Job ID = 7117906 SRX = SRX8639557 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T06:49:45 prefetch.2.10.7: 1) Downloading 'SRR12116995'... 2020-07-22T06:49:45 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T06:51:51 prefetch.2.10.7: HTTPS download succeed 2020-07-22T06:51:51 prefetch.2.10.7: 1) 'SRR12116995' was downloaded successfully 2020-07-22T06:51:51 prefetch.2.10.7: 'SRR12116995' has 0 unresolved dependencies Read 27245416 spots for SRR12116995/SRR12116995.sra Written 27245416 spots for SRR12116995/SRR12116995.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: 00:13:28 27245416 reads; of these: 27245416 (100.00%) were paired; of these: 5754803 (21.12%) aligned concordantly 0 times 19729584 (72.41%) aligned concordantly exactly 1 time 1761029 (6.46%) aligned concordantly >1 times ---- 5754803 pairs aligned concordantly 0 times; of these: 1078941 (18.75%) aligned discordantly 1 time ---- 4675862 pairs aligned 0 times concordantly or discordantly; of these: 9351724 mates make up the pairs; of these: 8833455 (94.46%) aligned 0 times 307810 (3.29%) aligned exactly 1 time 210459 (2.25%) aligned >1 times 83.79% overall alignment rate Time searching: 00:13:28 Overall time: 00:13:28 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] 274416 / 22459513 = 0.0122 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 16:16:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639557/SRX8639557.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639557/SRX8639557.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639557/SRX8639557.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639557/SRX8639557.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 16:16:52: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:16:52: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:16:57: 1000000 INFO @ Wed, 22 Jul 2020 16:17:01: 2000000 INFO @ Wed, 22 Jul 2020 16:17:06: 3000000 INFO @ Wed, 22 Jul 2020 16:17:11: 4000000 INFO @ Wed, 22 Jul 2020 16:17:16: 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 16:17:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639557/SRX8639557.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639557/SRX8639557.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639557/SRX8639557.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639557/SRX8639557.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 16:17:21: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:17:21: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:17:21: 6000000 INFO @ Wed, 22 Jul 2020 16:17:26: 7000000 INFO @ Wed, 22 Jul 2020 16:17:27: 1000000 INFO @ Wed, 22 Jul 2020 16:17:32: 8000000 INFO @ Wed, 22 Jul 2020 16:17:32: 2000000 INFO @ Wed, 22 Jul 2020 16:17:38: 9000000 INFO @ Wed, 22 Jul 2020 16:17:38: 3000000 INFO @ Wed, 22 Jul 2020 16:17:43: 10000000 INFO @ Wed, 22 Jul 2020 16:17:44: 4000000 INFO @ Wed, 22 Jul 2020 16:17:49: 11000000 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 16:17:50: 5000000 INFO @ Wed, 22 Jul 2020 16:17:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639557/SRX8639557.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639557/SRX8639557.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639557/SRX8639557.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639557/SRX8639557.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 16:17:51: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:17:51: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:17:54: 12000000 INFO @ Wed, 22 Jul 2020 16:17:55: 6000000 INFO @ Wed, 22 Jul 2020 16:17:57: 1000000 INFO @ Wed, 22 Jul 2020 16:18:00: 13000000 INFO @ Wed, 22 Jul 2020 16:18:01: 7000000 INFO @ Wed, 22 Jul 2020 16:18:03: 2000000 INFO @ Wed, 22 Jul 2020 16:18:05: 14000000 INFO @ Wed, 22 Jul 2020 16:18:07: 8000000 INFO @ Wed, 22 Jul 2020 16:18:08: 3000000 INFO @ Wed, 22 Jul 2020 16:18:11: 15000000 INFO @ Wed, 22 Jul 2020 16:18:13: 9000000 INFO @ Wed, 22 Jul 2020 16:18:14: 4000000 INFO @ Wed, 22 Jul 2020 16:18:17: 16000000 INFO @ Wed, 22 Jul 2020 16:18:19: 10000000 INFO @ Wed, 22 Jul 2020 16:18:20: 5000000 INFO @ Wed, 22 Jul 2020 16:18:22: 17000000 INFO @ Wed, 22 Jul 2020 16:18:25: 11000000 INFO @ Wed, 22 Jul 2020 16:18:26: 6000000 INFO @ Wed, 22 Jul 2020 16:18:28: 18000000 INFO @ Wed, 22 Jul 2020 16:18:30: 12000000 INFO @ Wed, 22 Jul 2020 16:18:32: 7000000 INFO @ Wed, 22 Jul 2020 16:18:34: 19000000 INFO @ Wed, 22 Jul 2020 16:18:36: 13000000 INFO @ Wed, 22 Jul 2020 16:18:38: 8000000 INFO @ Wed, 22 Jul 2020 16:18:39: 20000000 INFO @ Wed, 22 Jul 2020 16:18:42: 14000000 INFO @ Wed, 22 Jul 2020 16:18:44: 9000000 INFO @ Wed, 22 Jul 2020 16:18:45: 21000000 INFO @ Wed, 22 Jul 2020 16:18:48: 15000000 INFO @ Wed, 22 Jul 2020 16:18:50: 10000000 INFO @ Wed, 22 Jul 2020 16:18:51: 22000000 INFO @ Wed, 22 Jul 2020 16:18:54: 16000000 INFO @ Wed, 22 Jul 2020 16:18:56: 11000000 INFO @ Wed, 22 Jul 2020 16:18:56: 23000000 INFO @ Wed, 22 Jul 2020 16:19:00: 17000000 INFO @ Wed, 22 Jul 2020 16:19:01: 12000000 INFO @ Wed, 22 Jul 2020 16:19:02: 24000000 INFO @ Wed, 22 Jul 2020 16:19:05: 18000000 INFO @ Wed, 22 Jul 2020 16:19:07: 13000000 INFO @ Wed, 22 Jul 2020 16:19:08: 25000000 INFO @ Wed, 22 Jul 2020 16:19:11: 19000000 INFO @ Wed, 22 Jul 2020 16:19:13: 14000000 INFO @ Wed, 22 Jul 2020 16:19:14: 26000000 INFO @ Wed, 22 Jul 2020 16:19:17: 20000000 INFO @ Wed, 22 Jul 2020 16:19:19: 15000000 INFO @ Wed, 22 Jul 2020 16:19:20: 27000000 INFO @ Wed, 22 Jul 2020 16:19:23: 21000000 INFO @ Wed, 22 Jul 2020 16:19:25: 16000000 INFO @ Wed, 22 Jul 2020 16:19:26: 28000000 INFO @ Wed, 22 Jul 2020 16:19:29: 22000000 INFO @ Wed, 22 Jul 2020 16:19:31: 17000000 INFO @ Wed, 22 Jul 2020 16:19:31: 29000000 INFO @ Wed, 22 Jul 2020 16:19:35: 23000000 INFO @ Wed, 22 Jul 2020 16:19:37: 18000000 INFO @ Wed, 22 Jul 2020 16:19:37: 30000000 INFO @ Wed, 22 Jul 2020 16:19:41: 24000000 INFO @ Wed, 22 Jul 2020 16:19:43: 19000000 INFO @ Wed, 22 Jul 2020 16:19:43: 31000000 INFO @ Wed, 22 Jul 2020 16:19:47: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:19:49: 20000000 INFO @ Wed, 22 Jul 2020 16:19:49: 32000000 INFO @ Wed, 22 Jul 2020 16:19:53: 26000000 INFO @ Wed, 22 Jul 2020 16:19:55: 21000000 INFO @ Wed, 22 Jul 2020 16:19:55: 33000000 INFO @ Wed, 22 Jul 2020 16:19:59: 27000000 INFO @ Wed, 22 Jul 2020 16:20:00: 22000000 INFO @ Wed, 22 Jul 2020 16:20:00: 34000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:20:05: 28000000 INFO @ Wed, 22 Jul 2020 16:20:06: 23000000 INFO @ Wed, 22 Jul 2020 16:20:06: 35000000 INFO @ Wed, 22 Jul 2020 16:20:11: 29000000 INFO @ Wed, 22 Jul 2020 16:20:12: 24000000 INFO @ Wed, 22 Jul 2020 16:20:12: 36000000 INFO @ Wed, 22 Jul 2020 16:20:16: 30000000 INFO @ Wed, 22 Jul 2020 16:20:18: 25000000 INFO @ Wed, 22 Jul 2020 16:20:18: 37000000 INFO @ Wed, 22 Jul 2020 16:20:22: 31000000 INFO @ Wed, 22 Jul 2020 16:20:24: 26000000 INFO @ Wed, 22 Jul 2020 16:20:24: 38000000 INFO @ Wed, 22 Jul 2020 16:20:28: 32000000 INFO @ Wed, 22 Jul 2020 16:20:29: 27000000 INFO @ Wed, 22 Jul 2020 16:20:30: 39000000 INFO @ Wed, 22 Jul 2020 16:20:34: 33000000 INFO @ Wed, 22 Jul 2020 16:20:35: 28000000 INFO @ Wed, 22 Jul 2020 16:20:35: 40000000 INFO @ Wed, 22 Jul 2020 16:20:39: 34000000 INFO @ Wed, 22 Jul 2020 16:20:40: 29000000 INFO @ Wed, 22 Jul 2020 16:20:41: 41000000 INFO @ Wed, 22 Jul 2020 16:20:45: 35000000 INFO @ Wed, 22 Jul 2020 16:20:46: 30000000 INFO @ Wed, 22 Jul 2020 16:20:47: 42000000 INFO @ Wed, 22 Jul 2020 16:20:50: 36000000 INFO @ Wed, 22 Jul 2020 16:20:51: 31000000 INFO @ Wed, 22 Jul 2020 16:20:52: 43000000 INFO @ Wed, 22 Jul 2020 16:20:56: 37000000 INFO @ Wed, 22 Jul 2020 16:20:57: 32000000 INFO @ Wed, 22 Jul 2020 16:20:58: 44000000 INFO @ Wed, 22 Jul 2020 16:21:02: 38000000 INFO @ Wed, 22 Jul 2020 16:21:03: 33000000 INFO @ Wed, 22 Jul 2020 16:21:04: 45000000 INFO @ Wed, 22 Jul 2020 16:21:04: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:21:04: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:21:04: #1 total tags in treatment: 21220713 INFO @ Wed, 22 Jul 2020 16:21:04: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:21:04: #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 16:21:05: #1 tags after filtering in treatment: 11600279 INFO @ Wed, 22 Jul 2020 16:21:05: #1 Redundant rate of treatment: 0.45 INFO @ Wed, 22 Jul 2020 16:21:05: #1 finished! INFO @ Wed, 22 Jul 2020 16:21:05: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:21:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:21:06: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:21:06: 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 16:21:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639557/SRX8639557.05_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/SRX8639557/SRX8639557.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639557/SRX8639557.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639557/SRX8639557.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:21:08: 39000000 INFO @ Wed, 22 Jul 2020 16:21:08: 34000000 INFO @ Wed, 22 Jul 2020 16:21:13: 40000000 INFO @ Wed, 22 Jul 2020 16:21:14: 35000000 INFO @ Wed, 22 Jul 2020 16:21:19: 41000000 INFO @ Wed, 22 Jul 2020 16:21:19: 36000000 INFO @ Wed, 22 Jul 2020 16:21:24: 42000000 INFO @ Wed, 22 Jul 2020 16:21:25: 37000000 INFO @ Wed, 22 Jul 2020 16:21:30: 43000000 INFO @ Wed, 22 Jul 2020 16:21:30: 38000000 INFO @ Wed, 22 Jul 2020 16:21:35: 44000000 INFO @ Wed, 22 Jul 2020 16:21:36: 39000000 INFO @ Wed, 22 Jul 2020 16:21:41: 45000000 INFO @ Wed, 22 Jul 2020 16:21:41: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:21:41: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:21:41: #1 total tags in treatment: 21220713 INFO @ Wed, 22 Jul 2020 16:21:41: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:21:41: #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 16:21:41: 40000000 INFO @ Wed, 22 Jul 2020 16:21:42: #1 tags after filtering in treatment: 11600279 INFO @ Wed, 22 Jul 2020 16:21:42: #1 Redundant rate of treatment: 0.45 INFO @ Wed, 22 Jul 2020 16:21:42: #1 finished! INFO @ Wed, 22 Jul 2020 16:21:42: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:21:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:21:42: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:21:42: 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 16:21:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639557/SRX8639557.10_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/SRX8639557/SRX8639557.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639557/SRX8639557.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639557/SRX8639557.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:21:46: 41000000 INFO @ Wed, 22 Jul 2020 16:21:51: 42000000 INFO @ Wed, 22 Jul 2020 16:21:56: 43000000 INFO @ Wed, 22 Jul 2020 16:22:01: 44000000 INFO @ Wed, 22 Jul 2020 16:22:06: 45000000 INFO @ Wed, 22 Jul 2020 16:22:07: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:22:07: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:22:07: #1 total tags in treatment: 21220713 INFO @ Wed, 22 Jul 2020 16:22:07: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:22:07: #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 16:22:07: #1 tags after filtering in treatment: 11600279 INFO @ Wed, 22 Jul 2020 16:22:07: #1 Redundant rate of treatment: 0.45 INFO @ Wed, 22 Jul 2020 16:22:07: #1 finished! INFO @ Wed, 22 Jul 2020 16:22:07: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:22:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:22:08: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:22:08: 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 16:22:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639557/SRX8639557.20_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/SRX8639557/SRX8639557.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639557/SRX8639557.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639557/SRX8639557.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling