Job ID = 14521790 SRX = SRX9399061 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4854206 spots for SRR12935342/SRR12935342.sra Written 4854206 spots for SRR12935342/SRR12935342.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: 00:01:58 4854206 reads; of these: 4854206 (100.00%) were paired; of these: 646980 (13.33%) aligned concordantly 0 times 3701364 (76.25%) aligned concordantly exactly 1 time 505862 (10.42%) aligned concordantly >1 times ---- 646980 pairs aligned concordantly 0 times; of these: 174241 (26.93%) aligned discordantly 1 time ---- 472739 pairs aligned 0 times concordantly or discordantly; of these: 945478 mates make up the pairs; of these: 676394 (71.54%) aligned 0 times 199190 (21.07%) aligned exactly 1 time 69894 (7.39%) aligned >1 times 93.03% overall alignment rate Time searching: 00:01:58 Overall time: 00:01:58 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] 319871 / 4302507 = 0.0743 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 21:39:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399061/SRX9399061.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399061/SRX9399061.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399061/SRX9399061.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399061/SRX9399061.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 21:39:55: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:39:55: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:39:59: 1000000 INFO @ Sat, 15 Jan 2022 21:40:04: 2000000 INFO @ Sat, 15 Jan 2022 21:40:09: 3000000 INFO @ Sat, 15 Jan 2022 21:40:13: 4000000 INFO @ Sat, 15 Jan 2022 21:40:18: 5000000 INFO @ Sat, 15 Jan 2022 21:40:23: 6000000 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 21:40:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399061/SRX9399061.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399061/SRX9399061.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399061/SRX9399061.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399061/SRX9399061.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 21:40:25: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:40:25: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:40:27: 7000000 INFO @ Sat, 15 Jan 2022 21:40:30: 1000000 INFO @ Sat, 15 Jan 2022 21:40:32: 8000000 INFO @ Sat, 15 Jan 2022 21:40:34: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:40:34: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:40:34: #1 total tags in treatment: 3889821 INFO @ Sat, 15 Jan 2022 21:40:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:40:34: #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 21:40:34: #1 tags after filtering in treatment: 2810448 INFO @ Sat, 15 Jan 2022 21:40:34: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 21:40:34: #1 finished! INFO @ Sat, 15 Jan 2022 21:40:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:40:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:40:34: #2 number of paired peaks: 2 WARNING @ Sat, 15 Jan 2022 21:40:34: Too few paired peaks (2) 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 21:40:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399061/SRX9399061.05_peaks.narrowPeak: No such file or directory INFO @ Sat, 15 Jan 2022 21:40:34: 2000000 pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399061/SRX9399061.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399061/SRX9399061.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399061/SRX9399061.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:40:39: 3000000 INFO @ Sat, 15 Jan 2022 21:40:44: 4000000 INFO @ Sat, 15 Jan 2022 21:40:48: 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 21:40:53: 6000000 INFO @ Sat, 15 Jan 2022 21:40:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399061/SRX9399061.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399061/SRX9399061.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399061/SRX9399061.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399061/SRX9399061.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 21:40:55: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:40:55: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:40:58: 7000000 INFO @ Sat, 15 Jan 2022 21:40:59: 1000000 INFO @ Sat, 15 Jan 2022 21:41:03: 8000000 INFO @ Sat, 15 Jan 2022 21:41:03: 2000000 INFO @ Sat, 15 Jan 2022 21:41:05: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:41:05: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:41:05: #1 total tags in treatment: 3889821 INFO @ Sat, 15 Jan 2022 21:41:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:41:05: #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 21:41:05: #1 tags after filtering in treatment: 2810448 INFO @ Sat, 15 Jan 2022 21:41:05: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 21:41:05: #1 finished! INFO @ Sat, 15 Jan 2022 21:41:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:41:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:41:05: #2 number of paired peaks: 2 WARNING @ Sat, 15 Jan 2022 21:41:05: Too few paired peaks (2) 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 21:41:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399061/SRX9399061.10_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/SRX9399061/SRX9399061.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399061/SRX9399061.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399061/SRX9399061.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:41:08: 3000000 INFO @ Sat, 15 Jan 2022 21:41:12: 4000000 INFO @ Sat, 15 Jan 2022 21:41:16: 5000000 INFO @ Sat, 15 Jan 2022 21:41:20: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:41:24: 7000000 INFO @ Sat, 15 Jan 2022 21:41:28: 8000000 INFO @ Sat, 15 Jan 2022 21:41:29: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:41:29: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:41:29: #1 total tags in treatment: 3889821 INFO @ Sat, 15 Jan 2022 21:41:29: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:41:29: #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 21:41:29: #1 tags after filtering in treatment: 2810448 INFO @ Sat, 15 Jan 2022 21:41:29: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 21:41:29: #1 finished! INFO @ Sat, 15 Jan 2022 21:41:29: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:41:29: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:41:30: #2 number of paired peaks: 2 WARNING @ Sat, 15 Jan 2022 21:41:30: Too few paired peaks (2) 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 21:41:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399061/SRX9399061.20_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/SRX9399061/SRX9399061.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399061/SRX9399061.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399061/SRX9399061.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling