Job ID = 14519784 SRX = SRX9390804 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4611032 spots for SRR12926699/SRR12926699.sra Written 4611032 spots for SRR12926699/SRR12926699.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: 00:05:42 4611032 reads; of these: 4611032 (100.00%) were paired; of these: 2258888 (48.99%) aligned concordantly 0 times 1664192 (36.09%) aligned concordantly exactly 1 time 687952 (14.92%) aligned concordantly >1 times ---- 2258888 pairs aligned concordantly 0 times; of these: 282280 (12.50%) aligned discordantly 1 time ---- 1976608 pairs aligned 0 times concordantly or discordantly; of these: 3953216 mates make up the pairs; of these: 1773864 (44.87%) aligned 0 times 593217 (15.01%) aligned exactly 1 time 1586135 (40.12%) aligned >1 times 80.77% overall alignment rate Time searching: 00:05:42 Overall time: 00:05:42 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] 696514 / 2621981 = 0.2656 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 17:53:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9390804/SRX9390804.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9390804/SRX9390804.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9390804/SRX9390804.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9390804/SRX9390804.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 17:53:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:53:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:53:31: 1000000 INFO @ Sat, 15 Jan 2022 17:53:38: 2000000 INFO @ Sat, 15 Jan 2022 17:53:45: 3000000 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 17:53:51: 4000000 INFO @ Sat, 15 Jan 2022 17:53:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9390804/SRX9390804.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9390804/SRX9390804.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9390804/SRX9390804.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9390804/SRX9390804.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 17:53:54: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:53:54: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:53:58: 5000000 INFO @ Sat, 15 Jan 2022 17:54:01: 1000000 INFO @ Sat, 15 Jan 2022 17:54:05: 6000000 INFO @ Sat, 15 Jan 2022 17:54:06: #1 tag size is determined as 70 bps INFO @ Sat, 15 Jan 2022 17:54:06: #1 tag size = 70 INFO @ Sat, 15 Jan 2022 17:54:06: #1 total tags in treatment: 1709559 INFO @ Sat, 15 Jan 2022 17:54:06: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:54:06: #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 17:54:06: #1 tags after filtering in treatment: 1207501 INFO @ Sat, 15 Jan 2022 17:54:06: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 17:54:06: #1 finished! INFO @ Sat, 15 Jan 2022 17:54:06: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:54:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:54:06: #2 number of paired peaks: 35 WARNING @ Sat, 15 Jan 2022 17:54:06: Too few paired peaks (35) 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 17:54:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9390804/SRX9390804.05_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/SRX9390804/SRX9390804.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9390804/SRX9390804.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9390804/SRX9390804.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:54:09: 2000000 INFO @ Sat, 15 Jan 2022 17:54:16: 3000000 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 17:54:22: 4000000 INFO @ Sat, 15 Jan 2022 17:54:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9390804/SRX9390804.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9390804/SRX9390804.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9390804/SRX9390804.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9390804/SRX9390804.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 17:54:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:54:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:54:29: 5000000 INFO @ Sat, 15 Jan 2022 17:54:32: 1000000 INFO @ Sat, 15 Jan 2022 17:54:36: 6000000 INFO @ Sat, 15 Jan 2022 17:54:37: #1 tag size is determined as 70 bps INFO @ Sat, 15 Jan 2022 17:54:37: #1 tag size = 70 INFO @ Sat, 15 Jan 2022 17:54:37: #1 total tags in treatment: 1709559 INFO @ Sat, 15 Jan 2022 17:54:37: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:54:37: #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 17:54:37: #1 tags after filtering in treatment: 1207501 INFO @ Sat, 15 Jan 2022 17:54:37: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 17:54:37: #1 finished! INFO @ Sat, 15 Jan 2022 17:54:37: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:54:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:54:37: #2 number of paired peaks: 35 WARNING @ Sat, 15 Jan 2022 17:54:37: Too few paired peaks (35) 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 17:54:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9390804/SRX9390804.10_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/SRX9390804/SRX9390804.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9390804/SRX9390804.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9390804/SRX9390804.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:54:40: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:54:47: 3000000 INFO @ Sat, 15 Jan 2022 17:54:53: 4000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:55:00: 5000000 INFO @ Sat, 15 Jan 2022 17:55:07: 6000000 INFO @ Sat, 15 Jan 2022 17:55:08: #1 tag size is determined as 70 bps INFO @ Sat, 15 Jan 2022 17:55:08: #1 tag size = 70 INFO @ Sat, 15 Jan 2022 17:55:08: #1 total tags in treatment: 1709559 INFO @ Sat, 15 Jan 2022 17:55:08: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:55:08: #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 17:55:08: #1 tags after filtering in treatment: 1207501 INFO @ Sat, 15 Jan 2022 17:55:08: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 17:55:08: #1 finished! INFO @ Sat, 15 Jan 2022 17:55:08: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:55:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:55:08: #2 number of paired peaks: 35 WARNING @ Sat, 15 Jan 2022 17:55:08: Too few paired peaks (35) 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 17:55:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9390804/SRX9390804.20_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/SRX9390804/SRX9390804.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9390804/SRX9390804.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9390804/SRX9390804.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling