Job ID = 14521613 SRX = SRX9399005 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5671030 spots for SRR12935287/SRR12935287.sra Written 5671030 spots for SRR12935287/SRR12935287.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: 00:02:36 5671030 reads; of these: 5671030 (100.00%) were paired; of these: 1011016 (17.83%) aligned concordantly 0 times 3981685 (70.21%) aligned concordantly exactly 1 time 678329 (11.96%) aligned concordantly >1 times ---- 1011016 pairs aligned concordantly 0 times; of these: 142295 (14.07%) aligned discordantly 1 time ---- 868721 pairs aligned 0 times concordantly or discordantly; of these: 1737442 mates make up the pairs; of these: 1543363 (88.83%) aligned 0 times 123706 (7.12%) aligned exactly 1 time 70373 (4.05%) aligned >1 times 86.39% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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] 626783 / 4739146 = 0.1323 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 21:18:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399005/SRX9399005.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399005/SRX9399005.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399005/SRX9399005.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399005/SRX9399005.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 21:18:11: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:18:11: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:18:15: 1000000 INFO @ Sat, 15 Jan 2022 21:18:20: 2000000 INFO @ Sat, 15 Jan 2022 21:18:25: 3000000 INFO @ Sat, 15 Jan 2022 21:18:29: 4000000 INFO @ Sat, 15 Jan 2022 21:18:34: 5000000 INFO @ Sat, 15 Jan 2022 21:18:38: 6000000 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 21:18:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399005/SRX9399005.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399005/SRX9399005.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399005/SRX9399005.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399005/SRX9399005.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 21:18:41: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:18:41: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:18:43: 7000000 INFO @ Sat, 15 Jan 2022 21:18:46: 1000000 INFO @ Sat, 15 Jan 2022 21:18:47: 8000000 INFO @ Sat, 15 Jan 2022 21:18:50: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:18:50: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:18:50: #1 total tags in treatment: 4039610 INFO @ Sat, 15 Jan 2022 21:18:50: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:18:50: #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 21:18:50: #1 tags after filtering in treatment: 2842120 INFO @ Sat, 15 Jan 2022 21:18:50: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 21:18:50: #1 finished! INFO @ Sat, 15 Jan 2022 21:18:50: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:18:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:18:50: #2 number of paired peaks: 21 WARNING @ Sat, 15 Jan 2022 21:18:50: Too few paired peaks (21) 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 21:18:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399005/SRX9399005.05_peaks.narrowPeak: No such file or directory INFO @ Sat, 15 Jan 2022 21:18:51: 2000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399005/SRX9399005.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399005/SRX9399005.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399005/SRX9399005.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:18:56: 3000000 INFO @ Sat, 15 Jan 2022 21:19:01: 4000000 INFO @ Sat, 15 Jan 2022 21:19:06: 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 21:19:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399005/SRX9399005.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399005/SRX9399005.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399005/SRX9399005.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399005/SRX9399005.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 21:19:11: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:19:11: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:19:11: 6000000 INFO @ Sat, 15 Jan 2022 21:19:15: 1000000 INFO @ Sat, 15 Jan 2022 21:19:17: 7000000 INFO @ Sat, 15 Jan 2022 21:19:20: 2000000 INFO @ Sat, 15 Jan 2022 21:19:22: 8000000 INFO @ Sat, 15 Jan 2022 21:19:25: 3000000 INFO @ Sat, 15 Jan 2022 21:19:25: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:19:25: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:19:25: #1 total tags in treatment: 4039610 INFO @ Sat, 15 Jan 2022 21:19:25: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:19:25: #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 21:19:25: #1 tags after filtering in treatment: 2842120 INFO @ Sat, 15 Jan 2022 21:19:25: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 21:19:25: #1 finished! INFO @ Sat, 15 Jan 2022 21:19:25: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:19:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:19:25: #2 number of paired peaks: 21 WARNING @ Sat, 15 Jan 2022 21:19:25: Too few paired peaks (21) 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 21:19:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399005/SRX9399005.10_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/SRX9399005/SRX9399005.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399005/SRX9399005.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399005/SRX9399005.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:19:29: 4000000 INFO @ Sat, 15 Jan 2022 21:19:33: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:19:37: 6000000 INFO @ Sat, 15 Jan 2022 21:19:42: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:19:46: 8000000 INFO @ Sat, 15 Jan 2022 21:19:48: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:19:48: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:19:48: #1 total tags in treatment: 4039610 INFO @ Sat, 15 Jan 2022 21:19:48: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:19:48: #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 21:19:48: #1 tags after filtering in treatment: 2842120 INFO @ Sat, 15 Jan 2022 21:19:48: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 21:19:48: #1 finished! INFO @ Sat, 15 Jan 2022 21:19:48: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:19:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:19:49: #2 number of paired peaks: 21 WARNING @ Sat, 15 Jan 2022 21:19:49: Too few paired peaks (21) 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 21:19:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399005/SRX9399005.20_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/SRX9399005/SRX9399005.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399005/SRX9399005.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399005/SRX9399005.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling