Job ID = 14521757 SRX = SRX9399057 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4525164 spots for SRR12935338/SRR12935338.sra Written 4525164 spots for SRR12935338/SRR12935338.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: 00:01:58 4525164 reads; of these: 4525164 (100.00%) were paired; of these: 786990 (17.39%) aligned concordantly 0 times 3294379 (72.80%) aligned concordantly exactly 1 time 443795 (9.81%) aligned concordantly >1 times ---- 786990 pairs aligned concordantly 0 times; of these: 139898 (17.78%) aligned discordantly 1 time ---- 647092 pairs aligned 0 times concordantly or discordantly; of these: 1294184 mates make up the pairs; of these: 1001590 (77.39%) aligned 0 times 228789 (17.68%) aligned exactly 1 time 63805 (4.93%) aligned >1 times 88.93% overall alignment rate Time searching: 00:01:58 Overall time: 00:01:58 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] 275802 / 3829968 = 0.0720 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 21:36:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399057/SRX9399057.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399057/SRX9399057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399057/SRX9399057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399057/SRX9399057.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 21:36:51: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:36:51: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:36:56: 1000000 INFO @ Sat, 15 Jan 2022 21:37:02: 2000000 INFO @ Sat, 15 Jan 2022 21:37:07: 3000000 INFO @ Sat, 15 Jan 2022 21:37:12: 4000000 INFO @ Sat, 15 Jan 2022 21:37:18: 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 21:37:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399057/SRX9399057.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399057/SRX9399057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399057/SRX9399057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399057/SRX9399057.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 21:37:21: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:37:21: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:37:23: 6000000 INFO @ Sat, 15 Jan 2022 21:37:27: 1000000 INFO @ Sat, 15 Jan 2022 21:37:29: 7000000 INFO @ Sat, 15 Jan 2022 21:37:32: #1 tag size is determined as 32 bps INFO @ Sat, 15 Jan 2022 21:37:32: #1 tag size = 32 INFO @ Sat, 15 Jan 2022 21:37:32: #1 total tags in treatment: 3465537 INFO @ Sat, 15 Jan 2022 21:37:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:37:32: #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 21:37:32: #1 tags after filtering in treatment: 2573096 INFO @ Sat, 15 Jan 2022 21:37:32: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 21:37:32: #1 finished! INFO @ Sat, 15 Jan 2022 21:37:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:37:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:37:32: #2 number of paired peaks: 3 WARNING @ Sat, 15 Jan 2022 21:37:32: Too few paired peaks (3) 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 21:37:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399057/SRX9399057.05_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/SRX9399057/SRX9399057.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399057/SRX9399057.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399057/SRX9399057.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:37:33: 2000000 INFO @ Sat, 15 Jan 2022 21:37:39: 3000000 INFO @ Sat, 15 Jan 2022 21:37:44: 4000000 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 21:37:50: 5000000 INFO @ Sat, 15 Jan 2022 21:37:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399057/SRX9399057.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399057/SRX9399057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399057/SRX9399057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399057/SRX9399057.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 21:37:51: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:37:51: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:37:56: 6000000 INFO @ Sat, 15 Jan 2022 21:37:57: 1000000 INFO @ Sat, 15 Jan 2022 21:38:02: 7000000 INFO @ Sat, 15 Jan 2022 21:38:02: 2000000 INFO @ Sat, 15 Jan 2022 21:38:05: #1 tag size is determined as 32 bps INFO @ Sat, 15 Jan 2022 21:38:05: #1 tag size = 32 INFO @ Sat, 15 Jan 2022 21:38:05: #1 total tags in treatment: 3465537 INFO @ Sat, 15 Jan 2022 21:38:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:38:05: #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 21:38:05: #1 tags after filtering in treatment: 2573096 INFO @ Sat, 15 Jan 2022 21:38:05: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 21:38:05: #1 finished! INFO @ Sat, 15 Jan 2022 21:38:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:38:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:38:05: #2 number of paired peaks: 3 WARNING @ Sat, 15 Jan 2022 21:38:05: Too few paired peaks (3) 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 21:38:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399057/SRX9399057.10_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/SRX9399057/SRX9399057.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399057/SRX9399057.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399057/SRX9399057.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:38:07: 3000000 INFO @ Sat, 15 Jan 2022 21:38:11: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:38:16: 5000000 INFO @ Sat, 15 Jan 2022 21:38:20: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:38:25: 7000000 INFO @ Sat, 15 Jan 2022 21:38:27: #1 tag size is determined as 32 bps INFO @ Sat, 15 Jan 2022 21:38:27: #1 tag size = 32 INFO @ Sat, 15 Jan 2022 21:38:27: #1 total tags in treatment: 3465537 INFO @ Sat, 15 Jan 2022 21:38:27: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:38:27: #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 21:38:27: #1 tags after filtering in treatment: 2573096 INFO @ Sat, 15 Jan 2022 21:38:27: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 21:38:27: #1 finished! INFO @ Sat, 15 Jan 2022 21:38:27: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:38:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:38:27: #2 number of paired peaks: 3 WARNING @ Sat, 15 Jan 2022 21:38:27: Too few paired peaks (3) 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 21:38:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399057/SRX9399057.20_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/SRX9399057/SRX9399057.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399057/SRX9399057.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399057/SRX9399057.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling