Job ID = 7118014 SRX = SRX8639565 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T07:07:18 prefetch.2.10.7: 1) Downloading 'SRR12117003'... 2020-07-22T07:07:18 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T07:09:28 prefetch.2.10.7: HTTPS download succeed 2020-07-22T07:09:28 prefetch.2.10.7: 1) 'SRR12117003' was downloaded successfully 2020-07-22T07:09:28 prefetch.2.10.7: 'SRR12117003' has 0 unresolved dependencies Read 23018714 spots for SRR12117003/SRR12117003.sra Written 23018714 spots for SRR12117003/SRR12117003.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: 00:06:20 23018714 reads; of these: 23018714 (100.00%) were paired; of these: 13545276 (58.84%) aligned concordantly 0 times 8580325 (37.28%) aligned concordantly exactly 1 time 893113 (3.88%) aligned concordantly >1 times ---- 13545276 pairs aligned concordantly 0 times; of these: 290374 (2.14%) aligned discordantly 1 time ---- 13254902 pairs aligned 0 times concordantly or discordantly; of these: 26509804 mates make up the pairs; of these: 26239638 (98.98%) aligned 0 times 191104 (0.72%) aligned exactly 1 time 79062 (0.30%) aligned >1 times 43.00% overall alignment rate Time searching: 00:06:20 Overall time: 00:06:20 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 12 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] 110678 / 9737806 = 0.0114 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 16:22:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639565/SRX8639565.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639565/SRX8639565.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639565/SRX8639565.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639565/SRX8639565.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 @ Wed, 22 Jul 2020 16:22:00: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:22:00: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:22:04: 1000000 INFO @ Wed, 22 Jul 2020 16:22:09: 2000000 INFO @ Wed, 22 Jul 2020 16:22:13: 3000000 INFO @ Wed, 22 Jul 2020 16:22:18: 4000000 INFO @ Wed, 22 Jul 2020 16:22:22: 5000000 INFO @ Wed, 22 Jul 2020 16:22:27: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 16:22:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639565/SRX8639565.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639565/SRX8639565.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639565/SRX8639565.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639565/SRX8639565.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 @ Wed, 22 Jul 2020 16:22:30: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:22:30: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:22:31: 7000000 INFO @ Wed, 22 Jul 2020 16:22:35: 1000000 INFO @ Wed, 22 Jul 2020 16:22:36: 8000000 INFO @ Wed, 22 Jul 2020 16:22:40: 2000000 INFO @ Wed, 22 Jul 2020 16:22:42: 9000000 INFO @ Wed, 22 Jul 2020 16:22:45: 3000000 INFO @ Wed, 22 Jul 2020 16:22:47: 10000000 INFO @ Wed, 22 Jul 2020 16:22:50: 4000000 INFO @ Wed, 22 Jul 2020 16:22:53: 11000000 INFO @ Wed, 22 Jul 2020 16:22:55: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 16:22:59: 12000000 INFO @ Wed, 22 Jul 2020 16:23:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639565/SRX8639565.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639565/SRX8639565.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639565/SRX8639565.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639565/SRX8639565.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 @ Wed, 22 Jul 2020 16:23:00: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:23:00: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:23:01: 6000000 INFO @ Wed, 22 Jul 2020 16:23:05: 1000000 INFO @ Wed, 22 Jul 2020 16:23:05: 13000000 INFO @ Wed, 22 Jul 2020 16:23:06: 7000000 INFO @ Wed, 22 Jul 2020 16:23:10: 2000000 INFO @ Wed, 22 Jul 2020 16:23:11: 8000000 INFO @ Wed, 22 Jul 2020 16:23:11: 14000000 INFO @ Wed, 22 Jul 2020 16:23:16: 3000000 INFO @ Wed, 22 Jul 2020 16:23:16: 9000000 INFO @ Wed, 22 Jul 2020 16:23:17: 15000000 INFO @ Wed, 22 Jul 2020 16:23:21: 10000000 INFO @ Wed, 22 Jul 2020 16:23:22: 4000000 INFO @ Wed, 22 Jul 2020 16:23:23: 16000000 INFO @ Wed, 22 Jul 2020 16:23:27: 11000000 INFO @ Wed, 22 Jul 2020 16:23:28: 5000000 INFO @ Wed, 22 Jul 2020 16:23:30: 17000000 INFO @ Wed, 22 Jul 2020 16:23:32: 12000000 INFO @ Wed, 22 Jul 2020 16:23:33: 6000000 INFO @ Wed, 22 Jul 2020 16:23:36: 18000000 INFO @ Wed, 22 Jul 2020 16:23:37: 13000000 INFO @ Wed, 22 Jul 2020 16:23:39: 7000000 INFO @ Wed, 22 Jul 2020 16:23:42: 19000000 INFO @ Wed, 22 Jul 2020 16:23:42: 14000000 INFO @ Wed, 22 Jul 2020 16:23:45: 8000000 INFO @ Wed, 22 Jul 2020 16:23:45: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:23:45: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:23:45: #1 total tags in treatment: 9364152 INFO @ Wed, 22 Jul 2020 16:23:45: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:23:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 16:23:45: #1 tags after filtering in treatment: 6445887 INFO @ Wed, 22 Jul 2020 16:23:45: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 22 Jul 2020 16:23:45: #1 finished! INFO @ Wed, 22 Jul 2020 16:23:45: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:23:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:23:46: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:23:46: Too few paired peaks (0) 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 @ Wed, 22 Jul 2020 16:23:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639565/SRX8639565.05_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/SRX8639565/SRX8639565.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639565/SRX8639565.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639565/SRX8639565.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:23:47: 15000000 INFO @ Wed, 22 Jul 2020 16:23:51: 9000000 INFO @ Wed, 22 Jul 2020 16:23:52: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:23:56: 10000000 INFO @ Wed, 22 Jul 2020 16:23:58: 17000000 INFO @ Wed, 22 Jul 2020 16:24:02: 11000000 INFO @ Wed, 22 Jul 2020 16:24:03: 18000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:24:08: 12000000 INFO @ Wed, 22 Jul 2020 16:24:08: 19000000 INFO @ Wed, 22 Jul 2020 16:24:11: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:24:11: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:24:11: #1 total tags in treatment: 9364152 INFO @ Wed, 22 Jul 2020 16:24:11: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:24:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 16:24:11: #1 tags after filtering in treatment: 6445887 INFO @ Wed, 22 Jul 2020 16:24:11: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 22 Jul 2020 16:24:11: #1 finished! INFO @ Wed, 22 Jul 2020 16:24:11: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:24:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:24:11: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:24:11: Too few paired peaks (0) 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 @ Wed, 22 Jul 2020 16:24:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639565/SRX8639565.10_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/SRX8639565/SRX8639565.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639565/SRX8639565.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639565/SRX8639565.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:24:13: 13000000 INFO @ Wed, 22 Jul 2020 16:24:19: 14000000 INFO @ Wed, 22 Jul 2020 16:24:24: 15000000 INFO @ Wed, 22 Jul 2020 16:24:29: 16000000 INFO @ Wed, 22 Jul 2020 16:24:35: 17000000 INFO @ Wed, 22 Jul 2020 16:24:40: 18000000 INFO @ Wed, 22 Jul 2020 16:24:45: 19000000 INFO @ Wed, 22 Jul 2020 16:24:48: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:24:48: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:24:48: #1 total tags in treatment: 9364152 INFO @ Wed, 22 Jul 2020 16:24:48: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:24:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 16:24:48: #1 tags after filtering in treatment: 6445887 INFO @ Wed, 22 Jul 2020 16:24:48: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 22 Jul 2020 16:24:48: #1 finished! INFO @ Wed, 22 Jul 2020 16:24:48: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:24:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:24:49: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:24:49: Too few paired peaks (0) 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 @ Wed, 22 Jul 2020 16:24:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639565/SRX8639565.20_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/SRX8639565/SRX8639565.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639565/SRX8639565.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639565/SRX8639565.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling