Job ID = 7118302 SRX = SRX8639590 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T07:14:19 prefetch.2.10.7: 1) Downloading 'SRR12117028'... 2020-07-22T07:14:19 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T07:16:20 prefetch.2.10.7: HTTPS download succeed 2020-07-22T07:16:20 prefetch.2.10.7: 1) 'SRR12117028' was downloaded successfully 2020-07-22T07:16:20 prefetch.2.10.7: 'SRR12117028' has 0 unresolved dependencies Read 21601097 spots for SRR12117028/SRR12117028.sra Written 21601097 spots for SRR12117028/SRR12117028.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: 00:09:44 21601097 reads; of these: 21601097 (100.00%) were paired; of these: 4548549 (21.06%) aligned concordantly 0 times 15032644 (69.59%) aligned concordantly exactly 1 time 2019904 (9.35%) aligned concordantly >1 times ---- 4548549 pairs aligned concordantly 0 times; of these: 546672 (12.02%) aligned discordantly 1 time ---- 4001877 pairs aligned 0 times concordantly or discordantly; of these: 8003754 mates make up the pairs; of these: 7553417 (94.37%) aligned 0 times 232668 (2.91%) aligned exactly 1 time 217669 (2.72%) aligned >1 times 82.52% overall alignment rate Time searching: 00:09:44 Overall time: 00:09:44 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] 292103 / 17529935 = 0.0167 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 16:35:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639590/SRX8639590.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639590/SRX8639590.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639590/SRX8639590.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639590/SRX8639590.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 16:35:08: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:35:08: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:35:13: 1000000 INFO @ Wed, 22 Jul 2020 16:35:17: 2000000 INFO @ Wed, 22 Jul 2020 16:35:22: 3000000 INFO @ Wed, 22 Jul 2020 16:35:26: 4000000 INFO @ Wed, 22 Jul 2020 16:35:31: 5000000 INFO @ Wed, 22 Jul 2020 16:35:35: 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 16:35:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639590/SRX8639590.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639590/SRX8639590.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639590/SRX8639590.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639590/SRX8639590.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 16:35:38: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:35:38: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:35:40: 7000000 INFO @ Wed, 22 Jul 2020 16:35:43: 1000000 INFO @ Wed, 22 Jul 2020 16:35:45: 8000000 INFO @ Wed, 22 Jul 2020 16:35:48: 2000000 INFO @ Wed, 22 Jul 2020 16:35:49: 9000000 INFO @ Wed, 22 Jul 2020 16:35:53: 3000000 INFO @ Wed, 22 Jul 2020 16:35:54: 10000000 INFO @ Wed, 22 Jul 2020 16:35:58: 4000000 INFO @ Wed, 22 Jul 2020 16:35:59: 11000000 INFO @ Wed, 22 Jul 2020 16:36:02: 5000000 INFO @ Wed, 22 Jul 2020 16:36:04: 12000000 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 16:36:07: 6000000 INFO @ Wed, 22 Jul 2020 16:36:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639590/SRX8639590.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639590/SRX8639590.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639590/SRX8639590.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639590/SRX8639590.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 16:36:08: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:36:08: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:36:08: 13000000 INFO @ Wed, 22 Jul 2020 16:36:12: 7000000 INFO @ Wed, 22 Jul 2020 16:36:13: 14000000 INFO @ Wed, 22 Jul 2020 16:36:13: 1000000 INFO @ Wed, 22 Jul 2020 16:36:17: 8000000 INFO @ Wed, 22 Jul 2020 16:36:18: 15000000 INFO @ Wed, 22 Jul 2020 16:36:18: 2000000 INFO @ Wed, 22 Jul 2020 16:36:22: 9000000 INFO @ Wed, 22 Jul 2020 16:36:23: 16000000 INFO @ Wed, 22 Jul 2020 16:36:23: 3000000 INFO @ Wed, 22 Jul 2020 16:36:27: 10000000 INFO @ Wed, 22 Jul 2020 16:36:28: 17000000 INFO @ Wed, 22 Jul 2020 16:36:28: 4000000 INFO @ Wed, 22 Jul 2020 16:36:32: 11000000 INFO @ Wed, 22 Jul 2020 16:36:33: 18000000 INFO @ Wed, 22 Jul 2020 16:36:33: 5000000 INFO @ Wed, 22 Jul 2020 16:36:37: 12000000 INFO @ Wed, 22 Jul 2020 16:36:38: 19000000 INFO @ Wed, 22 Jul 2020 16:36:38: 6000000 INFO @ Wed, 22 Jul 2020 16:36:42: 13000000 INFO @ Wed, 22 Jul 2020 16:36:43: 20000000 INFO @ Wed, 22 Jul 2020 16:36:43: 7000000 INFO @ Wed, 22 Jul 2020 16:36:47: 14000000 INFO @ Wed, 22 Jul 2020 16:36:48: 21000000 INFO @ Wed, 22 Jul 2020 16:36:48: 8000000 INFO @ Wed, 22 Jul 2020 16:36:52: 15000000 INFO @ Wed, 22 Jul 2020 16:36:53: 22000000 INFO @ Wed, 22 Jul 2020 16:36:54: 9000000 INFO @ Wed, 22 Jul 2020 16:36:57: 16000000 INFO @ Wed, 22 Jul 2020 16:36:58: 23000000 INFO @ Wed, 22 Jul 2020 16:36:59: 10000000 INFO @ Wed, 22 Jul 2020 16:37:02: 17000000 INFO @ Wed, 22 Jul 2020 16:37:03: 24000000 INFO @ Wed, 22 Jul 2020 16:37:04: 11000000 INFO @ Wed, 22 Jul 2020 16:37:07: 18000000 INFO @ Wed, 22 Jul 2020 16:37:08: 25000000 INFO @ Wed, 22 Jul 2020 16:37:09: 12000000 INFO @ Wed, 22 Jul 2020 16:37:12: 19000000 INFO @ Wed, 22 Jul 2020 16:37:13: 26000000 INFO @ Wed, 22 Jul 2020 16:37:14: 13000000 INFO @ Wed, 22 Jul 2020 16:37:17: 20000000 INFO @ Wed, 22 Jul 2020 16:37:18: 27000000 INFO @ Wed, 22 Jul 2020 16:37:19: 14000000 INFO @ Wed, 22 Jul 2020 16:37:22: 21000000 INFO @ Wed, 22 Jul 2020 16:37:23: 28000000 INFO @ Wed, 22 Jul 2020 16:37:23: 15000000 INFO @ Wed, 22 Jul 2020 16:37:27: 22000000 INFO @ Wed, 22 Jul 2020 16:37:28: 29000000 INFO @ Wed, 22 Jul 2020 16:37:28: 16000000 INFO @ Wed, 22 Jul 2020 16:37:32: 23000000 INFO @ Wed, 22 Jul 2020 16:37:33: 30000000 INFO @ Wed, 22 Jul 2020 16:37:33: 17000000 INFO @ Wed, 22 Jul 2020 16:37:36: 24000000 INFO @ Wed, 22 Jul 2020 16:37:38: 31000000 INFO @ Wed, 22 Jul 2020 16:37:38: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:37:41: 25000000 INFO @ Wed, 22 Jul 2020 16:37:43: 32000000 INFO @ Wed, 22 Jul 2020 16:37:43: 19000000 INFO @ Wed, 22 Jul 2020 16:37:47: 26000000 INFO @ Wed, 22 Jul 2020 16:37:48: 33000000 INFO @ Wed, 22 Jul 2020 16:37:49: 20000000 INFO @ Wed, 22 Jul 2020 16:37:52: 27000000 INFO @ Wed, 22 Jul 2020 16:37:53: 34000000 INFO @ Wed, 22 Jul 2020 16:37:54: 21000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:37:57: 28000000 INFO @ Wed, 22 Jul 2020 16:37:58: 35000000 INFO @ Wed, 22 Jul 2020 16:37:58: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:37:58: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:37:58: #1 total tags in treatment: 16763588 INFO @ Wed, 22 Jul 2020 16:37:58: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:37:58: #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 16:37:59: #1 tags after filtering in treatment: 11325683 INFO @ Wed, 22 Jul 2020 16:37:59: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 22 Jul 2020 16:37:59: #1 finished! INFO @ Wed, 22 Jul 2020 16:37:59: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:37:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:37:59: 22000000 INFO @ Wed, 22 Jul 2020 16:37:59: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:37:59: 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 16:37:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639590/SRX8639590.05_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/SRX8639590/SRX8639590.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639590/SRX8639590.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639590/SRX8639590.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:38:02: 29000000 INFO @ Wed, 22 Jul 2020 16:38:04: 23000000 INFO @ Wed, 22 Jul 2020 16:38:07: 30000000 INFO @ Wed, 22 Jul 2020 16:38:09: 24000000 INFO @ Wed, 22 Jul 2020 16:38:12: 31000000 INFO @ Wed, 22 Jul 2020 16:38:14: 25000000 INFO @ Wed, 22 Jul 2020 16:38:17: 32000000 INFO @ Wed, 22 Jul 2020 16:38:19: 26000000 INFO @ Wed, 22 Jul 2020 16:38:22: 33000000 INFO @ Wed, 22 Jul 2020 16:38:24: 27000000 INFO @ Wed, 22 Jul 2020 16:38:27: 34000000 INFO @ Wed, 22 Jul 2020 16:38:29: 28000000 INFO @ Wed, 22 Jul 2020 16:38:32: 35000000 INFO @ Wed, 22 Jul 2020 16:38:32: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:38:32: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:38:32: #1 total tags in treatment: 16763588 INFO @ Wed, 22 Jul 2020 16:38:32: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:38:32: #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 16:38:32: #1 tags after filtering in treatment: 11325683 INFO @ Wed, 22 Jul 2020 16:38:32: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 22 Jul 2020 16:38:32: #1 finished! INFO @ Wed, 22 Jul 2020 16:38:32: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:38:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:38:33: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:38:33: 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 16:38:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639590/SRX8639590.10_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/SRX8639590/SRX8639590.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639590/SRX8639590.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639590/SRX8639590.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:38:33: 29000000 INFO @ Wed, 22 Jul 2020 16:38:38: 30000000 INFO @ Wed, 22 Jul 2020 16:38:43: 31000000 INFO @ Wed, 22 Jul 2020 16:38:48: 32000000 INFO @ Wed, 22 Jul 2020 16:38:52: 33000000 INFO @ Wed, 22 Jul 2020 16:38:57: 34000000 INFO @ Wed, 22 Jul 2020 16:39:02: 35000000 INFO @ Wed, 22 Jul 2020 16:39:02: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:39:02: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:39:02: #1 total tags in treatment: 16763588 INFO @ Wed, 22 Jul 2020 16:39:02: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:39:02: #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 16:39:03: #1 tags after filtering in treatment: 11325683 INFO @ Wed, 22 Jul 2020 16:39:03: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 22 Jul 2020 16:39:03: #1 finished! INFO @ Wed, 22 Jul 2020 16:39:03: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:39:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:39:03: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:39:03: 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 16:39:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639590/SRX8639590.20_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/SRX8639590/SRX8639590.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639590/SRX8639590.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639590/SRX8639590.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling