Job ID = 14521691 SRX = SRX9399031 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3610217 spots for SRR12935312/SRR12935312.sra Written 3610217 spots for SRR12935312/SRR12935312.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: 00:01:37 3610217 reads; of these: 3610217 (100.00%) were paired; of these: 653238 (18.09%) aligned concordantly 0 times 2513750 (69.63%) aligned concordantly exactly 1 time 443229 (12.28%) aligned concordantly >1 times ---- 653238 pairs aligned concordantly 0 times; of these: 243566 (37.29%) aligned discordantly 1 time ---- 409672 pairs aligned 0 times concordantly or discordantly; of these: 819344 mates make up the pairs; of these: 472513 (57.67%) aligned 0 times 226141 (27.60%) aligned exactly 1 time 120690 (14.73%) aligned >1 times 93.46% overall alignment rate Time searching: 00:01:37 Overall time: 00:01:37 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] 272584 / 3002562 = 0.0908 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 21:27:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399031/SRX9399031.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399031/SRX9399031.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399031/SRX9399031.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399031/SRX9399031.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 21:27:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:27:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:27:41: 1000000 INFO @ Sat, 15 Jan 2022 21:27:46: 2000000 INFO @ Sat, 15 Jan 2022 21:27:52: 3000000 INFO @ Sat, 15 Jan 2022 21:27:57: 4000000 INFO @ Sat, 15 Jan 2022 21:28:03: 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 21:28:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399031/SRX9399031.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399031/SRX9399031.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399031/SRX9399031.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399031/SRX9399031.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 21:28:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:28:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:28:08: 6000000 INFO @ Sat, 15 Jan 2022 21:28:09: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 21:28:09: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 21:28:09: #1 total tags in treatment: 2685818 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: 2019238 INFO @ Sat, 15 Jan 2022 21:28:09: #1 Redundant rate of treatment: 0.25 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 21:28:10: #2 number of paired peaks: 32 WARNING @ Sat, 15 Jan 2022 21:28:10: Too few paired peaks (32) 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 21:28:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399031/SRX9399031.05_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/SRX9399031/SRX9399031.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399031/SRX9399031.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399031/SRX9399031.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:28:11: 1000000 INFO @ Sat, 15 Jan 2022 21:28:16: 2000000 INFO @ Sat, 15 Jan 2022 21:28:22: 3000000 INFO @ Sat, 15 Jan 2022 21:28:27: 4000000 INFO @ Sat, 15 Jan 2022 21:28:32: 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 21:28:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399031/SRX9399031.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399031/SRX9399031.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399031/SRX9399031.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399031/SRX9399031.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 21:28:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:28:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:28:38: 6000000 INFO @ Sat, 15 Jan 2022 21:28:39: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 21:28:39: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 21:28:39: #1 total tags in treatment: 2685818 INFO @ Sat, 15 Jan 2022 21:28:39: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:28:39: #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 21:28:39: #1 tags after filtering in treatment: 2019238 INFO @ Sat, 15 Jan 2022 21:28:39: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 21:28:39: #1 finished! INFO @ Sat, 15 Jan 2022 21:28:39: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:28:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:28:39: #2 number of paired peaks: 32 WARNING @ Sat, 15 Jan 2022 21:28:39: Too few paired peaks (32) 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 21:28:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399031/SRX9399031.10_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/SRX9399031/SRX9399031.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399031/SRX9399031.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399031/SRX9399031.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:28:41: 1000000 INFO @ Sat, 15 Jan 2022 21:28:46: 2000000 INFO @ Sat, 15 Jan 2022 21:28:51: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:28:55: 4000000 INFO @ Sat, 15 Jan 2022 21:29:00: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:29:05: 6000000 INFO @ Sat, 15 Jan 2022 21:29:06: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 21:29:06: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 21:29:06: #1 total tags in treatment: 2685818 INFO @ Sat, 15 Jan 2022 21:29:06: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:29:06: #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 21:29:06: #1 tags after filtering in treatment: 2019238 INFO @ Sat, 15 Jan 2022 21:29:06: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 21:29:06: #1 finished! INFO @ Sat, 15 Jan 2022 21:29:06: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:29:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:29:06: #2 number of paired peaks: 32 WARNING @ Sat, 15 Jan 2022 21:29:06: Too few paired peaks (32) 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 21:29:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399031/SRX9399031.20_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/SRX9399031/SRX9399031.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399031/SRX9399031.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399031/SRX9399031.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling