Job ID = 14521665 SRX = SRX9399026 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3831644 spots for SRR12935308/SRR12935308.sra Written 3831644 spots for SRR12935308/SRR12935308.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: 00:01:44 3831644 reads; of these: 3831644 (100.00%) were paired; of these: 769434 (20.08%) aligned concordantly 0 times 2600463 (67.87%) aligned concordantly exactly 1 time 461747 (12.05%) aligned concordantly >1 times ---- 769434 pairs aligned concordantly 0 times; of these: 341538 (44.39%) aligned discordantly 1 time ---- 427896 pairs aligned 0 times concordantly or discordantly; of these: 855792 mates make up the pairs; of these: 439911 (51.40%) aligned 0 times 255531 (29.86%) aligned exactly 1 time 160350 (18.74%) aligned >1 times 94.26% overall alignment rate Time searching: 00:01:44 Overall time: 00:01:44 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] 271396 / 3128040 = 0.0868 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 21:25:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399026/SRX9399026.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399026/SRX9399026.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399026/SRX9399026.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399026/SRX9399026.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 21:25:52: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:25:52: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:25:57: 1000000 INFO @ Sat, 15 Jan 2022 21:26:01: 2000000 INFO @ Sat, 15 Jan 2022 21:26:05: 3000000 INFO @ Sat, 15 Jan 2022 21:26:09: 4000000 INFO @ Sat, 15 Jan 2022 21:26:13: 5000000 INFO @ Sat, 15 Jan 2022 21:26:18: 6000000 INFO @ Sat, 15 Jan 2022 21:26:20: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 21:26:20: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 21:26:20: #1 total tags in treatment: 2792463 INFO @ Sat, 15 Jan 2022 21:26:20: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:26:20: #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 21:26:21: #1 tags after filtering in treatment: 2074442 INFO @ Sat, 15 Jan 2022 21:26:21: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 21:26:21: #1 finished! INFO @ Sat, 15 Jan 2022 21:26:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:26:21: #2 looking for paired plus/minus strand peaks... 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 21:26:21: #2 number of paired peaks: 23 WARNING @ Sat, 15 Jan 2022 21:26:21: Too few paired peaks (23) 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 21:26:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399026/SRX9399026.05_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/SRX9399026/SRX9399026.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399026/SRX9399026.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399026/SRX9399026.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:26:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399026/SRX9399026.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399026/SRX9399026.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399026/SRX9399026.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399026/SRX9399026.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 21:26:22: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:26:22: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:26:27: 1000000 INFO @ Sat, 15 Jan 2022 21:26:30: 2000000 INFO @ Sat, 15 Jan 2022 21:26:34: 3000000 INFO @ Sat, 15 Jan 2022 21:26:38: 4000000 INFO @ Sat, 15 Jan 2022 21:26:42: 5000000 INFO @ Sat, 15 Jan 2022 21:26:45: 6000000 INFO @ Sat, 15 Jan 2022 21:26:48: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 21:26:48: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 21:26:48: #1 total tags in treatment: 2792463 INFO @ Sat, 15 Jan 2022 21:26:48: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:26:48: #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 21:26:48: #1 tags after filtering in treatment: 2074442 INFO @ Sat, 15 Jan 2022 21:26:48: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 21:26:48: #1 finished! INFO @ Sat, 15 Jan 2022 21:26:48: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:26:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:26:48: #2 number of paired peaks: 23 WARNING @ Sat, 15 Jan 2022 21:26:48: Too few paired peaks (23) 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 21:26:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399026/SRX9399026.10_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/SRX9399026/SRX9399026.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399026/SRX9399026.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399026/SRX9399026.10_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 21:26:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399026/SRX9399026.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399026/SRX9399026.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399026/SRX9399026.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399026/SRX9399026.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 21:26:52: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:26:52: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:26:57: 1000000 INFO @ Sat, 15 Jan 2022 21:27:01: 2000000 INFO @ Sat, 15 Jan 2022 21:27:05: 3000000 INFO @ Sat, 15 Jan 2022 21:27:10: 4000000 INFO @ Sat, 15 Jan 2022 21:27:14: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:27:18: 6000000 INFO @ Sat, 15 Jan 2022 21:27:21: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 21:27:21: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 21:27:21: #1 total tags in treatment: 2792463 INFO @ Sat, 15 Jan 2022 21:27:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:27:21: #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 21:27:21: #1 tags after filtering in treatment: 2074442 INFO @ Sat, 15 Jan 2022 21:27:21: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 21:27:21: #1 finished! INFO @ Sat, 15 Jan 2022 21:27:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:27:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:27:21: #2 number of paired peaks: 23 WARNING @ Sat, 15 Jan 2022 21:27:21: Too few paired peaks (23) 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 21:27:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399026/SRX9399026.20_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/SRX9399026/SRX9399026.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399026/SRX9399026.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399026/SRX9399026.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。