Job ID = 7117700 SRX = SRX8639550 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T06:43:23 prefetch.2.10.7: 1) Downloading 'SRR12116988'... 2020-07-22T06:43:23 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T06:45:19 prefetch.2.10.7: HTTPS download succeed 2020-07-22T06:45:19 prefetch.2.10.7: 1) 'SRR12116988' was downloaded successfully 2020-07-22T06:45:19 prefetch.2.10.7: 'SRR12116988' has 0 unresolved dependencies Read 21307589 spots for SRR12116988/SRR12116988.sra Written 21307589 spots for SRR12116988/SRR12116988.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: 00:12:25 21307589 reads; of these: 21307589 (100.00%) were paired; of these: 3264961 (15.32%) aligned concordantly 0 times 15816175 (74.23%) aligned concordantly exactly 1 time 2226453 (10.45%) aligned concordantly >1 times ---- 3264961 pairs aligned concordantly 0 times; of these: 361198 (11.06%) aligned discordantly 1 time ---- 2903763 pairs aligned 0 times concordantly or discordantly; of these: 5807526 mates make up the pairs; of these: 5418071 (93.29%) aligned 0 times 227406 (3.92%) aligned exactly 1 time 162049 (2.79%) aligned >1 times 87.29% overall alignment rate Time searching: 00:12:25 Overall time: 00:12:25 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 16 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] 288342 / 18361433 = 0.0157 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 16:07:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639550/SRX8639550.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639550/SRX8639550.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639550/SRX8639550.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639550/SRX8639550.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 16:07:45: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:07:45: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:07:50: 1000000 INFO @ Wed, 22 Jul 2020 16:07:55: 2000000 INFO @ Wed, 22 Jul 2020 16:08:00: 3000000 INFO @ Wed, 22 Jul 2020 16:08:05: 4000000 INFO @ Wed, 22 Jul 2020 16:08:10: 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 16:08:15: 6000000 INFO @ Wed, 22 Jul 2020 16:08:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639550/SRX8639550.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639550/SRX8639550.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639550/SRX8639550.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639550/SRX8639550.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 16:08:15: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:08:15: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:08:20: 7000000 INFO @ Wed, 22 Jul 2020 16:08:21: 1000000 INFO @ Wed, 22 Jul 2020 16:08:25: 8000000 INFO @ Wed, 22 Jul 2020 16:08:26: 2000000 INFO @ Wed, 22 Jul 2020 16:08:31: 9000000 INFO @ Wed, 22 Jul 2020 16:08:31: 3000000 INFO @ Wed, 22 Jul 2020 16:08:36: 10000000 INFO @ Wed, 22 Jul 2020 16:08:36: 4000000 INFO @ Wed, 22 Jul 2020 16:08:41: 11000000 INFO @ Wed, 22 Jul 2020 16:08:41: 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 16:08:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639550/SRX8639550.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639550/SRX8639550.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639550/SRX8639550.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639550/SRX8639550.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 16:08:45: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:08:45: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:08:46: 12000000 INFO @ Wed, 22 Jul 2020 16:08:47: 6000000 INFO @ Wed, 22 Jul 2020 16:08:51: 1000000 INFO @ Wed, 22 Jul 2020 16:08:52: 13000000 INFO @ Wed, 22 Jul 2020 16:08:52: 7000000 INFO @ Wed, 22 Jul 2020 16:08:56: 2000000 INFO @ Wed, 22 Jul 2020 16:08:57: 14000000 INFO @ Wed, 22 Jul 2020 16:08:57: 8000000 INFO @ Wed, 22 Jul 2020 16:09:01: 3000000 INFO @ Wed, 22 Jul 2020 16:09:02: 15000000 INFO @ Wed, 22 Jul 2020 16:09:03: 9000000 INFO @ Wed, 22 Jul 2020 16:09:07: 4000000 INFO @ Wed, 22 Jul 2020 16:09:08: 16000000 INFO @ Wed, 22 Jul 2020 16:09:08: 10000000 INFO @ Wed, 22 Jul 2020 16:09:12: 5000000 INFO @ Wed, 22 Jul 2020 16:09:13: 11000000 INFO @ Wed, 22 Jul 2020 16:09:13: 17000000 INFO @ Wed, 22 Jul 2020 16:09:17: 6000000 INFO @ Wed, 22 Jul 2020 16:09:18: 12000000 INFO @ Wed, 22 Jul 2020 16:09:18: 18000000 INFO @ Wed, 22 Jul 2020 16:09:23: 7000000 INFO @ Wed, 22 Jul 2020 16:09:24: 19000000 INFO @ Wed, 22 Jul 2020 16:09:24: 13000000 INFO @ Wed, 22 Jul 2020 16:09:28: 8000000 INFO @ Wed, 22 Jul 2020 16:09:29: 20000000 INFO @ Wed, 22 Jul 2020 16:09:30: 14000000 INFO @ Wed, 22 Jul 2020 16:09:34: 9000000 INFO @ Wed, 22 Jul 2020 16:09:35: 21000000 INFO @ Wed, 22 Jul 2020 16:09:35: 15000000 INFO @ Wed, 22 Jul 2020 16:09:39: 10000000 INFO @ Wed, 22 Jul 2020 16:09:40: 22000000 INFO @ Wed, 22 Jul 2020 16:09:41: 16000000 INFO @ Wed, 22 Jul 2020 16:09:45: 11000000 INFO @ Wed, 22 Jul 2020 16:09:46: 23000000 INFO @ Wed, 22 Jul 2020 16:09:46: 17000000 INFO @ Wed, 22 Jul 2020 16:09:50: 12000000 INFO @ Wed, 22 Jul 2020 16:09:51: 24000000 INFO @ Wed, 22 Jul 2020 16:09:52: 18000000 INFO @ Wed, 22 Jul 2020 16:09:56: 13000000 INFO @ Wed, 22 Jul 2020 16:09:56: 25000000 INFO @ Wed, 22 Jul 2020 16:09:57: 19000000 INFO @ Wed, 22 Jul 2020 16:10:01: 14000000 INFO @ Wed, 22 Jul 2020 16:10:02: 26000000 INFO @ Wed, 22 Jul 2020 16:10:02: 20000000 INFO @ Wed, 22 Jul 2020 16:10:07: 15000000 INFO @ Wed, 22 Jul 2020 16:10:07: 27000000 INFO @ Wed, 22 Jul 2020 16:10:08: 21000000 INFO @ Wed, 22 Jul 2020 16:10:12: 16000000 INFO @ Wed, 22 Jul 2020 16:10:13: 28000000 INFO @ Wed, 22 Jul 2020 16:10:13: 22000000 INFO @ Wed, 22 Jul 2020 16:10:17: 17000000 INFO @ Wed, 22 Jul 2020 16:10:19: 23000000 INFO @ Wed, 22 Jul 2020 16:10:19: 29000000 INFO @ Wed, 22 Jul 2020 16:10:23: 18000000 INFO @ Wed, 22 Jul 2020 16:10:24: 24000000 INFO @ Wed, 22 Jul 2020 16:10:25: 30000000 INFO @ Wed, 22 Jul 2020 16:10:28: 19000000 INFO @ Wed, 22 Jul 2020 16:10:29: 25000000 INFO @ Wed, 22 Jul 2020 16:10:31: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:10:34: 20000000 INFO @ Wed, 22 Jul 2020 16:10:35: 26000000 INFO @ Wed, 22 Jul 2020 16:10:36: 32000000 INFO @ Wed, 22 Jul 2020 16:10:39: 21000000 INFO @ Wed, 22 Jul 2020 16:10:40: 27000000 INFO @ Wed, 22 Jul 2020 16:10:42: 33000000 INFO @ Wed, 22 Jul 2020 16:10:44: 22000000 INFO @ Wed, 22 Jul 2020 16:10:46: 28000000 INFO @ Wed, 22 Jul 2020 16:10:48: 34000000 INFO @ Wed, 22 Jul 2020 16:10:50: 23000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:10:52: 29000000 INFO @ Wed, 22 Jul 2020 16:10:54: 35000000 INFO @ Wed, 22 Jul 2020 16:10:55: 24000000 INFO @ Wed, 22 Jul 2020 16:10:58: 30000000 INFO @ Wed, 22 Jul 2020 16:10:59: 36000000 INFO @ Wed, 22 Jul 2020 16:11:00: 25000000 INFO @ Wed, 22 Jul 2020 16:11:02: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:11:02: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:11:02: #1 total tags in treatment: 17755542 INFO @ Wed, 22 Jul 2020 16:11:02: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:11:02: #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 16:11:03: #1 tags after filtering in treatment: 11746281 INFO @ Wed, 22 Jul 2020 16:11:03: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 22 Jul 2020 16:11:03: #1 finished! INFO @ Wed, 22 Jul 2020 16:11:03: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:11:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:11:03: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:11:03: 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 16:11:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639550/SRX8639550.05_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/SRX8639550/SRX8639550.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639550/SRX8639550.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639550/SRX8639550.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:11:04: 31000000 INFO @ Wed, 22 Jul 2020 16:11:06: 26000000 INFO @ Wed, 22 Jul 2020 16:11:10: 32000000 INFO @ Wed, 22 Jul 2020 16:11:11: 27000000 INFO @ Wed, 22 Jul 2020 16:11:15: 33000000 INFO @ Wed, 22 Jul 2020 16:11:16: 28000000 INFO @ Wed, 22 Jul 2020 16:11:21: 34000000 INFO @ Wed, 22 Jul 2020 16:11:22: 29000000 INFO @ Wed, 22 Jul 2020 16:11:27: 35000000 INFO @ Wed, 22 Jul 2020 16:11:28: 30000000 INFO @ Wed, 22 Jul 2020 16:11:32: 36000000 INFO @ Wed, 22 Jul 2020 16:11:34: 31000000 INFO @ Wed, 22 Jul 2020 16:11:35: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:11:35: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:11:35: #1 total tags in treatment: 17755542 INFO @ Wed, 22 Jul 2020 16:11:35: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:11:35: #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 16:11:36: #1 tags after filtering in treatment: 11746281 INFO @ Wed, 22 Jul 2020 16:11:36: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 22 Jul 2020 16:11:36: #1 finished! INFO @ Wed, 22 Jul 2020 16:11:36: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:11:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:11:36: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:11:36: 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 16:11:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639550/SRX8639550.10_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/SRX8639550/SRX8639550.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639550/SRX8639550.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639550/SRX8639550.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:11:40: 32000000 INFO @ Wed, 22 Jul 2020 16:11:46: 33000000 INFO @ Wed, 22 Jul 2020 16:11:51: 34000000 INFO @ Wed, 22 Jul 2020 16:11:56: 35000000 INFO @ Wed, 22 Jul 2020 16:12:01: 36000000 INFO @ Wed, 22 Jul 2020 16:12:04: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:12:04: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:12:04: #1 total tags in treatment: 17755542 INFO @ Wed, 22 Jul 2020 16:12:04: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:12:04: #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 16:12:04: #1 tags after filtering in treatment: 11746281 INFO @ Wed, 22 Jul 2020 16:12:04: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 22 Jul 2020 16:12:04: #1 finished! INFO @ Wed, 22 Jul 2020 16:12:04: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:12:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:12:05: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:12:05: 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 16:12:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639550/SRX8639550.20_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/SRX8639550/SRX8639550.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639550/SRX8639550.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639550/SRX8639550.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling