Job ID = 14521667 SRX = SRX9399028 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4098017 spots for SRR12935309/SRR12935309.sra Written 4098017 spots for SRR12935309/SRR12935309.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: 00:02:37 4098017 reads; of these: 4098017 (100.00%) were paired; of these: 808172 (19.72%) aligned concordantly 0 times 2792294 (68.14%) aligned concordantly exactly 1 time 497551 (12.14%) aligned concordantly >1 times ---- 808172 pairs aligned concordantly 0 times; of these: 325179 (40.24%) aligned discordantly 1 time ---- 482993 pairs aligned 0 times concordantly or discordantly; of these: 965986 mates make up the pairs; of these: 527204 (54.58%) aligned 0 times 280256 (29.01%) aligned exactly 1 time 158526 (16.41%) aligned >1 times 93.57% overall alignment rate Time searching: 00:02:37 Overall time: 00:02:37 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] 312057 / 3356003 = 0.0930 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 21:26:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399028/SRX9399028.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399028/SRX9399028.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399028/SRX9399028.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399028/SRX9399028.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 21:26:50: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:26:50: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:26:57: 1000000 INFO @ Sat, 15 Jan 2022 21:27:04: 2000000 INFO @ Sat, 15 Jan 2022 21:27:11: 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 21:27:19: 4000000 INFO @ Sat, 15 Jan 2022 21:27:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399028/SRX9399028.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399028/SRX9399028.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399028/SRX9399028.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399028/SRX9399028.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 21:27:20: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:27:20: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:27:27: 5000000 INFO @ Sat, 15 Jan 2022 21:27:27: 1000000 INFO @ Sat, 15 Jan 2022 21:27:34: 6000000 INFO @ Sat, 15 Jan 2022 21:27:35: 2000000 INFO @ Sat, 15 Jan 2022 21:27:42: 7000000 INFO @ Sat, 15 Jan 2022 21:27:42: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:27:42: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:27:42: #1 total tags in treatment: 2979471 INFO @ Sat, 15 Jan 2022 21:27:42: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:27:42: #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 21:27:42: #1 tags after filtering in treatment: 2188996 INFO @ Sat, 15 Jan 2022 21:27:42: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:27:42: #1 finished! INFO @ Sat, 15 Jan 2022 21:27:42: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:27:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:27:42: #2 number of paired peaks: 30 WARNING @ Sat, 15 Jan 2022 21:27:42: Too few paired peaks (30) 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 21:27:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399028/SRX9399028.05_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/SRX9399028/SRX9399028.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399028/SRX9399028.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399028/SRX9399028.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:27:43: 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 21:27:49: 4000000 INFO @ Sat, 15 Jan 2022 21:27:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399028/SRX9399028.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399028/SRX9399028.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399028/SRX9399028.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399028/SRX9399028.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 21:27:50: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:27:50: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:27:55: 5000000 INFO @ Sat, 15 Jan 2022 21:27:57: 1000000 INFO @ Sat, 15 Jan 2022 21:28:02: 6000000 INFO @ Sat, 15 Jan 2022 21:28:04: 2000000 INFO @ Sat, 15 Jan 2022 21:28:09: 7000000 INFO @ Sat, 15 Jan 2022 21:28:09: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:28:09: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:28:09: #1 total tags in treatment: 2979471 INFO @ Sat, 15 Jan 2022 21:28:09: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:28:09: #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 21:28:09: #1 tags after filtering in treatment: 2188996 INFO @ Sat, 15 Jan 2022 21:28:09: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:28:09: #1 finished! INFO @ Sat, 15 Jan 2022 21:28:09: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:28:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:28:09: #2 number of paired peaks: 30 WARNING @ Sat, 15 Jan 2022 21:28:09: Too few paired peaks (30) 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 21:28:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399028/SRX9399028.10_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/SRX9399028/SRX9399028.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399028/SRX9399028.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399028/SRX9399028.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:28:10: 3000000 INFO @ Sat, 15 Jan 2022 21:28:16: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:28:23: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:28:30: 6000000 INFO @ Sat, 15 Jan 2022 21:28:37: 7000000 INFO @ Sat, 15 Jan 2022 21:28:37: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:28:37: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:28:37: #1 total tags in treatment: 2979471 INFO @ Sat, 15 Jan 2022 21:28:37: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:28:37: #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 21:28:37: #1 tags after filtering in treatment: 2188996 INFO @ Sat, 15 Jan 2022 21:28:37: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:28:37: #1 finished! INFO @ Sat, 15 Jan 2022 21:28:37: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:28:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:28:37: #2 number of paired peaks: 30 WARNING @ Sat, 15 Jan 2022 21:28:37: Too few paired peaks (30) 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 21:28:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399028/SRX9399028.20_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/SRX9399028/SRX9399028.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399028/SRX9399028.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399028/SRX9399028.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling