Job ID = 14521643 SRX = SRX9399135 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7664407 spots for SRR12935416/SRR12935416.sra Written 7664407 spots for SRR12935416/SRR12935416.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: 00:04:15 7664407 reads; of these: 7664407 (100.00%) were paired; of these: 2287471 (29.85%) aligned concordantly 0 times 4296605 (56.06%) aligned concordantly exactly 1 time 1080331 (14.10%) aligned concordantly >1 times ---- 2287471 pairs aligned concordantly 0 times; of these: 208530 (9.12%) aligned discordantly 1 time ---- 2078941 pairs aligned 0 times concordantly or discordantly; of these: 4157882 mates make up the pairs; of these: 3615415 (86.95%) aligned 0 times 356941 (8.58%) aligned exactly 1 time 185526 (4.46%) aligned >1 times 76.41% overall alignment rate Time searching: 00:04:15 Overall time: 00:04:15 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] 2276802 / 5560314 = 0.4095 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 21:25:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399135/SRX9399135.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399135/SRX9399135.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399135/SRX9399135.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399135/SRX9399135.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 21:25:51: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:25:51: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:25:59: 1000000 INFO @ Sat, 15 Jan 2022 21:26:05: 2000000 INFO @ Sat, 15 Jan 2022 21:26:12: 3000000 INFO @ Sat, 15 Jan 2022 21:26:18: 4000000 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: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399135/SRX9399135.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399135/SRX9399135.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399135/SRX9399135.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399135/SRX9399135.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 21:26:21: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:26:21: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:26:25: 5000000 INFO @ Sat, 15 Jan 2022 21:26:28: 1000000 INFO @ Sat, 15 Jan 2022 21:26:31: 6000000 INFO @ Sat, 15 Jan 2022 21:26:35: 2000000 INFO @ Sat, 15 Jan 2022 21:26:37: 7000000 INFO @ Sat, 15 Jan 2022 21:26:38: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:26:38: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:26:38: #1 total tags in treatment: 3159376 INFO @ Sat, 15 Jan 2022 21:26:38: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:26:38: #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 21:26:38: #1 tags after filtering in treatment: 2306219 INFO @ Sat, 15 Jan 2022 21:26:38: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:26:38: #1 finished! INFO @ Sat, 15 Jan 2022 21:26:38: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:26:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:26:38: #2 number of paired peaks: 28 WARNING @ Sat, 15 Jan 2022 21:26:38: Too few paired peaks (28) 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 21:26:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399135/SRX9399135.05_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/SRX9399135/SRX9399135.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399135/SRX9399135.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399135/SRX9399135.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:26:41: 3000000 INFO @ Sat, 15 Jan 2022 21:26:48: 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 21:26:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399135/SRX9399135.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399135/SRX9399135.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399135/SRX9399135.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399135/SRX9399135.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 21:26:51: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:26:51: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:26:55: 5000000 INFO @ Sat, 15 Jan 2022 21:26:58: 1000000 INFO @ Sat, 15 Jan 2022 21:27:02: 6000000 INFO @ Sat, 15 Jan 2022 21:27:06: 2000000 INFO @ Sat, 15 Jan 2022 21:27:09: 7000000 INFO @ Sat, 15 Jan 2022 21:27:10: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:27:10: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:27:10: #1 total tags in treatment: 3159376 INFO @ Sat, 15 Jan 2022 21:27:10: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:27:10: #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 21:27:10: #1 tags after filtering in treatment: 2306219 INFO @ Sat, 15 Jan 2022 21:27:10: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:27:10: #1 finished! INFO @ Sat, 15 Jan 2022 21:27:10: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:27:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:27:10: #2 number of paired peaks: 28 WARNING @ Sat, 15 Jan 2022 21:27:10: Too few paired peaks (28) 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 21:27:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399135/SRX9399135.10_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/SRX9399135/SRX9399135.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399135/SRX9399135.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399135/SRX9399135.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:27:13: 3000000 INFO @ Sat, 15 Jan 2022 21:27:20: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:27:28: 5000000 INFO @ Sat, 15 Jan 2022 21:27:35: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:27:43: 7000000 INFO @ Sat, 15 Jan 2022 21:27:44: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:27:44: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:27:44: #1 total tags in treatment: 3159376 INFO @ Sat, 15 Jan 2022 21:27:44: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:27:44: #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 21:27:44: #1 tags after filtering in treatment: 2306219 INFO @ Sat, 15 Jan 2022 21:27:44: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:27:44: #1 finished! INFO @ Sat, 15 Jan 2022 21:27:44: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:27:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:27:44: #2 number of paired peaks: 28 WARNING @ Sat, 15 Jan 2022 21:27:44: Too few paired peaks (28) 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 21:27:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399135/SRX9399135.20_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/SRX9399135/SRX9399135.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399135/SRX9399135.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399135/SRX9399135.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling