Job ID = 7116128 SRX = SRX8639469 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T06:15:06 prefetch.2.10.7: 1) Downloading 'SRR12116969'... 2020-07-22T06:15:06 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T06:17:29 prefetch.2.10.7: HTTPS download succeed 2020-07-22T06:17:29 prefetch.2.10.7: 1) 'SRR12116969' was downloaded successfully 2020-07-22T06:17:29 prefetch.2.10.7: 'SRR12116969' has 0 unresolved dependencies Read 26805704 spots for SRR12116969/SRR12116969.sra Written 26805704 spots for SRR12116969/SRR12116969.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: 00:12:01 26805704 reads; of these: 26805704 (100.00%) were paired; of these: 5176810 (19.31%) aligned concordantly 0 times 19117044 (71.32%) aligned concordantly exactly 1 time 2511850 (9.37%) aligned concordantly >1 times ---- 5176810 pairs aligned concordantly 0 times; of these: 213529 (4.12%) aligned discordantly 1 time ---- 4963281 pairs aligned 0 times concordantly or discordantly; of these: 9926562 mates make up the pairs; of these: 9602669 (96.74%) aligned 0 times 225283 (2.27%) aligned exactly 1 time 98610 (0.99%) aligned >1 times 82.09% overall alignment rate Time searching: 00:12:01 Overall time: 00:12:01 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] 448574 / 21820049 = 0.0206 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 15:40:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639469/SRX8639469.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639469/SRX8639469.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639469/SRX8639469.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639469/SRX8639469.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 15:40:39: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:40:39: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:40:44: 1000000 INFO @ Wed, 22 Jul 2020 15:40:49: 2000000 INFO @ Wed, 22 Jul 2020 15:40:54: 3000000 INFO @ Wed, 22 Jul 2020 15:40:59: 4000000 INFO @ Wed, 22 Jul 2020 15:41:04: 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 15:41:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639469/SRX8639469.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639469/SRX8639469.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639469/SRX8639469.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639469/SRX8639469.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 15:41:09: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:41:09: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:41:10: 6000000 INFO @ Wed, 22 Jul 2020 15:41:15: 1000000 INFO @ Wed, 22 Jul 2020 15:41:16: 7000000 INFO @ Wed, 22 Jul 2020 15:41:22: 8000000 INFO @ Wed, 22 Jul 2020 15:41:22: 2000000 INFO @ Wed, 22 Jul 2020 15:41:28: 9000000 INFO @ Wed, 22 Jul 2020 15:41:29: 3000000 INFO @ Wed, 22 Jul 2020 15:41:35: 10000000 INFO @ Wed, 22 Jul 2020 15:41:36: 4000000 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 15:41:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639469/SRX8639469.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639469/SRX8639469.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639469/SRX8639469.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639469/SRX8639469.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 15:41:39: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:41:39: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:41:41: 11000000 INFO @ Wed, 22 Jul 2020 15:41:43: 5000000 INFO @ Wed, 22 Jul 2020 15:41:46: 1000000 INFO @ Wed, 22 Jul 2020 15:41:47: 12000000 INFO @ Wed, 22 Jul 2020 15:41:50: 6000000 INFO @ Wed, 22 Jul 2020 15:41:53: 2000000 INFO @ Wed, 22 Jul 2020 15:41:53: 13000000 INFO @ Wed, 22 Jul 2020 15:41:57: 7000000 INFO @ Wed, 22 Jul 2020 15:42:00: 14000000 INFO @ Wed, 22 Jul 2020 15:42:00: 3000000 INFO @ Wed, 22 Jul 2020 15:42:04: 8000000 INFO @ Wed, 22 Jul 2020 15:42:06: 15000000 INFO @ Wed, 22 Jul 2020 15:42:07: 4000000 INFO @ Wed, 22 Jul 2020 15:42:11: 9000000 INFO @ Wed, 22 Jul 2020 15:42:12: 16000000 INFO @ Wed, 22 Jul 2020 15:42:14: 5000000 INFO @ Wed, 22 Jul 2020 15:42:18: 10000000 INFO @ Wed, 22 Jul 2020 15:42:19: 17000000 INFO @ Wed, 22 Jul 2020 15:42:21: 6000000 INFO @ Wed, 22 Jul 2020 15:42:25: 18000000 INFO @ Wed, 22 Jul 2020 15:42:25: 11000000 INFO @ Wed, 22 Jul 2020 15:42:28: 7000000 INFO @ Wed, 22 Jul 2020 15:42:31: 19000000 INFO @ Wed, 22 Jul 2020 15:42:32: 12000000 INFO @ Wed, 22 Jul 2020 15:42:35: 8000000 INFO @ Wed, 22 Jul 2020 15:42:38: 20000000 INFO @ Wed, 22 Jul 2020 15:42:39: 13000000 INFO @ Wed, 22 Jul 2020 15:42:42: 9000000 INFO @ Wed, 22 Jul 2020 15:42:44: 21000000 INFO @ Wed, 22 Jul 2020 15:42:46: 14000000 INFO @ Wed, 22 Jul 2020 15:42:50: 10000000 INFO @ Wed, 22 Jul 2020 15:42:50: 22000000 INFO @ Wed, 22 Jul 2020 15:42:53: 15000000 INFO @ Wed, 22 Jul 2020 15:42:57: 11000000 INFO @ Wed, 22 Jul 2020 15:42:58: 23000000 INFO @ Wed, 22 Jul 2020 15:43:00: 16000000 INFO @ Wed, 22 Jul 2020 15:43:04: 12000000 INFO @ Wed, 22 Jul 2020 15:43:05: 24000000 INFO @ Wed, 22 Jul 2020 15:43:07: 17000000 INFO @ Wed, 22 Jul 2020 15:43:11: 13000000 INFO @ Wed, 22 Jul 2020 15:43:12: 25000000 INFO @ Wed, 22 Jul 2020 15:43:15: 18000000 INFO @ Wed, 22 Jul 2020 15:43:18: 14000000 INFO @ Wed, 22 Jul 2020 15:43:18: 26000000 INFO @ Wed, 22 Jul 2020 15:43:22: 19000000 INFO @ Wed, 22 Jul 2020 15:43:24: 27000000 INFO @ Wed, 22 Jul 2020 15:43:25: 15000000 INFO @ Wed, 22 Jul 2020 15:43:29: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 15:43:31: 28000000 INFO @ Wed, 22 Jul 2020 15:43:32: 16000000 INFO @ Wed, 22 Jul 2020 15:43:36: 21000000 INFO @ Wed, 22 Jul 2020 15:43:37: 29000000 INFO @ Wed, 22 Jul 2020 15:43:39: 17000000 INFO @ Wed, 22 Jul 2020 15:43:43: 22000000 INFO @ Wed, 22 Jul 2020 15:43:43: 30000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 15:43:46: 18000000 INFO @ Wed, 22 Jul 2020 15:43:49: 23000000 INFO @ Wed, 22 Jul 2020 15:43:50: 31000000 INFO @ Wed, 22 Jul 2020 15:43:53: 19000000 INFO @ Wed, 22 Jul 2020 15:43:56: 24000000 INFO @ Wed, 22 Jul 2020 15:43:56: 32000000 INFO @ Wed, 22 Jul 2020 15:44:00: 20000000 INFO @ Wed, 22 Jul 2020 15:44:02: 25000000 INFO @ Wed, 22 Jul 2020 15:44:03: 33000000 INFO @ Wed, 22 Jul 2020 15:44:07: 21000000 INFO @ Wed, 22 Jul 2020 15:44:09: 34000000 INFO @ Wed, 22 Jul 2020 15:44:09: 26000000 INFO @ Wed, 22 Jul 2020 15:44:14: 22000000 INFO @ Wed, 22 Jul 2020 15:44:15: 35000000 INFO @ Wed, 22 Jul 2020 15:44:16: 27000000 INFO @ Wed, 22 Jul 2020 15:44:20: 23000000 INFO @ Wed, 22 Jul 2020 15:44:22: 36000000 INFO @ Wed, 22 Jul 2020 15:44:23: 28000000 INFO @ Wed, 22 Jul 2020 15:44:27: 24000000 INFO @ Wed, 22 Jul 2020 15:44:28: 37000000 INFO @ Wed, 22 Jul 2020 15:44:31: 29000000 INFO @ Wed, 22 Jul 2020 15:44:34: 25000000 INFO @ Wed, 22 Jul 2020 15:44:34: 38000000 INFO @ Wed, 22 Jul 2020 15:44:38: 30000000 INFO @ Wed, 22 Jul 2020 15:44:40: 39000000 INFO @ Wed, 22 Jul 2020 15:44:41: 26000000 INFO @ Wed, 22 Jul 2020 15:44:45: 31000000 INFO @ Wed, 22 Jul 2020 15:44:47: 40000000 INFO @ Wed, 22 Jul 2020 15:44:48: 27000000 INFO @ Wed, 22 Jul 2020 15:44:53: 32000000 INFO @ Wed, 22 Jul 2020 15:44:53: 41000000 INFO @ Wed, 22 Jul 2020 15:44:55: 28000000 INFO @ Wed, 22 Jul 2020 15:44:59: 42000000 INFO @ Wed, 22 Jul 2020 15:45:00: 33000000 INFO @ Wed, 22 Jul 2020 15:45:02: 29000000 INFO @ Wed, 22 Jul 2020 15:45:06: 43000000 INFO @ Wed, 22 Jul 2020 15:45:07: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 15:45:07: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 15:45:07: #1 total tags in treatment: 21180606 INFO @ Wed, 22 Jul 2020 15:45:07: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:45:07: #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 15:45:07: #1 tags after filtering in treatment: 13221970 INFO @ Wed, 22 Jul 2020 15:45:07: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 22 Jul 2020 15:45:07: #1 finished! INFO @ Wed, 22 Jul 2020 15:45:07: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:45:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:45:07: 34000000 INFO @ Wed, 22 Jul 2020 15:45:08: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 15:45:08: 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 15:45:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639469/SRX8639469.05_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/SRX8639469/SRX8639469.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639469/SRX8639469.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639469/SRX8639469.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:45:09: 30000000 INFO @ Wed, 22 Jul 2020 15:45:14: 35000000 INFO @ Wed, 22 Jul 2020 15:45:15: 31000000 INFO @ Wed, 22 Jul 2020 15:45:21: 36000000 INFO @ Wed, 22 Jul 2020 15:45:22: 32000000 INFO @ Wed, 22 Jul 2020 15:45:28: 37000000 INFO @ Wed, 22 Jul 2020 15:45:29: 33000000 INFO @ Wed, 22 Jul 2020 15:45:35: 38000000 INFO @ Wed, 22 Jul 2020 15:45:36: 34000000 INFO @ Wed, 22 Jul 2020 15:45:42: 39000000 INFO @ Wed, 22 Jul 2020 15:45:42: 35000000 INFO @ Wed, 22 Jul 2020 15:45:48: 40000000 INFO @ Wed, 22 Jul 2020 15:45:49: 36000000 INFO @ Wed, 22 Jul 2020 15:45:55: 41000000 INFO @ Wed, 22 Jul 2020 15:45:56: 37000000 INFO @ Wed, 22 Jul 2020 15:46:02: 42000000 INFO @ Wed, 22 Jul 2020 15:46:03: 38000000 INFO @ Wed, 22 Jul 2020 15:46:09: 43000000 INFO @ Wed, 22 Jul 2020 15:46:09: 39000000 INFO @ Wed, 22 Jul 2020 15:46:09: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 15:46:09: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 15:46:09: #1 total tags in treatment: 21180606 INFO @ Wed, 22 Jul 2020 15:46:09: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:46:09: #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 15:46:10: #1 tags after filtering in treatment: 13221970 INFO @ Wed, 22 Jul 2020 15:46:10: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 22 Jul 2020 15:46:10: #1 finished! INFO @ Wed, 22 Jul 2020 15:46:10: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:46:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:46:10: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 15:46:10: 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 15:46:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639469/SRX8639469.10_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/SRX8639469/SRX8639469.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639469/SRX8639469.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639469/SRX8639469.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:46:15: 40000000 INFO @ Wed, 22 Jul 2020 15:46:21: 41000000 INFO @ Wed, 22 Jul 2020 15:46:27: 42000000 INFO @ Wed, 22 Jul 2020 15:46:33: 43000000 INFO @ Wed, 22 Jul 2020 15:46:34: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 15:46:34: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 15:46:34: #1 total tags in treatment: 21180606 INFO @ Wed, 22 Jul 2020 15:46:34: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:46:34: #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 15:46:34: #1 tags after filtering in treatment: 13221970 INFO @ Wed, 22 Jul 2020 15:46:34: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 22 Jul 2020 15:46:34: #1 finished! INFO @ Wed, 22 Jul 2020 15:46:34: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:46:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:46:35: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 15:46:35: 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 15:46:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639469/SRX8639469.20_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/SRX8639469/SRX8639469.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639469/SRX8639469.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639469/SRX8639469.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling