Job ID = 14522051 SRX = SRX9067204 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4900561 spots for SRR12580357/SRR12580357.sra Written 4900561 spots for SRR12580357/SRR12580357.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: 00:02:10 4900561 reads; of these: 4900561 (100.00%) were paired; of these: 1238427 (25.27%) aligned concordantly 0 times 3194149 (65.18%) aligned concordantly exactly 1 time 467985 (9.55%) aligned concordantly >1 times ---- 1238427 pairs aligned concordantly 0 times; of these: 415562 (33.56%) aligned discordantly 1 time ---- 822865 pairs aligned 0 times concordantly or discordantly; of these: 1645730 mates make up the pairs; of these: 1159362 (70.45%) aligned 0 times 324727 (19.73%) aligned exactly 1 time 161641 (9.82%) aligned >1 times 88.17% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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] 328161 / 3749253 = 0.0875 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 22:08:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067204/SRX9067204.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067204/SRX9067204.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067204/SRX9067204.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067204/SRX9067204.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 22:08:57: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:08:57: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:09:02: 1000000 INFO @ Sat, 15 Jan 2022 22:09:06: 2000000 INFO @ Sat, 15 Jan 2022 22:09:11: 3000000 INFO @ Sat, 15 Jan 2022 22:09:16: 4000000 INFO @ Sat, 15 Jan 2022 22:09:21: 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 22:09:26: 6000000 INFO @ Sat, 15 Jan 2022 22:09:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067204/SRX9067204.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067204/SRX9067204.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067204/SRX9067204.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067204/SRX9067204.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 22:09:27: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:09:27: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:09:31: 7000000 INFO @ Sat, 15 Jan 2022 22:09:31: 1000000 INFO @ Sat, 15 Jan 2022 22:09:36: 2000000 INFO @ Sat, 15 Jan 2022 22:09:36: #1 tag size is determined as 32 bps INFO @ Sat, 15 Jan 2022 22:09:36: #1 tag size = 32 INFO @ Sat, 15 Jan 2022 22:09:36: #1 total tags in treatment: 3335797 INFO @ Sat, 15 Jan 2022 22:09:36: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:09:36: #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 22:09:37: #1 tags after filtering in treatment: 2443942 INFO @ Sat, 15 Jan 2022 22:09:37: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 22:09:37: #1 finished! INFO @ Sat, 15 Jan 2022 22:09:37: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:09:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:09:37: #2 number of paired peaks: 11 WARNING @ Sat, 15 Jan 2022 22:09:37: Too few paired peaks (11) 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 22:09:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067204/SRX9067204.05_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/SRX9067204/SRX9067204.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067204/SRX9067204.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067204/SRX9067204.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:09:41: 3000000 INFO @ Sat, 15 Jan 2022 22:09:46: 4000000 INFO @ Sat, 15 Jan 2022 22:09:50: 5000000 INFO @ Sat, 15 Jan 2022 22:09:54: 6000000 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 22:09:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067204/SRX9067204.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067204/SRX9067204.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067204/SRX9067204.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067204/SRX9067204.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 22:09:57: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:09:57: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:09:59: 7000000 INFO @ Sat, 15 Jan 2022 22:10:02: 1000000 INFO @ Sat, 15 Jan 2022 22:10:03: #1 tag size is determined as 32 bps INFO @ Sat, 15 Jan 2022 22:10:03: #1 tag size = 32 INFO @ Sat, 15 Jan 2022 22:10:03: #1 total tags in treatment: 3335797 INFO @ Sat, 15 Jan 2022 22:10:03: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:10:03: #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 22:10:03: #1 tags after filtering in treatment: 2443942 INFO @ Sat, 15 Jan 2022 22:10:03: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 22:10:03: #1 finished! INFO @ Sat, 15 Jan 2022 22:10:03: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:10:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:10:03: #2 number of paired peaks: 11 WARNING @ Sat, 15 Jan 2022 22:10:03: Too few paired peaks (11) 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 22:10:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067204/SRX9067204.10_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/SRX9067204/SRX9067204.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067204/SRX9067204.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067204/SRX9067204.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:10:06: 2000000 INFO @ Sat, 15 Jan 2022 22:10:11: 3000000 INFO @ Sat, 15 Jan 2022 22:10:15: 4000000 INFO @ Sat, 15 Jan 2022 22:10:19: 5000000 INFO @ Sat, 15 Jan 2022 22:10:23: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:10:28: 7000000 INFO @ Sat, 15 Jan 2022 22:10:32: #1 tag size is determined as 32 bps INFO @ Sat, 15 Jan 2022 22:10:32: #1 tag size = 32 INFO @ Sat, 15 Jan 2022 22:10:32: #1 total tags in treatment: 3335797 INFO @ Sat, 15 Jan 2022 22:10:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:10:32: #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 22:10:32: #1 tags after filtering in treatment: 2443942 INFO @ Sat, 15 Jan 2022 22:10:32: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 22:10:32: #1 finished! INFO @ Sat, 15 Jan 2022 22:10:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:10:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:10:32: #2 number of paired peaks: 11 WARNING @ Sat, 15 Jan 2022 22:10:32: Too few paired peaks (11) 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 22:10:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067204/SRX9067204.20_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/SRX9067204/SRX9067204.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067204/SRX9067204.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067204/SRX9067204.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。