Job ID = 14521639 SRX = SRX9399131 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7146327 spots for SRR12935412/SRR12935412.sra Written 7146327 spots for SRR12935412/SRR12935412.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: 00:02:53 7146327 reads; of these: 7146327 (100.00%) were paired; of these: 674645 (9.44%) aligned concordantly 0 times 5323052 (74.49%) aligned concordantly exactly 1 time 1148630 (16.07%) aligned concordantly >1 times ---- 674645 pairs aligned concordantly 0 times; of these: 74103 (10.98%) aligned discordantly 1 time ---- 600542 pairs aligned 0 times concordantly or discordantly; of these: 1201084 mates make up the pairs; of these: 1002904 (83.50%) aligned 0 times 142962 (11.90%) aligned exactly 1 time 55218 (4.60%) aligned >1 times 92.98% overall alignment rate Time searching: 00:02:53 Overall time: 00:02:53 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_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] 1213553 / 6532628 = 0.1858 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 21:23:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399131/SRX9399131.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399131/SRX9399131.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399131/SRX9399131.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399131/SRX9399131.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 21:23:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:23:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:23:40: 1000000 INFO @ Sat, 15 Jan 2022 21:23:45: 2000000 INFO @ Sat, 15 Jan 2022 21:23:50: 3000000 INFO @ Sat, 15 Jan 2022 21:23:55: 4000000 INFO @ Sat, 15 Jan 2022 21:23:59: 5000000 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 21:24:04: 6000000 INFO @ Sat, 15 Jan 2022 21:24:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399131/SRX9399131.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399131/SRX9399131.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399131/SRX9399131.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399131/SRX9399131.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 21:24:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:24:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:24:10: 7000000 INFO @ Sat, 15 Jan 2022 21:24:10: 1000000 INFO @ Sat, 15 Jan 2022 21:24:15: 8000000 INFO @ Sat, 15 Jan 2022 21:24:16: 2000000 INFO @ Sat, 15 Jan 2022 21:24:21: 9000000 INFO @ Sat, 15 Jan 2022 21:24:22: 3000000 INFO @ Sat, 15 Jan 2022 21:24:27: 10000000 INFO @ Sat, 15 Jan 2022 21:24:27: 4000000 INFO @ Sat, 15 Jan 2022 21:24:31: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 21:24:31: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 21:24:31: #1 total tags in treatment: 5260967 INFO @ Sat, 15 Jan 2022 21:24:31: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:24:31: #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 21:24:31: #1 tags after filtering in treatment: 3436982 INFO @ Sat, 15 Jan 2022 21:24:31: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 21:24:31: #1 finished! INFO @ Sat, 15 Jan 2022 21:24:31: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:24:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:24:32: #2 number of paired peaks: 5 WARNING @ Sat, 15 Jan 2022 21:24:32: Too few paired peaks (5) 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 21:24:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399131/SRX9399131.05_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/SRX9399131/SRX9399131.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399131/SRX9399131.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399131/SRX9399131.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 21:24:33: 5000000 INFO @ Sat, 15 Jan 2022 21:24:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399131/SRX9399131.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399131/SRX9399131.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399131/SRX9399131.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399131/SRX9399131.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 21:24:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:24:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:24:39: 6000000 INFO @ Sat, 15 Jan 2022 21:24:41: 1000000 INFO @ Sat, 15 Jan 2022 21:24:45: 7000000 INFO @ Sat, 15 Jan 2022 21:24:47: 2000000 INFO @ Sat, 15 Jan 2022 21:24:50: 8000000 INFO @ Sat, 15 Jan 2022 21:24:53: 3000000 INFO @ Sat, 15 Jan 2022 21:24:56: 9000000 INFO @ Sat, 15 Jan 2022 21:24:59: 4000000 INFO @ Sat, 15 Jan 2022 21:25:02: 10000000 INFO @ Sat, 15 Jan 2022 21:25:05: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:25:07: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 21:25:07: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 21:25:07: #1 total tags in treatment: 5260967 INFO @ Sat, 15 Jan 2022 21:25:07: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:25:07: #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 21:25:07: #1 tags after filtering in treatment: 3436982 INFO @ Sat, 15 Jan 2022 21:25:07: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 21:25:07: #1 finished! INFO @ Sat, 15 Jan 2022 21:25:07: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:25:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:25:08: #2 number of paired peaks: 5 WARNING @ Sat, 15 Jan 2022 21:25:08: Too few paired peaks (5) 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 21:25:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399131/SRX9399131.10_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/SRX9399131/SRX9399131.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399131/SRX9399131.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399131/SRX9399131.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:25:10: 6000000 INFO @ Sat, 15 Jan 2022 21:25:15: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:25:20: 8000000 INFO @ Sat, 15 Jan 2022 21:25:26: 9000000 INFO @ Sat, 15 Jan 2022 21:25:30: 10000000 INFO @ Sat, 15 Jan 2022 21:25:35: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 21:25:35: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 21:25:35: #1 total tags in treatment: 5260967 INFO @ Sat, 15 Jan 2022 21:25:35: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:25:35: #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 21:25:35: #1 tags after filtering in treatment: 3436982 INFO @ Sat, 15 Jan 2022 21:25:35: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 21:25:35: #1 finished! INFO @ Sat, 15 Jan 2022 21:25:35: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:25:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:25:35: #2 number of paired peaks: 5 WARNING @ Sat, 15 Jan 2022 21:25:35: Too few paired peaks (5) 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 21:25:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399131/SRX9399131.20_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/SRX9399131/SRX9399131.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399131/SRX9399131.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399131/SRX9399131.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling