Job ID = 7116764 SRX = SRX8639484 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T06:17:14 prefetch.2.10.7: 1) Downloading 'SRR12117048'... 2020-07-22T06:17:14 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T06:19:35 prefetch.2.10.7: HTTPS download succeed 2020-07-22T06:19:35 prefetch.2.10.7: 1) 'SRR12117048' was downloaded successfully 2020-07-22T06:19:35 prefetch.2.10.7: 'SRR12117048' has 0 unresolved dependencies Read 23502378 spots for SRR12117048/SRR12117048.sra Written 23502378 spots for SRR12117048/SRR12117048.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: 00:07:40 23502378 reads; of these: 23502378 (100.00%) were paired; of these: 12788295 (54.41%) aligned concordantly 0 times 9798607 (41.69%) aligned concordantly exactly 1 time 915476 (3.90%) aligned concordantly >1 times ---- 12788295 pairs aligned concordantly 0 times; of these: 56165 (0.44%) aligned discordantly 1 time ---- 12732130 pairs aligned 0 times concordantly or discordantly; of these: 25464260 mates make up the pairs; of these: 25285763 (99.30%) aligned 0 times 147857 (0.58%) aligned exactly 1 time 30640 (0.12%) aligned >1 times 46.21% overall alignment rate Time searching: 00:07:40 Overall time: 00:07:40 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] 122705 / 10757671 = 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 15:34:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639484/SRX8639484.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639484/SRX8639484.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639484/SRX8639484.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639484/SRX8639484.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 15:34:10: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:34:10: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:34:15: 1000000 INFO @ Wed, 22 Jul 2020 15:34:20: 2000000 INFO @ Wed, 22 Jul 2020 15:34:25: 3000000 INFO @ Wed, 22 Jul 2020 15:34:30: 4000000 INFO @ Wed, 22 Jul 2020 15:34:35: 5000000 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 15:34:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639484/SRX8639484.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639484/SRX8639484.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639484/SRX8639484.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639484/SRX8639484.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 15:34:39: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:34:39: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:34:40: 6000000 INFO @ Wed, 22 Jul 2020 15:34:44: 1000000 INFO @ Wed, 22 Jul 2020 15:34:45: 7000000 INFO @ Wed, 22 Jul 2020 15:34:50: 2000000 INFO @ Wed, 22 Jul 2020 15:34:50: 8000000 INFO @ Wed, 22 Jul 2020 15:34:55: 3000000 INFO @ Wed, 22 Jul 2020 15:34:56: 9000000 INFO @ Wed, 22 Jul 2020 15:35:00: 4000000 INFO @ Wed, 22 Jul 2020 15:35:01: 10000000 INFO @ Wed, 22 Jul 2020 15:35:05: 5000000 INFO @ Wed, 22 Jul 2020 15:35:06: 11000000 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 15:35:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639484/SRX8639484.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639484/SRX8639484.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639484/SRX8639484.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639484/SRX8639484.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 15:35:09: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:35:09: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:35:11: 6000000 INFO @ Wed, 22 Jul 2020 15:35:11: 12000000 INFO @ Wed, 22 Jul 2020 15:35:15: 1000000 INFO @ Wed, 22 Jul 2020 15:35:16: 7000000 INFO @ Wed, 22 Jul 2020 15:35:17: 13000000 INFO @ Wed, 22 Jul 2020 15:35:20: 2000000 INFO @ Wed, 22 Jul 2020 15:35:21: 8000000 INFO @ Wed, 22 Jul 2020 15:35:22: 14000000 INFO @ Wed, 22 Jul 2020 15:35:25: 3000000 INFO @ Wed, 22 Jul 2020 15:35:27: 9000000 INFO @ Wed, 22 Jul 2020 15:35:28: 15000000 INFO @ Wed, 22 Jul 2020 15:35:31: 4000000 INFO @ Wed, 22 Jul 2020 15:35:32: 10000000 INFO @ Wed, 22 Jul 2020 15:35:33: 16000000 INFO @ Wed, 22 Jul 2020 15:35:36: 5000000 INFO @ Wed, 22 Jul 2020 15:35:37: 11000000 INFO @ Wed, 22 Jul 2020 15:35:38: 17000000 INFO @ Wed, 22 Jul 2020 15:35:42: 6000000 INFO @ Wed, 22 Jul 2020 15:35:43: 12000000 INFO @ Wed, 22 Jul 2020 15:35:44: 18000000 INFO @ Wed, 22 Jul 2020 15:35:47: 7000000 INFO @ Wed, 22 Jul 2020 15:35:48: 13000000 INFO @ Wed, 22 Jul 2020 15:35:49: 19000000 INFO @ Wed, 22 Jul 2020 15:35:52: 8000000 INFO @ Wed, 22 Jul 2020 15:35:53: 14000000 INFO @ Wed, 22 Jul 2020 15:35:55: 20000000 INFO @ Wed, 22 Jul 2020 15:35:58: 9000000 INFO @ Wed, 22 Jul 2020 15:35:59: 15000000 INFO @ Wed, 22 Jul 2020 15:36:00: 21000000 INFO @ Wed, 22 Jul 2020 15:36:03: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 15:36:03: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 15:36:03: #1 total tags in treatment: 10591435 INFO @ Wed, 22 Jul 2020 15:36:03: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:36:03: #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 15:36:03: #1 tags after filtering in treatment: 7546408 INFO @ Wed, 22 Jul 2020 15:36:03: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 22 Jul 2020 15:36:03: #1 finished! INFO @ Wed, 22 Jul 2020 15:36:03: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:36:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:36:04: 10000000 INFO @ Wed, 22 Jul 2020 15:36:04: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 15:36:04: 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 15:36:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639484/SRX8639484.05_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/SRX8639484/SRX8639484.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639484/SRX8639484.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639484/SRX8639484.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:36:04: 16000000 INFO @ Wed, 22 Jul 2020 15:36:09: 11000000 INFO @ Wed, 22 Jul 2020 15:36:10: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 15:36:14: 12000000 INFO @ Wed, 22 Jul 2020 15:36:15: 18000000 INFO @ Wed, 22 Jul 2020 15:36:20: 13000000 INFO @ Wed, 22 Jul 2020 15:36:20: 19000000 INFO @ Wed, 22 Jul 2020 15:36:25: 14000000 INFO @ Wed, 22 Jul 2020 15:36:26: 20000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 15:36:30: 15000000 INFO @ Wed, 22 Jul 2020 15:36:31: 21000000 INFO @ Wed, 22 Jul 2020 15:36:34: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 15:36:34: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 15:36:34: #1 total tags in treatment: 10591435 INFO @ Wed, 22 Jul 2020 15:36:34: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:36:34: #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 15:36:34: #1 tags after filtering in treatment: 7546408 INFO @ Wed, 22 Jul 2020 15:36:34: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 22 Jul 2020 15:36:34: #1 finished! INFO @ Wed, 22 Jul 2020 15:36:34: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:36:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:36:34: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 15:36:34: 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 15:36:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639484/SRX8639484.10_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/SRX8639484/SRX8639484.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639484/SRX8639484.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639484/SRX8639484.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:36:35: 16000000 INFO @ Wed, 22 Jul 2020 15:36:40: 17000000 INFO @ Wed, 22 Jul 2020 15:36:45: 18000000 INFO @ Wed, 22 Jul 2020 15:36:50: 19000000 INFO @ Wed, 22 Jul 2020 15:36:55: 20000000 INFO @ Wed, 22 Jul 2020 15:37:00: 21000000 INFO @ Wed, 22 Jul 2020 15:37:02: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 15:37:02: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 15:37:02: #1 total tags in treatment: 10591435 INFO @ Wed, 22 Jul 2020 15:37:02: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:37:02: #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 15:37:02: #1 tags after filtering in treatment: 7546408 INFO @ Wed, 22 Jul 2020 15:37:02: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 22 Jul 2020 15:37:02: #1 finished! INFO @ Wed, 22 Jul 2020 15:37:02: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:37:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:37:03: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 15:37:03: 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 15:37:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639484/SRX8639484.20_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/SRX8639484/SRX8639484.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639484/SRX8639484.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639484/SRX8639484.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling