Job ID = 7117768 SRX = SRX8639553 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T06:45:11 prefetch.2.10.7: 1) Downloading 'SRR12116991'... 2020-07-22T06:45:11 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T06:47:08 prefetch.2.10.7: HTTPS download succeed 2020-07-22T06:47:08 prefetch.2.10.7: 1) 'SRR12116991' was downloaded successfully 2020-07-22T06:47:08 prefetch.2.10.7: 'SRR12116991' has 0 unresolved dependencies Read 23882241 spots for SRR12116991/SRR12116991.sra Written 23882241 spots for SRR12116991/SRR12116991.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: 00:12:53 23882241 reads; of these: 23882241 (100.00%) were paired; of these: 4087604 (17.12%) aligned concordantly 0 times 17419156 (72.94%) aligned concordantly exactly 1 time 2375481 (9.95%) aligned concordantly >1 times ---- 4087604 pairs aligned concordantly 0 times; of these: 171244 (4.19%) aligned discordantly 1 time ---- 3916360 pairs aligned 0 times concordantly or discordantly; of these: 7832720 mates make up the pairs; of these: 7512168 (95.91%) aligned 0 times 228811 (2.92%) aligned exactly 1 time 91741 (1.17%) aligned >1 times 84.27% overall alignment rate Time searching: 00:12:53 Overall time: 00:12:53 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 20 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] 356136 / 19939492 = 0.0179 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 16:10:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639553/SRX8639553.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639553/SRX8639553.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639553/SRX8639553.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639553/SRX8639553.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 16:10:58: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:10:58: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:11:03: 1000000 INFO @ Wed, 22 Jul 2020 16:11:08: 2000000 INFO @ Wed, 22 Jul 2020 16:11:12: 3000000 INFO @ Wed, 22 Jul 2020 16:11:17: 4000000 INFO @ Wed, 22 Jul 2020 16:11:22: 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 16:11:26: 6000000 INFO @ Wed, 22 Jul 2020 16:11:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639553/SRX8639553.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639553/SRX8639553.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639553/SRX8639553.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639553/SRX8639553.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 16:11:28: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:11:28: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:11:31: 7000000 INFO @ Wed, 22 Jul 2020 16:11:33: 1000000 INFO @ Wed, 22 Jul 2020 16:11:36: 8000000 INFO @ Wed, 22 Jul 2020 16:11:38: 2000000 INFO @ Wed, 22 Jul 2020 16:11:41: 9000000 INFO @ Wed, 22 Jul 2020 16:11:43: 3000000 INFO @ Wed, 22 Jul 2020 16:11:46: 10000000 INFO @ Wed, 22 Jul 2020 16:11:48: 4000000 INFO @ Wed, 22 Jul 2020 16:11:51: 11000000 INFO @ Wed, 22 Jul 2020 16:11:53: 5000000 INFO @ Wed, 22 Jul 2020 16:11:55: 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 16:11:58: 6000000 INFO @ Wed, 22 Jul 2020 16:11:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639553/SRX8639553.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639553/SRX8639553.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639553/SRX8639553.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639553/SRX8639553.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 16:11:58: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:11:58: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:12:00: 13000000 INFO @ Wed, 22 Jul 2020 16:12:03: 7000000 INFO @ Wed, 22 Jul 2020 16:12:03: 1000000 INFO @ Wed, 22 Jul 2020 16:12:06: 14000000 INFO @ Wed, 22 Jul 2020 16:12:07: 8000000 INFO @ Wed, 22 Jul 2020 16:12:09: 2000000 INFO @ Wed, 22 Jul 2020 16:12:11: 15000000 INFO @ Wed, 22 Jul 2020 16:12:12: 9000000 INFO @ Wed, 22 Jul 2020 16:12:14: 3000000 INFO @ Wed, 22 Jul 2020 16:12:16: 16000000 INFO @ Wed, 22 Jul 2020 16:12:18: 10000000 INFO @ Wed, 22 Jul 2020 16:12:19: 4000000 INFO @ Wed, 22 Jul 2020 16:12:21: 17000000 INFO @ Wed, 22 Jul 2020 16:12:24: 11000000 INFO @ Wed, 22 Jul 2020 16:12:24: 5000000 INFO @ Wed, 22 Jul 2020 16:12:26: 18000000 INFO @ Wed, 22 Jul 2020 16:12:29: 6000000 INFO @ Wed, 22 Jul 2020 16:12:30: 12000000 INFO @ Wed, 22 Jul 2020 16:12:31: 19000000 INFO @ Wed, 22 Jul 2020 16:12:34: 7000000 INFO @ Wed, 22 Jul 2020 16:12:36: 20000000 INFO @ Wed, 22 Jul 2020 16:12:37: 13000000 INFO @ Wed, 22 Jul 2020 16:12:40: 8000000 INFO @ Wed, 22 Jul 2020 16:12:41: 21000000 INFO @ Wed, 22 Jul 2020 16:12:44: 14000000 INFO @ Wed, 22 Jul 2020 16:12:45: 9000000 INFO @ Wed, 22 Jul 2020 16:12:46: 22000000 INFO @ Wed, 22 Jul 2020 16:12:50: 10000000 INFO @ Wed, 22 Jul 2020 16:12:51: 15000000 INFO @ Wed, 22 Jul 2020 16:12:51: 23000000 INFO @ Wed, 22 Jul 2020 16:12:55: 11000000 INFO @ Wed, 22 Jul 2020 16:12:56: 24000000 INFO @ Wed, 22 Jul 2020 16:12:57: 16000000 INFO @ Wed, 22 Jul 2020 16:13:01: 12000000 INFO @ Wed, 22 Jul 2020 16:13:01: 25000000 INFO @ Wed, 22 Jul 2020 16:13:03: 17000000 INFO @ Wed, 22 Jul 2020 16:13:06: 13000000 INFO @ Wed, 22 Jul 2020 16:13:06: 26000000 INFO @ Wed, 22 Jul 2020 16:13:10: 18000000 INFO @ Wed, 22 Jul 2020 16:13:11: 27000000 INFO @ Wed, 22 Jul 2020 16:13:11: 14000000 INFO @ Wed, 22 Jul 2020 16:13:16: 28000000 INFO @ Wed, 22 Jul 2020 16:13:16: 19000000 INFO @ Wed, 22 Jul 2020 16:13:17: 15000000 INFO @ Wed, 22 Jul 2020 16:13:21: 29000000 INFO @ Wed, 22 Jul 2020 16:13:22: 16000000 INFO @ Wed, 22 Jul 2020 16:13:23: 20000000 INFO @ Wed, 22 Jul 2020 16:13:26: 30000000 INFO @ Wed, 22 Jul 2020 16:13:27: 17000000 INFO @ Wed, 22 Jul 2020 16:13:30: 21000000 INFO @ Wed, 22 Jul 2020 16:13:31: 31000000 INFO @ Wed, 22 Jul 2020 16:13:33: 18000000 INFO @ Wed, 22 Jul 2020 16:13:36: 32000000 INFO @ Wed, 22 Jul 2020 16:13:36: 22000000 INFO @ Wed, 22 Jul 2020 16:13:38: 19000000 INFO @ Wed, 22 Jul 2020 16:13:41: 33000000 INFO @ Wed, 22 Jul 2020 16:13:43: 23000000 INFO @ Wed, 22 Jul 2020 16:13:43: 20000000 INFO @ Wed, 22 Jul 2020 16:13:46: 34000000 INFO @ Wed, 22 Jul 2020 16:13:48: 21000000 INFO @ Wed, 22 Jul 2020 16:13:49: 24000000 INFO @ Wed, 22 Jul 2020 16:13:51: 35000000 INFO @ Wed, 22 Jul 2020 16:13:53: 22000000 INFO @ Wed, 22 Jul 2020 16:13:55: 36000000 INFO @ Wed, 22 Jul 2020 16:13:56: 25000000 INFO @ Wed, 22 Jul 2020 16:13:58: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:14:00: 37000000 INFO @ Wed, 22 Jul 2020 16:14:02: 26000000 INFO @ Wed, 22 Jul 2020 16:14:03: 24000000 INFO @ Wed, 22 Jul 2020 16:14:05: 38000000 INFO @ Wed, 22 Jul 2020 16:14:08: 25000000 INFO @ Wed, 22 Jul 2020 16:14:08: 27000000 INFO @ Wed, 22 Jul 2020 16:14:10: 39000000 INFO @ Wed, 22 Jul 2020 16:14:13: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:14:13: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:14:13: #1 total tags in treatment: 19438781 INFO @ Wed, 22 Jul 2020 16:14:13: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:14:13: #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 16:14:13: 26000000 INFO @ Wed, 22 Jul 2020 16:14:14: #1 tags after filtering in treatment: 12445073 INFO @ Wed, 22 Jul 2020 16:14:14: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Jul 2020 16:14:14: #1 finished! INFO @ Wed, 22 Jul 2020 16:14:14: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:14:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:14:15: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:14:15: 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 16:14:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639553/SRX8639553.05_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/SRX8639553/SRX8639553.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639553/SRX8639553.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639553/SRX8639553.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:14:15: 28000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:14:19: 27000000 INFO @ Wed, 22 Jul 2020 16:14:22: 29000000 INFO @ Wed, 22 Jul 2020 16:14:24: 28000000 INFO @ Wed, 22 Jul 2020 16:14:28: 30000000 INFO @ Wed, 22 Jul 2020 16:14:29: 29000000 INFO @ Wed, 22 Jul 2020 16:14:34: 30000000 INFO @ Wed, 22 Jul 2020 16:14:35: 31000000 INFO @ Wed, 22 Jul 2020 16:14:39: 31000000 INFO @ Wed, 22 Jul 2020 16:14:41: 32000000 INFO @ Wed, 22 Jul 2020 16:14:44: 32000000 INFO @ Wed, 22 Jul 2020 16:14:48: 33000000 INFO @ Wed, 22 Jul 2020 16:14:49: 33000000 INFO @ Wed, 22 Jul 2020 16:14:54: 34000000 INFO @ Wed, 22 Jul 2020 16:14:55: 34000000 INFO @ Wed, 22 Jul 2020 16:15:00: 35000000 INFO @ Wed, 22 Jul 2020 16:15:01: 35000000 INFO @ Wed, 22 Jul 2020 16:15:06: 36000000 INFO @ Wed, 22 Jul 2020 16:15:07: 36000000 INFO @ Wed, 22 Jul 2020 16:15:11: 37000000 INFO @ Wed, 22 Jul 2020 16:15:13: 37000000 INFO @ Wed, 22 Jul 2020 16:15:16: 38000000 INFO @ Wed, 22 Jul 2020 16:15:20: 38000000 INFO @ Wed, 22 Jul 2020 16:15:21: 39000000 INFO @ Wed, 22 Jul 2020 16:15:24: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:15:24: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:15:24: #1 total tags in treatment: 19438781 INFO @ Wed, 22 Jul 2020 16:15:24: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:15:24: #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 16:15:25: #1 tags after filtering in treatment: 12445073 INFO @ Wed, 22 Jul 2020 16:15:25: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Jul 2020 16:15:25: #1 finished! INFO @ Wed, 22 Jul 2020 16:15:25: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:15:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:15:25: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:15:25: 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 16:15:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639553/SRX8639553.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis INFO @ Wed, 22 Jul 2020 16:15:26: 39000000 needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639553/SRX8639553.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639553/SRX8639553.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639553/SRX8639553.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:15:29: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:15:29: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:15:29: #1 total tags in treatment: 19438781 INFO @ Wed, 22 Jul 2020 16:15:29: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:15:29: #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 16:15:30: #1 tags after filtering in treatment: 12445073 INFO @ Wed, 22 Jul 2020 16:15:30: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Jul 2020 16:15:30: #1 finished! INFO @ Wed, 22 Jul 2020 16:15:30: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:15:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:15:31: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:15:31: 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 16:15:31: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639553/SRX8639553.10_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/SRX8639553/SRX8639553.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639553/SRX8639553.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639553/SRX8639553.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling