Job ID = 14521833 SRX = SRX9399086 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4021240 spots for SRR12935367/SRR12935367.sra Written 4021240 spots for SRR12935367/SRR12935367.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: 00:01:33 4021240 reads; of these: 4021240 (100.00%) were paired; of these: 594234 (14.78%) aligned concordantly 0 times 3148392 (78.29%) aligned concordantly exactly 1 time 278614 (6.93%) aligned concordantly >1 times ---- 594234 pairs aligned concordantly 0 times; of these: 97957 (16.48%) aligned discordantly 1 time ---- 496277 pairs aligned 0 times concordantly or discordantly; of these: 992554 mates make up the pairs; of these: 828478 (83.47%) aligned 0 times 134364 (13.54%) aligned exactly 1 time 29712 (2.99%) aligned >1 times 89.70% overall alignment rate Time searching: 00:01:33 Overall time: 00:01:33 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] 262733 / 3472243 = 0.0757 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 21:44:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399086/SRX9399086.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399086/SRX9399086.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399086/SRX9399086.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399086/SRX9399086.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 21:44:02: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:44:02: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:44:07: 1000000 INFO @ Sat, 15 Jan 2022 21:44:11: 2000000 INFO @ Sat, 15 Jan 2022 21:44:16: 3000000 INFO @ Sat, 15 Jan 2022 21:44:21: 4000000 INFO @ Sat, 15 Jan 2022 21:44:26: 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 21:44:30: 6000000 INFO @ Sat, 15 Jan 2022 21:44:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399086/SRX9399086.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399086/SRX9399086.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399086/SRX9399086.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399086/SRX9399086.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 21:44:32: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:44:32: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:44:34: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:44:34: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:44:34: #1 total tags in treatment: 3165700 INFO @ Sat, 15 Jan 2022 21:44:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:44:34: #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 21:44:34: #1 tags after filtering in treatment: 2324626 INFO @ Sat, 15 Jan 2022 21:44:34: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:44:34: #1 finished! INFO @ Sat, 15 Jan 2022 21:44:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:44:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:44:34: #2 number of paired peaks: 3 WARNING @ Sat, 15 Jan 2022 21:44:34: 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 21:44:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399086/SRX9399086.05_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/SRX9399086/SRX9399086.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399086/SRX9399086.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399086/SRX9399086.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:44:38: 1000000 INFO @ Sat, 15 Jan 2022 21:44:45: 2000000 INFO @ Sat, 15 Jan 2022 21:44:52: 3000000 INFO @ Sat, 15 Jan 2022 21:44:58: 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 21:45:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399086/SRX9399086.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399086/SRX9399086.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399086/SRX9399086.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399086/SRX9399086.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 21:45:02: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:45:02: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:45:05: 5000000 INFO @ Sat, 15 Jan 2022 21:45:09: 1000000 INFO @ Sat, 15 Jan 2022 21:45:12: 6000000 INFO @ Sat, 15 Jan 2022 21:45:15: 2000000 INFO @ Sat, 15 Jan 2022 21:45:17: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:45:17: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:45:17: #1 total tags in treatment: 3165700 INFO @ Sat, 15 Jan 2022 21:45:17: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:45:17: #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 21:45:17: #1 tags after filtering in treatment: 2324626 INFO @ Sat, 15 Jan 2022 21:45:17: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:45:17: #1 finished! INFO @ Sat, 15 Jan 2022 21:45:17: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:45:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:45:17: #2 number of paired peaks: 3 WARNING @ Sat, 15 Jan 2022 21:45:17: 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 21:45:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399086/SRX9399086.10_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/SRX9399086/SRX9399086.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399086/SRX9399086.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399086/SRX9399086.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:45:22: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:45:28: 4000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:45:34: 5000000 INFO @ Sat, 15 Jan 2022 21:45:40: 6000000 INFO @ Sat, 15 Jan 2022 21:45:44: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:45:44: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:45:44: #1 total tags in treatment: 3165700 INFO @ Sat, 15 Jan 2022 21:45:44: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:45:44: #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 21:45:44: #1 tags after filtering in treatment: 2324626 INFO @ Sat, 15 Jan 2022 21:45:44: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:45:44: #1 finished! INFO @ Sat, 15 Jan 2022 21:45:44: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:45:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:45:44: #2 number of paired peaks: 3 WARNING @ Sat, 15 Jan 2022 21:45:44: 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 21:45:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399086/SRX9399086.20_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/SRX9399086/SRX9399086.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399086/SRX9399086.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399086/SRX9399086.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling