Job ID = 14519690 SRX = SRX9067178 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4516969 spots for SRR12580331/SRR12580331.sra Written 4516969 spots for SRR12580331/SRR12580331.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: 00:01:47 4516969 reads; of these: 4516969 (100.00%) were paired; of these: 513575 (11.37%) aligned concordantly 0 times 3631842 (80.40%) aligned concordantly exactly 1 time 371552 (8.23%) aligned concordantly >1 times ---- 513575 pairs aligned concordantly 0 times; of these: 140051 (27.27%) aligned discordantly 1 time ---- 373524 pairs aligned 0 times concordantly or discordantly; of these: 747048 mates make up the pairs; of these: 500813 (67.04%) aligned 0 times 199901 (26.76%) aligned exactly 1 time 46334 (6.20%) aligned >1 times 94.46% overall alignment rate Time searching: 00:01:47 Overall time: 00:01:47 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] 370049 / 4074676 = 0.0908 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 17:28:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067178/SRX9067178.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067178/SRX9067178.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067178/SRX9067178.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067178/SRX9067178.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 17:28:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:28:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:28:47: 1000000 INFO @ Sat, 15 Jan 2022 17:28:52: 2000000 INFO @ Sat, 15 Jan 2022 17:28:56: 3000000 INFO @ Sat, 15 Jan 2022 17:29:01: 4000000 INFO @ Sat, 15 Jan 2022 17:29:06: 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 17:29:10: 6000000 INFO @ Sat, 15 Jan 2022 17:29:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067178/SRX9067178.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067178/SRX9067178.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067178/SRX9067178.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067178/SRX9067178.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 17:29:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:29:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:29:15: 7000000 INFO @ Sat, 15 Jan 2022 17:29:17: 1000000 INFO @ Sat, 15 Jan 2022 17:29:19: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 17:29:19: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 17:29:19: #1 total tags in treatment: 3636126 INFO @ Sat, 15 Jan 2022 17:29:19: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:29:19: #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 17:29:19: #1 tags after filtering in treatment: 2602895 INFO @ Sat, 15 Jan 2022 17:29:19: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 17:29:19: #1 finished! INFO @ Sat, 15 Jan 2022 17:29:19: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:29:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:29:19: #2 number of paired peaks: 2 WARNING @ Sat, 15 Jan 2022 17:29:19: Too few paired peaks (2) 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 17:29:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067178/SRX9067178.05_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/SRX9067178/SRX9067178.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067178/SRX9067178.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067178/SRX9067178.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:29:21: 2000000 INFO @ Sat, 15 Jan 2022 17:29:26: 3000000 INFO @ Sat, 15 Jan 2022 17:29:31: 4000000 INFO @ Sat, 15 Jan 2022 17:29:35: 5000000 INFO @ Sat, 15 Jan 2022 17:29:40: 6000000 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 17:29:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067178/SRX9067178.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067178/SRX9067178.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067178/SRX9067178.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067178/SRX9067178.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 17:29:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:29:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:29:44: 7000000 INFO @ Sat, 15 Jan 2022 17:29:48: 1000000 INFO @ Sat, 15 Jan 2022 17:29:48: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 17:29:48: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 17:29:48: #1 total tags in treatment: 3636126 INFO @ Sat, 15 Jan 2022 17:29:48: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:29:48: #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 17:29:49: #1 tags after filtering in treatment: 2602895 INFO @ Sat, 15 Jan 2022 17:29:49: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 17:29:49: #1 finished! INFO @ Sat, 15 Jan 2022 17:29:49: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:29:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:29:49: #2 number of paired peaks: 2 WARNING @ Sat, 15 Jan 2022 17:29:49: Too few paired peaks (2) 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 17:29:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067178/SRX9067178.10_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/SRX9067178/SRX9067178.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067178/SRX9067178.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067178/SRX9067178.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:29:52: 2000000 INFO @ Sat, 15 Jan 2022 17:29:57: 3000000 INFO @ Sat, 15 Jan 2022 17:30:02: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:30:07: 5000000 INFO @ Sat, 15 Jan 2022 17:30:11: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:30:16: 7000000 INFO @ Sat, 15 Jan 2022 17:30:20: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 17:30:20: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 17:30:20: #1 total tags in treatment: 3636126 INFO @ Sat, 15 Jan 2022 17:30:20: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:30:20: #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 17:30:20: #1 tags after filtering in treatment: 2602895 INFO @ Sat, 15 Jan 2022 17:30:20: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 17:30:20: #1 finished! INFO @ Sat, 15 Jan 2022 17:30:20: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:30:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:30:20: #2 number of paired peaks: 2 WARNING @ Sat, 15 Jan 2022 17:30:20: Too few paired peaks (2) 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 17:30:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067178/SRX9067178.20_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/SRX9067178/SRX9067178.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067178/SRX9067178.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067178/SRX9067178.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling