Job ID = 14521756 SRX = SRX9399056 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5460720 spots for SRR12935337/SRR12935337.sra Written 5460720 spots for SRR12935337/SRR12935337.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: 00:02:21 5460720 reads; of these: 5460720 (100.00%) were paired; of these: 901871 (16.52%) aligned concordantly 0 times 4023143 (73.67%) aligned concordantly exactly 1 time 535706 (9.81%) aligned concordantly >1 times ---- 901871 pairs aligned concordantly 0 times; of these: 178852 (19.83%) aligned discordantly 1 time ---- 723019 pairs aligned 0 times concordantly or discordantly; of these: 1446038 mates make up the pairs; of these: 1129285 (78.10%) aligned 0 times 242360 (16.76%) aligned exactly 1 time 74393 (5.14%) aligned >1 times 89.66% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:21 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] 352388 / 4670081 = 0.0755 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 21:37:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399056/SRX9399056.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399056/SRX9399056.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399056/SRX9399056.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399056/SRX9399056.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 21:37:32: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:37:32: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:37:36: 1000000 INFO @ Sat, 15 Jan 2022 21:37:40: 2000000 INFO @ Sat, 15 Jan 2022 21:37:44: 3000000 INFO @ Sat, 15 Jan 2022 21:37:48: 4000000 INFO @ Sat, 15 Jan 2022 21:37:52: 5000000 INFO @ Sat, 15 Jan 2022 21:37:56: 6000000 INFO @ Sat, 15 Jan 2022 21:38:00: 7000000 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 21:38:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399056/SRX9399056.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399056/SRX9399056.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399056/SRX9399056.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399056/SRX9399056.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 21:38:02: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:38:02: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:38:03: 8000000 INFO @ Sat, 15 Jan 2022 21:38:06: 1000000 INFO @ Sat, 15 Jan 2022 21:38:07: 9000000 INFO @ Sat, 15 Jan 2022 21:38:08: #1 tag size is determined as 45 bps INFO @ Sat, 15 Jan 2022 21:38:08: #1 tag size = 45 INFO @ Sat, 15 Jan 2022 21:38:08: #1 total tags in treatment: 4209734 INFO @ Sat, 15 Jan 2022 21:38:08: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:38:08: #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 21:38:08: #1 tags after filtering in treatment: 2989037 INFO @ Sat, 15 Jan 2022 21:38:08: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 21:38:08: #1 finished! INFO @ Sat, 15 Jan 2022 21:38:08: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:38:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:38:08: #2 number of paired peaks: 1 WARNING @ Sat, 15 Jan 2022 21:38:08: Too few paired peaks (1) 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 21:38:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399056/SRX9399056.05_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/SRX9399056/SRX9399056.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399056/SRX9399056.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399056/SRX9399056.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:38:10: 2000000 INFO @ Sat, 15 Jan 2022 21:38:14: 3000000 INFO @ Sat, 15 Jan 2022 21:38:18: 4000000 INFO @ Sat, 15 Jan 2022 21:38:22: 5000000 INFO @ Sat, 15 Jan 2022 21:38:26: 6000000 INFO @ Sat, 15 Jan 2022 21:38:29: 7000000 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 21:38:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399056/SRX9399056.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399056/SRX9399056.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399056/SRX9399056.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399056/SRX9399056.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 21:38:32: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:38:32: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:38:33: 8000000 INFO @ Sat, 15 Jan 2022 21:38:37: 1000000 INFO @ Sat, 15 Jan 2022 21:38:37: 9000000 INFO @ Sat, 15 Jan 2022 21:38:38: #1 tag size is determined as 45 bps INFO @ Sat, 15 Jan 2022 21:38:38: #1 tag size = 45 INFO @ Sat, 15 Jan 2022 21:38:38: #1 total tags in treatment: 4209734 INFO @ Sat, 15 Jan 2022 21:38:38: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:38:38: #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 21:38:38: #1 tags after filtering in treatment: 2989037 INFO @ Sat, 15 Jan 2022 21:38:38: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 21:38:38: #1 finished! INFO @ Sat, 15 Jan 2022 21:38:38: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:38:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:38:38: #2 number of paired peaks: 1 WARNING @ Sat, 15 Jan 2022 21:38:38: Too few paired peaks (1) 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 21:38:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399056/SRX9399056.10_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/SRX9399056/SRX9399056.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399056/SRX9399056.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399056/SRX9399056.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:38:41: 2000000 INFO @ Sat, 15 Jan 2022 21:38:46: 3000000 INFO @ Sat, 15 Jan 2022 21:38:50: 4000000 INFO @ Sat, 15 Jan 2022 21:38:55: 5000000 INFO @ Sat, 15 Jan 2022 21:38:59: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:39:03: 7000000 INFO @ Sat, 15 Jan 2022 21:39:08: 8000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:39:12: 9000000 INFO @ Sat, 15 Jan 2022 21:39:12: #1 tag size is determined as 45 bps INFO @ Sat, 15 Jan 2022 21:39:12: #1 tag size = 45 INFO @ Sat, 15 Jan 2022 21:39:12: #1 total tags in treatment: 4209734 INFO @ Sat, 15 Jan 2022 21:39:12: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:39:12: #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 21:39:13: #1 tags after filtering in treatment: 2989037 INFO @ Sat, 15 Jan 2022 21:39:13: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 21:39:13: #1 finished! INFO @ Sat, 15 Jan 2022 21:39:13: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:39:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:39:13: #2 number of paired peaks: 1 WARNING @ Sat, 15 Jan 2022 21:39:13: Too few paired peaks (1) 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 21:39:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399056/SRX9399056.20_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/SRX9399056/SRX9399056.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399056/SRX9399056.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399056/SRX9399056.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling