the pairs; of these: 497921 (72.35%) aligned 0 times 158544 (23.04%) aligned exactly 1 time 31757 (4.61%) aligned >1 times 94.50% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 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] 255159 / 4136985 = 0.0617 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 21:45:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399085/SRX9399085.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399085/SRX9399085.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399085/SRX9399085.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399085/SRX9399085.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 @ Sat, 15 Jan 2022 21:45:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:45:48: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:45:54: 1000000 INFO @ Sat, 15 Jan 2022 21:46:00: 2000000 INFO @ Sat, 15 Jan 2022 21:46:05: 3000000 INFO @ Sat, 15 Jan 2022 21:46:11: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 21:46:17: 5000000 INFO @ Sat, 15 Jan 2022 21:46:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399085/SRX9399085.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399085/SRX9399085.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399085/SRX9399085.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399085/SRX9399085.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 @ Sat, 15 Jan 2022 21:46:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:46:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:46:23: 6000000 INFO @ Sat, 15 Jan 2022 21:46:23: 1000000 INFO @ Sat, 15 Jan 2022 21:46:28: 2000000 INFO @ Sat, 15 Jan 2022 21:46:29: 7000000 INFO @ Sat, 15 Jan 2022 21:46:34: 3000000 INFO @ Sat, 15 Jan 2022 21:46:35: 8000000 INFO @ Sat, 15 Jan 2022 21:46:35: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:46:35: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:46:35: #1 total tags in treatment: 3809810 INFO @ Sat, 15 Jan 2022 21:46:35: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:46:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 21:46:35: #1 tags after filtering in treatment: 2716431 INFO @ Sat, 15 Jan 2022 21:46:35: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 21:46:35: #1 finished! INFO @ Sat, 15 Jan 2022 21:46:35: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:46:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:46:36: #2 number of paired peaks: 0 WARNING @ Sat, 15 Jan 2022 21:46:36: 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 @ Sat, 15 Jan 2022 21:46:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399085/SRX9399085.05_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/SRX9399085/SRX9399085.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399085/SRX9399085.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399085/SRX9399085.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:46:39: 4000000 INFO @ Sat, 15 Jan 2022 21:46:44: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 21:46:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399085/SRX9399085.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399085/SRX9399085.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399085/SRX9399085.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399085/SRX9399085.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 @ Sat, 15 Jan 2022 21:46:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:46:48: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:46:49: 6000000 INFO @ Sat, 15 Jan 2022 21:46:54: 1000000 INFO @ Sat, 15 Jan 2022 21:46:54: 7000000 INFO @ Sat, 15 Jan 2022 21:46:59: 2000000 INFO @ Sat, 15 Jan 2022 21:47:00: 8000000 INFO @ Sat, 15 Jan 2022 21:47:00: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:47:00: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:47:00: #1 total tags in treatment: 3809810 INFO @ Sat, 15 Jan 2022 21:47:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:47:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 21:47:00: #1 tags after filtering in treatment: 2716431 INFO @ Sat, 15 Jan 2022 21:47:00: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 21:47:00: #1 finished! INFO @ Sat, 15 Jan 2022 21:47:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:47:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:47:00: #2 number of paired peaks: 0 WARNING @ Sat, 15 Jan 2022 21:47:00: 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 @ Sat, 15 Jan 2022 21:47:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399085/SRX9399085.10_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/SRX9399085/SRX9399085.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399085/SRX9399085.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399085/SRX9399085.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:47:04: 3000000 INFO @ Sat, 15 Jan 2022 21:47:10: 4000000 INFO @ Sat, 15 Jan 2022 21:47:15: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:47:20: 6000000 INFO @ Sat, 15 Jan 2022 21:47:25: 7000000 INFO @ Sat, 15 Jan 2022 21:47:30: 8000000 INFO @ Sat, 15 Jan 2022 21:47:30: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:47:30: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:47:30: #1 total tags in treatment: 3809810 INFO @ Sat, 15 Jan 2022 21:47:30: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:47:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 21:47:31: #1 tags after filtering in treatment: 2716431 INFO @ Sat, 15 Jan 2022 21:47:31: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 21:47:31: #1 finished! INFO @ Sat, 15 Jan 2022 21:47:31: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:47:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:47:31: #2 number of paired peaks: 0 WARNING @ Sat, 15 Jan 2022 21:47:31: 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 @ Sat, 15 Jan 2022 21:47:31: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399085/SRX9399085.20_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/SRX9399085/SRX9399085.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399085/SRX9399085.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399085/SRX9399085.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。