Job ID = 12531572 SRX = SRX3353405 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19287330 spots for SRR6246284/SRR6246284.sra Written 19287330 spots for SRR6246284/SRR6246284.sra Read 12919937 spots for SRR6246285/SRR6246285.sra Written 12919937 spots for SRR6246285/SRR6246285.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: 00:22:33 32207267 reads; of these: 32207267 (100.00%) were paired; of these: 4662849 (14.48%) aligned concordantly 0 times 10951641 (34.00%) aligned concordantly exactly 1 time 16592777 (51.52%) aligned concordantly >1 times ---- 4662849 pairs aligned concordantly 0 times; of these: 1001492 (21.48%) aligned discordantly 1 time ---- 3661357 pairs aligned 0 times concordantly or discordantly; of these: 7322714 mates make up the pairs; of these: 4402029 (60.11%) aligned 0 times 235576 (3.22%) aligned exactly 1 time 2685109 (36.67%) aligned >1 times 93.17% overall alignment rate Time searching: 00:22:33 Overall time: 00:22:33 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_sort_core] merging from 28 files... [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] 17179175 / 28377844 = 0.6054 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 08:58:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3353405/SRX3353405.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3353405/SRX3353405.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3353405/SRX3353405.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3353405/SRX3353405.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, 17 Apr 2021 08:58:31: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:58:31: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:58:36: 1000000 INFO @ Sat, 17 Apr 2021 08:58:42: 2000000 INFO @ Sat, 17 Apr 2021 08:58:48: 3000000 INFO @ Sat, 17 Apr 2021 08:58:54: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 08:59:00: 5000000 INFO @ Sat, 17 Apr 2021 08:59:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3353405/SRX3353405.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3353405/SRX3353405.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3353405/SRX3353405.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3353405/SRX3353405.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, 17 Apr 2021 08:59:00: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:59:00: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:59:06: 6000000 INFO @ Sat, 17 Apr 2021 08:59:07: 1000000 INFO @ Sat, 17 Apr 2021 08:59:13: 7000000 INFO @ Sat, 17 Apr 2021 08:59:13: 2000000 INFO @ Sat, 17 Apr 2021 08:59:19: 8000000 INFO @ Sat, 17 Apr 2021 08:59:19: 3000000 INFO @ Sat, 17 Apr 2021 08:59:25: 9000000 INFO @ Sat, 17 Apr 2021 08:59:25: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 08:59:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3353405/SRX3353405.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3353405/SRX3353405.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3353405/SRX3353405.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3353405/SRX3353405.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, 17 Apr 2021 08:59:31: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:59:31: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:59:31: 10000000 INFO @ Sat, 17 Apr 2021 08:59:31: 5000000 INFO @ Sat, 17 Apr 2021 08:59:37: 1000000 INFO @ Sat, 17 Apr 2021 08:59:38: 11000000 INFO @ Sat, 17 Apr 2021 08:59:38: 6000000 INFO @ Sat, 17 Apr 2021 08:59:44: 2000000 INFO @ Sat, 17 Apr 2021 08:59:44: 12000000 INFO @ Sat, 17 Apr 2021 08:59:44: 7000000 INFO @ Sat, 17 Apr 2021 08:59:50: 3000000 INFO @ Sat, 17 Apr 2021 08:59:50: 13000000 INFO @ Sat, 17 Apr 2021 08:59:51: 8000000 INFO @ Sat, 17 Apr 2021 08:59:56: 14000000 INFO @ Sat, 17 Apr 2021 08:59:57: 4000000 INFO @ Sat, 17 Apr 2021 08:59:57: 9000000 INFO @ Sat, 17 Apr 2021 09:00:03: 15000000 INFO @ Sat, 17 Apr 2021 09:00:03: 5000000 INFO @ Sat, 17 Apr 2021 09:00:03: 10000000 INFO @ Sat, 17 Apr 2021 09:00:09: 16000000 INFO @ Sat, 17 Apr 2021 09:00:10: 6000000 INFO @ Sat, 17 Apr 2021 09:00:10: 11000000 INFO @ Sat, 17 Apr 2021 09:00:15: 17000000 INFO @ Sat, 17 Apr 2021 09:00:16: 12000000 INFO @ Sat, 17 Apr 2021 09:00:16: 7000000 INFO @ Sat, 17 Apr 2021 09:00:21: 18000000 INFO @ Sat, 17 Apr 2021 09:00:22: 13000000 INFO @ Sat, 17 Apr 2021 09:00:23: 8000000 INFO @ Sat, 17 Apr 2021 09:00:27: 19000000 INFO @ Sat, 17 Apr 2021 09:00:29: 14000000 INFO @ Sat, 17 Apr 2021 09:00:29: 9000000 INFO @ Sat, 17 Apr 2021 09:00:33: 20000000 INFO @ Sat, 17 Apr 2021 09:00:35: 15000000 INFO @ Sat, 17 Apr 2021 09:00:36: 10000000 INFO @ Sat, 17 Apr 2021 09:00:40: 21000000 INFO @ Sat, 17 Apr 2021 09:00:41: 16000000 INFO @ Sat, 17 Apr 2021 09:00:44: 11000000 INFO @ Sat, 17 Apr 2021 09:00:48: 17000000 INFO @ Sat, 17 Apr 2021 09:00:49: 22000000 INFO @ Sat, 17 Apr 2021 09:00:52: 12000000 INFO @ Sat, 17 Apr 2021 09:00:54: 18000000 INFO @ Sat, 17 Apr 2021 09:00:56: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 09:01:01: 19000000 INFO @ Sat, 17 Apr 2021 09:01:01: 13000000 INFO @ Sat, 17 Apr 2021 09:01:03: 24000000 INFO @ Sat, 17 Apr 2021 09:01:08: 20000000 INFO @ Sat, 17 Apr 2021 09:01:09: 25000000 INFO @ Sat, 17 Apr 2021 09:01:10: 14000000 BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 09:01:14: #1 tag size is determined as 51 bps INFO @ Sat, 17 Apr 2021 09:01:14: #1 tag size = 51 INFO @ Sat, 17 Apr 2021 09:01:14: #1 total tags in treatment: 10528285 INFO @ Sat, 17 Apr 2021 09:01:14: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:01:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:01:14: #1 tags after filtering in treatment: 3742232 INFO @ Sat, 17 Apr 2021 09:01:14: #1 Redundant rate of treatment: 0.64 INFO @ Sat, 17 Apr 2021 09:01:14: #1 finished! INFO @ Sat, 17 Apr 2021 09:01:14: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:01:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:01:14: 21000000 INFO @ Sat, 17 Apr 2021 09:01:14: #2 number of paired peaks: 31 WARNING @ Sat, 17 Apr 2021 09:01:14: Too few paired peaks (31) 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, 17 Apr 2021 09:01:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3353405/SRX3353405.05_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/SRX3353405/SRX3353405.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3353405/SRX3353405.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3353405/SRX3353405.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:01:18: 15000000 INFO @ Sat, 17 Apr 2021 09:01:21: 22000000 INFO @ Sat, 17 Apr 2021 09:01:26: 16000000 INFO @ Sat, 17 Apr 2021 09:01:27: 23000000 INFO @ Sat, 17 Apr 2021 09:01:33: 17000000 INFO @ Sat, 17 Apr 2021 09:01:34: 24000000 INFO @ Sat, 17 Apr 2021 09:01:40: 25000000 INFO @ Sat, 17 Apr 2021 09:01:41: 18000000 INFO @ Sat, 17 Apr 2021 09:01:44: #1 tag size is determined as 51 bps INFO @ Sat, 17 Apr 2021 09:01:44: #1 tag size = 51 INFO @ Sat, 17 Apr 2021 09:01:44: #1 total tags in treatment: 10528285 INFO @ Sat, 17 Apr 2021 09:01:44: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:01:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:01:44: #1 tags after filtering in treatment: 3742232 INFO @ Sat, 17 Apr 2021 09:01:44: #1 Redundant rate of treatment: 0.64 INFO @ Sat, 17 Apr 2021 09:01:44: #1 finished! INFO @ Sat, 17 Apr 2021 09:01:44: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:01:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:01:45: #2 number of paired peaks: 31 WARNING @ Sat, 17 Apr 2021 09:01:45: Too few paired peaks (31) 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, 17 Apr 2021 09:01:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3353405/SRX3353405.10_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/SRX3353405/SRX3353405.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3353405/SRX3353405.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3353405/SRX3353405.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:01:49: 19000000 INFO @ Sat, 17 Apr 2021 09:01:57: 20000000 INFO @ Sat, 17 Apr 2021 09:02:04: 21000000 INFO @ Sat, 17 Apr 2021 09:02:11: 22000000 INFO @ Sat, 17 Apr 2021 09:02:17: 23000000 INFO @ Sat, 17 Apr 2021 09:02:23: 24000000 INFO @ Sat, 17 Apr 2021 09:02:29: 25000000 INFO @ Sat, 17 Apr 2021 09:02:33: #1 tag size is determined as 51 bps INFO @ Sat, 17 Apr 2021 09:02:33: #1 tag size = 51 INFO @ Sat, 17 Apr 2021 09:02:33: #1 total tags in treatment: 10528285 INFO @ Sat, 17 Apr 2021 09:02:33: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:02:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 09:02:33: #1 tags after filtering in treatment: 3742232 INFO @ Sat, 17 Apr 2021 09:02:33: #1 Redundant rate of treatment: 0.64 INFO @ Sat, 17 Apr 2021 09:02:33: #1 finished! INFO @ Sat, 17 Apr 2021 09:02:33: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:02:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:02:33: #2 number of paired peaks: 31 WARNING @ Sat, 17 Apr 2021 09:02:33: Too few paired peaks (31) 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, 17 Apr 2021 09:02:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3353405/SRX3353405.20_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/SRX3353405/SRX3353405.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3353405/SRX3353405.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3353405/SRX3353405.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling