Job ID = 14521601 SRX = SRX9399113 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6378792 spots for SRR12935394/SRR12935394.sra Written 6378792 spots for SRR12935394/SRR12935394.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: 00:02:47 6378792 reads; of these: 6378792 (100.00%) were paired; of these: 494997 (7.76%) aligned concordantly 0 times 4195192 (65.77%) aligned concordantly exactly 1 time 1688603 (26.47%) aligned concordantly >1 times ---- 494997 pairs aligned concordantly 0 times; of these: 45496 (9.19%) aligned discordantly 1 time ---- 449501 pairs aligned 0 times concordantly or discordantly; of these: 899002 mates make up the pairs; of these: 737963 (82.09%) aligned 0 times 100103 (11.13%) aligned exactly 1 time 60936 (6.78%) aligned >1 times 94.22% overall alignment rate Time searching: 00:02:47 Overall time: 00:02:47 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] 1915098 / 5921289 = 0.3234 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 21:17:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399113/SRX9399113.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399113/SRX9399113.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399113/SRX9399113.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399113/SRX9399113.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 21:17:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:17:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:17:17: 1000000 INFO @ Sat, 15 Jan 2022 21:17:23: 2000000 INFO @ Sat, 15 Jan 2022 21:17:29: 3000000 INFO @ Sat, 15 Jan 2022 21:17:34: 4000000 INFO @ Sat, 15 Jan 2022 21:17:40: 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 21:17:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399113/SRX9399113.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399113/SRX9399113.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399113/SRX9399113.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399113/SRX9399113.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 21:17:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:17:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:17:45: 6000000 INFO @ Sat, 15 Jan 2022 21:17:48: 1000000 INFO @ Sat, 15 Jan 2022 21:17:51: 7000000 INFO @ Sat, 15 Jan 2022 21:17:53: 2000000 INFO @ Sat, 15 Jan 2022 21:17:57: 8000000 INFO @ Sat, 15 Jan 2022 21:17:58: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 21:17:58: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 21:17:58: #1 total tags in treatment: 3973365 INFO @ Sat, 15 Jan 2022 21:17:58: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:17:58: #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 21:17:58: #1 tags after filtering in treatment: 2638989 INFO @ Sat, 15 Jan 2022 21:17:58: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 15 Jan 2022 21:17:58: #1 finished! INFO @ Sat, 15 Jan 2022 21:17:58: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:17:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:17:58: #2 number of paired peaks: 27 WARNING @ Sat, 15 Jan 2022 21:17:58: Too few paired peaks (27) 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 21:17:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399113/SRX9399113.05_peaks.narrowPeak: No such file or directory INFO @ Sat, 15 Jan 2022 21:17:58: 3000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399113/SRX9399113.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399113/SRX9399113.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399113/SRX9399113.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:18:04: 4000000 INFO @ Sat, 15 Jan 2022 21:18:09: 5000000 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 21:18:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399113/SRX9399113.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399113/SRX9399113.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399113/SRX9399113.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399113/SRX9399113.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 21:18:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:18:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:18:14: 6000000 INFO @ Sat, 15 Jan 2022 21:18:17: 1000000 INFO @ Sat, 15 Jan 2022 21:18:19: 7000000 INFO @ Sat, 15 Jan 2022 21:18:22: 2000000 INFO @ Sat, 15 Jan 2022 21:18:24: 8000000 INFO @ Sat, 15 Jan 2022 21:18:25: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 21:18:25: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 21:18:25: #1 total tags in treatment: 3973365 INFO @ Sat, 15 Jan 2022 21:18:25: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:18:25: #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 21:18:25: #1 tags after filtering in treatment: 2638989 INFO @ Sat, 15 Jan 2022 21:18:25: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 15 Jan 2022 21:18:25: #1 finished! INFO @ Sat, 15 Jan 2022 21:18:25: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:18:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:18:25: #2 number of paired peaks: 27 WARNING @ Sat, 15 Jan 2022 21:18:25: Too few paired peaks (27) 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 21:18:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399113/SRX9399113.10_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/SRX9399113/SRX9399113.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399113/SRX9399113.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399113/SRX9399113.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:18:27: 3000000 INFO @ Sat, 15 Jan 2022 21:18:32: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:18:37: 5000000 INFO @ Sat, 15 Jan 2022 21:18:42: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:18:47: 7000000 INFO @ Sat, 15 Jan 2022 21:18:52: 8000000 INFO @ Sat, 15 Jan 2022 21:18:53: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 21:18:53: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 21:18:53: #1 total tags in treatment: 3973365 INFO @ Sat, 15 Jan 2022 21:18:53: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:18:53: #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 21:18:53: #1 tags after filtering in treatment: 2638989 INFO @ Sat, 15 Jan 2022 21:18:53: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 15 Jan 2022 21:18:53: #1 finished! INFO @ Sat, 15 Jan 2022 21:18:53: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:18:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:18:53: #2 number of paired peaks: 27 WARNING @ Sat, 15 Jan 2022 21:18:53: Too few paired peaks (27) 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 21:18:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399113/SRX9399113.20_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/SRX9399113/SRX9399113.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399113/SRX9399113.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399113/SRX9399113.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling