Job ID = 14520543 SRX = SRX3659075 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5091958 spots for SRR6682790/SRR6682790.sra Written 5091958 spots for SRR6682790/SRR6682790.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: 00:06:47 5091958 reads; of these: 5091958 (100.00%) were paired; of these: 125038 (2.46%) aligned concordantly 0 times 4395159 (86.32%) aligned concordantly exactly 1 time 571761 (11.23%) aligned concordantly >1 times ---- 125038 pairs aligned concordantly 0 times; of these: 35579 (28.45%) aligned discordantly 1 time ---- 89459 pairs aligned 0 times concordantly or discordantly; of these: 178918 mates make up the pairs; of these: 112492 (62.87%) aligned 0 times 49813 (27.84%) aligned exactly 1 time 16613 (9.29%) aligned >1 times 98.90% overall alignment rate Time searching: 00:06:48 Overall time: 00:06:48 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 8 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] 491306 / 4937424 = 0.0995 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 19:36:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3659075/SRX3659075.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3659075/SRX3659075.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3659075/SRX3659075.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3659075/SRX3659075.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 19:36:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:36:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:36:19: 1000000 INFO @ Sat, 15 Jan 2022 19:36:32: 2000000 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 19:36:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3659075/SRX3659075.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3659075/SRX3659075.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3659075/SRX3659075.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3659075/SRX3659075.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 19:36:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:36:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:36:46: 3000000 INFO @ Sat, 15 Jan 2022 19:36:48: 1000000 INFO @ Sat, 15 Jan 2022 19:37:00: 4000000 BedGraph に変換中... INFO @ Sat, 15 Jan 2022 19:37:02: 2000000 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 19:37:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3659075/SRX3659075.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3659075/SRX3659075.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3659075/SRX3659075.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3659075/SRX3659075.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 19:37:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:37:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:37:15: 5000000 INFO @ Sat, 15 Jan 2022 19:37:17: 3000000 INFO @ Sat, 15 Jan 2022 19:37:18: 1000000 INFO @ Sat, 15 Jan 2022 19:37:30: 6000000 INFO @ Sat, 15 Jan 2022 19:37:30: 2000000 INFO @ Sat, 15 Jan 2022 19:37:31: 4000000 INFO @ Sat, 15 Jan 2022 19:37:42: 3000000 INFO @ Sat, 15 Jan 2022 19:37:45: 7000000 INFO @ Sat, 15 Jan 2022 19:37:46: 5000000 INFO @ Sat, 15 Jan 2022 19:37:53: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:37:59: 8000000 INFO @ Sat, 15 Jan 2022 19:38:00: 6000000 INFO @ Sat, 15 Jan 2022 19:38:05: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:38:13: 9000000 INFO @ Sat, 15 Jan 2022 19:38:14: 7000000 INFO @ Sat, 15 Jan 2022 19:38:15: #1 tag size is determined as 89 bps INFO @ Sat, 15 Jan 2022 19:38:15: #1 tag size = 89 INFO @ Sat, 15 Jan 2022 19:38:15: #1 total tags in treatment: 4475940 INFO @ Sat, 15 Jan 2022 19:38:15: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:38:15: #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 19:38:15: #1 tags after filtering in treatment: 3064950 INFO @ Sat, 15 Jan 2022 19:38:15: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 15 Jan 2022 19:38:15: #1 finished! INFO @ Sat, 15 Jan 2022 19:38:15: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:38:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:38:15: #2 number of paired peaks: 7 WARNING @ Sat, 15 Jan 2022 19:38:15: Too few paired peaks (7) 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 19:38:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3659075/SRX3659075.05_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/SRX3659075/SRX3659075.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3659075/SRX3659075.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3659075/SRX3659075.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:38:16: 6000000 INFO @ Sat, 15 Jan 2022 19:38:27: 7000000 INFO @ Sat, 15 Jan 2022 19:38:28: 8000000 INFO @ Sat, 15 Jan 2022 19:38:38: 8000000 INFO @ Sat, 15 Jan 2022 19:38:41: 9000000 INFO @ Sat, 15 Jan 2022 19:38:42: #1 tag size is determined as 89 bps INFO @ Sat, 15 Jan 2022 19:38:42: #1 tag size = 89 INFO @ Sat, 15 Jan 2022 19:38:42: #1 total tags in treatment: 4475940 INFO @ Sat, 15 Jan 2022 19:38:42: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:38:42: #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 19:38:42: #1 tags after filtering in treatment: 3064950 INFO @ Sat, 15 Jan 2022 19:38:42: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 15 Jan 2022 19:38:42: #1 finished! INFO @ Sat, 15 Jan 2022 19:38:42: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:38:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:38:42: #2 number of paired peaks: 7 WARNING @ Sat, 15 Jan 2022 19:38:42: Too few paired peaks (7) 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 19:38:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3659075/SRX3659075.10_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/SRX3659075/SRX3659075.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3659075/SRX3659075.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3659075/SRX3659075.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:38:48: 9000000 INFO @ Sat, 15 Jan 2022 19:38:49: #1 tag size is determined as 89 bps INFO @ Sat, 15 Jan 2022 19:38:49: #1 tag size = 89 INFO @ Sat, 15 Jan 2022 19:38:49: #1 total tags in treatment: 4475940 INFO @ Sat, 15 Jan 2022 19:38:49: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:38:49: #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 19:38:49: #1 tags after filtering in treatment: 3064950 INFO @ Sat, 15 Jan 2022 19:38:49: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 15 Jan 2022 19:38:49: #1 finished! INFO @ Sat, 15 Jan 2022 19:38:49: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:38:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:38:49: #2 number of paired peaks: 7 WARNING @ Sat, 15 Jan 2022 19:38:49: Too few paired peaks (7) 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 19:38:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3659075/SRX3659075.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3659075/SRX3659075.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3659075/SRX3659075.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3659075/SRX3659075.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling