Job ID = 7113627 SRX = SRX8462178 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T05:44:41 prefetch.2.10.7: 1) Downloading 'SRR11915637'... 2020-07-22T05:44:41 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:45:51 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:45:52 prefetch.2.10.7: 'SRR11915637' is valid 2020-07-22T05:45:52 prefetch.2.10.7: 1) 'SRR11915637' was downloaded successfully 2020-07-22T05:45:52 prefetch.2.10.7: 'SRR11915637' has 0 unresolved dependencies Read 5966274 spots for SRR11915637/SRR11915637.sra Written 5966274 spots for SRR11915637/SRR11915637.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: 00:05:19 5966274 reads; of these: 5966274 (100.00%) were paired; of these: 706481 (11.84%) aligned concordantly 0 times 4374397 (73.32%) aligned concordantly exactly 1 time 885396 (14.84%) aligned concordantly >1 times ---- 706481 pairs aligned concordantly 0 times; of these: 16332 (2.31%) aligned discordantly 1 time ---- 690149 pairs aligned 0 times concordantly or discordantly; of these: 1380298 mates make up the pairs; of these: 1248404 (90.44%) aligned 0 times 100738 (7.30%) aligned exactly 1 time 31156 (2.26%) aligned >1 times 89.54% overall alignment rate Time searching: 00:05:19 Overall time: 00:05:19 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] 1548165 / 5273070 = 0.2936 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 14:55:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462178/SRX8462178.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462178/SRX8462178.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462178/SRX8462178.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462178/SRX8462178.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 14:55:45: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:55:45: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:55:51: 1000000 INFO @ Wed, 22 Jul 2020 14:55:57: 2000000 INFO @ Wed, 22 Jul 2020 14:56:02: 3000000 INFO @ Wed, 22 Jul 2020 14:56:08: 4000000 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 14:56:14: 5000000 INFO @ Wed, 22 Jul 2020 14:56:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462178/SRX8462178.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462178/SRX8462178.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462178/SRX8462178.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462178/SRX8462178.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 14:56:15: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:56:15: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:56:19: 6000000 INFO @ Wed, 22 Jul 2020 14:56:21: 1000000 INFO @ Wed, 22 Jul 2020 14:56:25: 7000000 INFO @ Wed, 22 Jul 2020 14:56:28: 2000000 INFO @ Wed, 22 Jul 2020 14:56:29: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 14:56:29: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 14:56:29: #1 total tags in treatment: 3712556 INFO @ Wed, 22 Jul 2020 14:56:29: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:56:29: #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 14:56:29: #1 tags after filtering in treatment: 2855569 INFO @ Wed, 22 Jul 2020 14:56:29: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 22 Jul 2020 14:56:29: #1 finished! INFO @ Wed, 22 Jul 2020 14:56:29: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:56:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:56:29: #2 number of paired peaks: 29 WARNING @ Wed, 22 Jul 2020 14:56:29: Too few paired peaks (29) 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 14:56:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462178/SRX8462178.05_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/SRX8462178/SRX8462178.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462178/SRX8462178.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462178/SRX8462178.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 14:56:34: 3000000 INFO @ Wed, 22 Jul 2020 14:56:40: 4000000 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 14:56:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462178/SRX8462178.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462178/SRX8462178.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462178/SRX8462178.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462178/SRX8462178.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 14:56:45: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:56:45: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:56:45: 5000000 INFO @ Wed, 22 Jul 2020 14:56:52: 6000000 INFO @ Wed, 22 Jul 2020 14:56:52: 1000000 INFO @ Wed, 22 Jul 2020 14:56:58: 7000000 INFO @ Wed, 22 Jul 2020 14:56:59: 2000000 INFO @ Wed, 22 Jul 2020 14:57:01: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 14:57:01: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 14:57:01: #1 total tags in treatment: 3712556 INFO @ Wed, 22 Jul 2020 14:57:01: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:57:01: #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 14:57:01: #1 tags after filtering in treatment: 2855569 INFO @ Wed, 22 Jul 2020 14:57:01: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 22 Jul 2020 14:57:01: #1 finished! INFO @ Wed, 22 Jul 2020 14:57:01: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:57:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:57:02: #2 number of paired peaks: 29 WARNING @ Wed, 22 Jul 2020 14:57:02: Too few paired peaks (29) 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 14:57:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462178/SRX8462178.10_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/SRX8462178/SRX8462178.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462178/SRX8462178.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462178/SRX8462178.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 14:57:05: 3000000 INFO @ Wed, 22 Jul 2020 14:57:12: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 14:57:18: 5000000 INFO @ Wed, 22 Jul 2020 14:57:24: 6000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 14:57:31: 7000000 INFO @ Wed, 22 Jul 2020 14:57:34: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 14:57:34: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 14:57:34: #1 total tags in treatment: 3712556 INFO @ Wed, 22 Jul 2020 14:57:34: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:57:34: #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 14:57:34: #1 tags after filtering in treatment: 2855569 INFO @ Wed, 22 Jul 2020 14:57:34: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 22 Jul 2020 14:57:34: #1 finished! INFO @ Wed, 22 Jul 2020 14:57:34: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:57:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:57:35: #2 number of paired peaks: 29 WARNING @ Wed, 22 Jul 2020 14:57:35: Too few paired peaks (29) 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 14:57:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462178/SRX8462178.20_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/SRX8462178/SRX8462178.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462178/SRX8462178.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462178/SRX8462178.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling