Job ID = 7117368 SRX = SRX8639503 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T06:38:24 prefetch.2.10.7: 1) Downloading 'SRR12117067'... 2020-07-22T06:38:24 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T06:44:45 prefetch.2.10.7: HTTPS download succeed 2020-07-22T06:44:45 prefetch.2.10.7: 1) 'SRR12117067' was downloaded successfully 2020-07-22T06:44:45 prefetch.2.10.7: 'SRR12117067' has 0 unresolved dependencies Read 29854645 spots for SRR12117067/SRR12117067.sra Written 29854645 spots for SRR12117067/SRR12117067.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: 00:14:15 29854645 reads; of these: 29854645 (100.00%) were paired; of these: 4434044 (14.85%) aligned concordantly 0 times 22118105 (74.09%) aligned concordantly exactly 1 time 3302496 (11.06%) aligned concordantly >1 times ---- 4434044 pairs aligned concordantly 0 times; of these: 339378 (7.65%) aligned discordantly 1 time ---- 4094666 pairs aligned 0 times concordantly or discordantly; of these: 8189332 mates make up the pairs; of these: 7619992 (93.05%) aligned 0 times 377526 (4.61%) aligned exactly 1 time 191814 (2.34%) aligned >1 times 87.24% overall alignment rate Time searching: 00:14:15 Overall time: 00:14:15 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 24 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] 715053 / 25604661 = 0.0279 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 16:11:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639503/SRX8639503.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639503/SRX8639503.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639503/SRX8639503.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639503/SRX8639503.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 16:11:56: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:11:56: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:12:01: 1000000 INFO @ Wed, 22 Jul 2020 16:12:06: 2000000 INFO @ Wed, 22 Jul 2020 16:12:11: 3000000 INFO @ Wed, 22 Jul 2020 16:12:16: 4000000 INFO @ Wed, 22 Jul 2020 16:12:21: 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 16:12:26: 6000000 INFO @ Wed, 22 Jul 2020 16:12:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639503/SRX8639503.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639503/SRX8639503.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639503/SRX8639503.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639503/SRX8639503.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 16:12:26: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:12:26: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:12:31: 7000000 INFO @ Wed, 22 Jul 2020 16:12:32: 1000000 INFO @ Wed, 22 Jul 2020 16:12:36: 8000000 INFO @ Wed, 22 Jul 2020 16:12:37: 2000000 INFO @ Wed, 22 Jul 2020 16:12:42: 9000000 INFO @ Wed, 22 Jul 2020 16:12:42: 3000000 INFO @ Wed, 22 Jul 2020 16:12:47: 10000000 INFO @ Wed, 22 Jul 2020 16:12:47: 4000000 INFO @ Wed, 22 Jul 2020 16:12:52: 11000000 INFO @ Wed, 22 Jul 2020 16:12:53: 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 16:12:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639503/SRX8639503.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639503/SRX8639503.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639503/SRX8639503.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639503/SRX8639503.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 16:12:56: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:12:56: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:12:58: 12000000 INFO @ Wed, 22 Jul 2020 16:12:58: 6000000 INFO @ Wed, 22 Jul 2020 16:13:02: 1000000 INFO @ Wed, 22 Jul 2020 16:13:03: 13000000 INFO @ Wed, 22 Jul 2020 16:13:03: 7000000 INFO @ Wed, 22 Jul 2020 16:13:07: 2000000 INFO @ Wed, 22 Jul 2020 16:13:08: 14000000 INFO @ Wed, 22 Jul 2020 16:13:09: 8000000 INFO @ Wed, 22 Jul 2020 16:13:13: 3000000 INFO @ Wed, 22 Jul 2020 16:13:14: 15000000 INFO @ Wed, 22 Jul 2020 16:13:14: 9000000 INFO @ Wed, 22 Jul 2020 16:13:18: 4000000 INFO @ Wed, 22 Jul 2020 16:13:19: 16000000 INFO @ Wed, 22 Jul 2020 16:13:20: 10000000 INFO @ Wed, 22 Jul 2020 16:13:23: 5000000 INFO @ Wed, 22 Jul 2020 16:13:24: 17000000 INFO @ Wed, 22 Jul 2020 16:13:25: 11000000 INFO @ Wed, 22 Jul 2020 16:13:29: 6000000 INFO @ Wed, 22 Jul 2020 16:13:29: 18000000 INFO @ Wed, 22 Jul 2020 16:13:31: 12000000 INFO @ Wed, 22 Jul 2020 16:13:34: 7000000 INFO @ Wed, 22 Jul 2020 16:13:35: 19000000 INFO @ Wed, 22 Jul 2020 16:13:36: 13000000 INFO @ Wed, 22 Jul 2020 16:13:39: 8000000 INFO @ Wed, 22 Jul 2020 16:13:40: 20000000 INFO @ Wed, 22 Jul 2020 16:13:41: 14000000 INFO @ Wed, 22 Jul 2020 16:13:45: 9000000 INFO @ Wed, 22 Jul 2020 16:13:45: 21000000 INFO @ Wed, 22 Jul 2020 16:13:46: 15000000 INFO @ Wed, 22 Jul 2020 16:13:50: 10000000 INFO @ Wed, 22 Jul 2020 16:13:51: 22000000 INFO @ Wed, 22 Jul 2020 16:13:52: 16000000 INFO @ Wed, 22 Jul 2020 16:13:55: 11000000 INFO @ Wed, 22 Jul 2020 16:13:56: 23000000 INFO @ Wed, 22 Jul 2020 16:13:57: 17000000 INFO @ Wed, 22 Jul 2020 16:14:01: 12000000 INFO @ Wed, 22 Jul 2020 16:14:02: 24000000 INFO @ Wed, 22 Jul 2020 16:14:02: 18000000 INFO @ Wed, 22 Jul 2020 16:14:06: 13000000 INFO @ Wed, 22 Jul 2020 16:14:07: 25000000 INFO @ Wed, 22 Jul 2020 16:14:08: 19000000 INFO @ Wed, 22 Jul 2020 16:14:11: 14000000 INFO @ Wed, 22 Jul 2020 16:14:12: 26000000 INFO @ Wed, 22 Jul 2020 16:14:13: 20000000 INFO @ Wed, 22 Jul 2020 16:14:17: 15000000 INFO @ Wed, 22 Jul 2020 16:14:18: 27000000 INFO @ Wed, 22 Jul 2020 16:14:18: 21000000 INFO @ Wed, 22 Jul 2020 16:14:22: 16000000 INFO @ Wed, 22 Jul 2020 16:14:23: 28000000 INFO @ Wed, 22 Jul 2020 16:14:24: 22000000 INFO @ Wed, 22 Jul 2020 16:14:27: 17000000 INFO @ Wed, 22 Jul 2020 16:14:28: 29000000 INFO @ Wed, 22 Jul 2020 16:14:29: 23000000 INFO @ Wed, 22 Jul 2020 16:14:33: 18000000 INFO @ Wed, 22 Jul 2020 16:14:34: 30000000 INFO @ Wed, 22 Jul 2020 16:14:35: 24000000 INFO @ Wed, 22 Jul 2020 16:14:38: 19000000 INFO @ Wed, 22 Jul 2020 16:14:39: 31000000 INFO @ Wed, 22 Jul 2020 16:14:40: 25000000 INFO @ Wed, 22 Jul 2020 16:14:44: 20000000 INFO @ Wed, 22 Jul 2020 16:14:44: 32000000 INFO @ Wed, 22 Jul 2020 16:14:45: 26000000 INFO @ Wed, 22 Jul 2020 16:14:49: 21000000 INFO @ Wed, 22 Jul 2020 16:14:49: 33000000 INFO @ Wed, 22 Jul 2020 16:14:51: 27000000 INFO @ Wed, 22 Jul 2020 16:14:54: 22000000 INFO @ Wed, 22 Jul 2020 16:14:54: 34000000 INFO @ Wed, 22 Jul 2020 16:14:56: 28000000 INFO @ Wed, 22 Jul 2020 16:15:00: 23000000 INFO @ Wed, 22 Jul 2020 16:15:00: 35000000 INFO @ Wed, 22 Jul 2020 16:15:01: 29000000 INFO @ Wed, 22 Jul 2020 16:15:05: 24000000 INFO @ Wed, 22 Jul 2020 16:15:05: 36000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:15:07: 30000000 INFO @ Wed, 22 Jul 2020 16:15:10: 37000000 INFO @ Wed, 22 Jul 2020 16:15:10: 25000000 INFO @ Wed, 22 Jul 2020 16:15:12: 31000000 INFO @ Wed, 22 Jul 2020 16:15:15: 38000000 INFO @ Wed, 22 Jul 2020 16:15:16: 26000000 INFO @ Wed, 22 Jul 2020 16:15:17: 32000000 INFO @ Wed, 22 Jul 2020 16:15:21: 39000000 INFO @ Wed, 22 Jul 2020 16:15:21: 27000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:15:23: 33000000 INFO @ Wed, 22 Jul 2020 16:15:26: 40000000 INFO @ Wed, 22 Jul 2020 16:15:26: 28000000 INFO @ Wed, 22 Jul 2020 16:15:28: 34000000 INFO @ Wed, 22 Jul 2020 16:15:31: 41000000 INFO @ Wed, 22 Jul 2020 16:15:32: 29000000 INFO @ Wed, 22 Jul 2020 16:15:33: 35000000 INFO @ Wed, 22 Jul 2020 16:15:37: 42000000 INFO @ Wed, 22 Jul 2020 16:15:37: 30000000 INFO @ Wed, 22 Jul 2020 16:15:39: 36000000 INFO @ Wed, 22 Jul 2020 16:15:42: 43000000 INFO @ Wed, 22 Jul 2020 16:15:42: 31000000 INFO @ Wed, 22 Jul 2020 16:15:44: 37000000 INFO @ Wed, 22 Jul 2020 16:15:47: 44000000 INFO @ Wed, 22 Jul 2020 16:15:48: 32000000 INFO @ Wed, 22 Jul 2020 16:15:49: 38000000 INFO @ Wed, 22 Jul 2020 16:15:52: 45000000 INFO @ Wed, 22 Jul 2020 16:15:53: 33000000 INFO @ Wed, 22 Jul 2020 16:15:55: 39000000 INFO @ Wed, 22 Jul 2020 16:15:58: 46000000 INFO @ Wed, 22 Jul 2020 16:15:58: 34000000 INFO @ Wed, 22 Jul 2020 16:16:00: 40000000 INFO @ Wed, 22 Jul 2020 16:16:03: 47000000 INFO @ Wed, 22 Jul 2020 16:16:04: 35000000 INFO @ Wed, 22 Jul 2020 16:16:05: 41000000 INFO @ Wed, 22 Jul 2020 16:16:08: 48000000 INFO @ Wed, 22 Jul 2020 16:16:09: 36000000 INFO @ Wed, 22 Jul 2020 16:16:11: 42000000 INFO @ Wed, 22 Jul 2020 16:16:13: 49000000 INFO @ Wed, 22 Jul 2020 16:16:14: 37000000 INFO @ Wed, 22 Jul 2020 16:16:16: 43000000 INFO @ Wed, 22 Jul 2020 16:16:18: 50000000 INFO @ Wed, 22 Jul 2020 16:16:19: 38000000 INFO @ Wed, 22 Jul 2020 16:16:21: 44000000 INFO @ Wed, 22 Jul 2020 16:16:22: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:16:22: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:16:22: #1 total tags in treatment: 24706648 INFO @ Wed, 22 Jul 2020 16:16:22: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:16:22: #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 16:16:23: #1 tags after filtering in treatment: 14403335 INFO @ Wed, 22 Jul 2020 16:16:23: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 22 Jul 2020 16:16:23: #1 finished! INFO @ Wed, 22 Jul 2020 16:16:23: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:16:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:16:23: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:16:23: 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 16:16:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639503/SRX8639503.05_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/SRX8639503/SRX8639503.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639503/SRX8639503.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639503/SRX8639503.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:16:25: 39000000 INFO @ Wed, 22 Jul 2020 16:16:27: 45000000 INFO @ Wed, 22 Jul 2020 16:16:30: 40000000 INFO @ Wed, 22 Jul 2020 16:16:32: 46000000 INFO @ Wed, 22 Jul 2020 16:16:35: 41000000 INFO @ Wed, 22 Jul 2020 16:16:37: 47000000 INFO @ Wed, 22 Jul 2020 16:16:41: 42000000 INFO @ Wed, 22 Jul 2020 16:16:42: 48000000 INFO @ Wed, 22 Jul 2020 16:16:46: 43000000 INFO @ Wed, 22 Jul 2020 16:16:48: 49000000 INFO @ Wed, 22 Jul 2020 16:16:51: 44000000 INFO @ Wed, 22 Jul 2020 16:16:53: 50000000 INFO @ Wed, 22 Jul 2020 16:16:56: 45000000 INFO @ Wed, 22 Jul 2020 16:16:56: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:16:56: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:16:56: #1 total tags in treatment: 24706648 INFO @ Wed, 22 Jul 2020 16:16:56: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:16:56: #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 16:16:57: #1 tags after filtering in treatment: 14403335 INFO @ Wed, 22 Jul 2020 16:16:57: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 22 Jul 2020 16:16:57: #1 finished! INFO @ Wed, 22 Jul 2020 16:16:57: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:16:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:16:58: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:16:58: 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 16:16:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639503/SRX8639503.10_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/SRX8639503/SRX8639503.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639503/SRX8639503.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639503/SRX8639503.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:17:01: 46000000 INFO @ Wed, 22 Jul 2020 16:17:06: 47000000 INFO @ Wed, 22 Jul 2020 16:17:11: 48000000 INFO @ Wed, 22 Jul 2020 16:17:16: 49000000 INFO @ Wed, 22 Jul 2020 16:17:21: 50000000 INFO @ Wed, 22 Jul 2020 16:17:25: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:17:25: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:17:25: #1 total tags in treatment: 24706648 INFO @ Wed, 22 Jul 2020 16:17:25: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:17:25: #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 16:17:25: #1 tags after filtering in treatment: 14403335 INFO @ Wed, 22 Jul 2020 16:17:25: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 22 Jul 2020 16:17:25: #1 finished! INFO @ Wed, 22 Jul 2020 16:17:25: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:17:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:17:26: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:17:26: 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 16:17:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639503/SRX8639503.20_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/SRX8639503/SRX8639503.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639503/SRX8639503.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639503/SRX8639503.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling