Job ID = 2640751 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T09:53:44 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 10,871,824 reads read : 21,743,648 reads written : 21,743,648 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:07:40 10871824 reads; of these: 10871824 (100.00%) were paired; of these: 421367 (3.88%) aligned concordantly 0 times 9124449 (83.93%) aligned concordantly exactly 1 time 1326008 (12.20%) aligned concordantly >1 times ---- 421367 pairs aligned concordantly 0 times; of these: 101162 (24.01%) aligned discordantly 1 time ---- 320205 pairs aligned 0 times concordantly or discordantly; of these: 640410 mates make up the pairs; of these: 516432 (80.64%) aligned 0 times 77704 (12.13%) aligned exactly 1 time 46274 (7.23%) aligned >1 times 97.62% overall alignment rate Time searching: 00:07:40 Overall time: 00:07:40 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 8 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] 548274 / 10462489 = 0.0524 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:13:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732442/ERX2732442.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732442/ERX2732442.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732442/ERX2732442.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732442/ERX2732442.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 @ Sat, 24 Aug 2019 19:13:25: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:13:25: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:13:32: 1000000 INFO @ Sat, 24 Aug 2019 19:13:38: 2000000 INFO @ Sat, 24 Aug 2019 19:13:44: 3000000 INFO @ Sat, 24 Aug 2019 19:13:50: 4000000 INFO @ Sat, 24 Aug 2019 19:13:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732442/ERX2732442.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732442/ERX2732442.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732442/ERX2732442.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732442/ERX2732442.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 @ Sat, 24 Aug 2019 19:13:55: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:13:55: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:13:56: 5000000 INFO @ Sat, 24 Aug 2019 19:14:02: 6000000 INFO @ Sat, 24 Aug 2019 19:14:03: 1000000 INFO @ Sat, 24 Aug 2019 19:14:09: 7000000 INFO @ Sat, 24 Aug 2019 19:14:12: 2000000 INFO @ Sat, 24 Aug 2019 19:14:15: 8000000 INFO @ Sat, 24 Aug 2019 19:14:21: 3000000 INFO @ Sat, 24 Aug 2019 19:14:21: 9000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:14:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732442/ERX2732442.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732442/ERX2732442.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732442/ERX2732442.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732442/ERX2732442.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 @ Sat, 24 Aug 2019 19:14:25: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:14:25: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:14:28: 10000000 INFO @ Sat, 24 Aug 2019 19:14:29: 4000000 INFO @ Sat, 24 Aug 2019 19:14:32: 1000000 INFO @ Sat, 24 Aug 2019 19:14:34: 11000000 INFO @ Sat, 24 Aug 2019 19:14:38: 5000000 INFO @ Sat, 24 Aug 2019 19:14:39: 2000000 INFO @ Sat, 24 Aug 2019 19:14:40: 12000000 INFO @ Sat, 24 Aug 2019 19:14:46: 3000000 INFO @ Sat, 24 Aug 2019 19:14:46: 13000000 INFO @ Sat, 24 Aug 2019 19:14:46: 6000000 INFO @ Sat, 24 Aug 2019 19:14:53: 14000000 INFO @ Sat, 24 Aug 2019 19:14:53: 4000000 INFO @ Sat, 24 Aug 2019 19:14:55: 7000000 INFO @ Sat, 24 Aug 2019 19:14:59: 15000000 INFO @ Sat, 24 Aug 2019 19:15:00: 5000000 INFO @ Sat, 24 Aug 2019 19:15:04: 8000000 INFO @ Sat, 24 Aug 2019 19:15:05: 16000000 INFO @ Sat, 24 Aug 2019 19:15:07: 6000000 INFO @ Sat, 24 Aug 2019 19:15:12: 17000000 INFO @ Sat, 24 Aug 2019 19:15:12: 9000000 INFO @ Sat, 24 Aug 2019 19:15:14: 7000000 INFO @ Sat, 24 Aug 2019 19:15:18: 18000000 INFO @ Sat, 24 Aug 2019 19:15:21: 10000000 INFO @ Sat, 24 Aug 2019 19:15:22: 8000000 INFO @ Sat, 24 Aug 2019 19:15:24: 19000000 INFO @ Sat, 24 Aug 2019 19:15:29: 9000000 INFO @ Sat, 24 Aug 2019 19:15:29: 11000000 INFO @ Sat, 24 Aug 2019 19:15:31: 20000000 INFO @ Sat, 24 Aug 2019 19:15:31: #1 tag size is determined as 34 bps INFO @ Sat, 24 Aug 2019 19:15:31: #1 tag size = 34 INFO @ Sat, 24 Aug 2019 19:15:31: #1 total tags in treatment: 9902671 INFO @ Sat, 24 Aug 2019 19:15:31: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:15:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:15:32: #1 tags after filtering in treatment: 7491896 INFO @ Sat, 24 Aug 2019 19:15:32: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 24 Aug 2019 19:15:32: #1 finished! INFO @ Sat, 24 Aug 2019 19:15:32: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:15:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:15:32: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:15:32: 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 @ Sat, 24 Aug 2019 19:15:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732442/ERX2732442.05_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/ERX2732442/ERX2732442.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732442/ERX2732442.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732442/ERX2732442.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:15:36: 10000000 INFO @ Sat, 24 Aug 2019 19:15:38: 12000000 INFO @ Sat, 24 Aug 2019 19:15:43: 11000000 INFO @ Sat, 24 Aug 2019 19:15:46: 13000000 INFO @ Sat, 24 Aug 2019 19:15:50: 12000000 INFO @ Sat, 24 Aug 2019 19:15:55: 14000000 INFO @ Sat, 24 Aug 2019 19:15:57: 13000000 INFO @ Sat, 24 Aug 2019 19:16:04: 15000000 INFO @ Sat, 24 Aug 2019 19:16:04: 14000000 INFO @ Sat, 24 Aug 2019 19:16:11: 15000000 INFO @ Sat, 24 Aug 2019 19:16:12: 16000000 INFO @ Sat, 24 Aug 2019 19:16:18: 16000000 INFO @ Sat, 24 Aug 2019 19:16:20: 17000000 INFO @ Sat, 24 Aug 2019 19:16:25: 17000000 INFO @ Sat, 24 Aug 2019 19:16:29: 18000000 INFO @ Sat, 24 Aug 2019 19:16:32: 18000000 INFO @ Sat, 24 Aug 2019 19:16:37: 19000000 INFO @ Sat, 24 Aug 2019 19:16:39: 19000000 INFO @ Sat, 24 Aug 2019 19:16:46: 20000000 INFO @ Sat, 24 Aug 2019 19:16:46: 20000000 INFO @ Sat, 24 Aug 2019 19:16:47: #1 tag size is determined as 34 bps INFO @ Sat, 24 Aug 2019 19:16:47: #1 tag size = 34 INFO @ Sat, 24 Aug 2019 19:16:47: #1 total tags in treatment: 9902671 INFO @ Sat, 24 Aug 2019 19:16:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:16:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:16:47: #1 tags after filtering in treatment: 7491896 INFO @ Sat, 24 Aug 2019 19:16:47: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 24 Aug 2019 19:16:47: #1 finished! INFO @ Sat, 24 Aug 2019 19:16:47: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:16:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:16:47: #1 tag size is determined as 34 bps INFO @ Sat, 24 Aug 2019 19:16:47: #1 tag size = 34 INFO @ Sat, 24 Aug 2019 19:16:47: #1 total tags in treatment: 9902671 INFO @ Sat, 24 Aug 2019 19:16:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:16:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:16:47: #1 tags after filtering in treatment: 7491896 INFO @ Sat, 24 Aug 2019 19:16:47: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 24 Aug 2019 19:16:47: #1 finished! INFO @ Sat, 24 Aug 2019 19:16:47: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:16:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:16:48: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:16:48: 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 @ Sat, 24 Aug 2019 19:16:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732442/ERX2732442.10_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/ERX2732442/ERX2732442.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732442/ERX2732442.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732442/ERX2732442.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:16:48: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:16:48: 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 @ Sat, 24 Aug 2019 19:16:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732442/ERX2732442.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732442/ERX2732442.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732442/ERX2732442.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732442/ERX2732442.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。