Job ID = 2640750 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T09:55:10 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 : 11,157,104 reads read : 22,314,208 reads written : 22,314,208 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: 00:07:25 11157104 reads; of these: 11157104 (100.00%) were paired; of these: 422125 (3.78%) aligned concordantly 0 times 9515080 (85.28%) aligned concordantly exactly 1 time 1219899 (10.93%) aligned concordantly >1 times ---- 422125 pairs aligned concordantly 0 times; of these: 122878 (29.11%) aligned discordantly 1 time ---- 299247 pairs aligned 0 times concordantly or discordantly; of these: 598494 mates make up the pairs; of these: 482168 (80.56%) aligned 0 times 69777 (11.66%) aligned exactly 1 time 46549 (7.78%) aligned >1 times 97.84% overall alignment rate Time searching: 00:07:25 Overall time: 00:07:25 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] 452281 / 10758877 = 0.0420 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:12:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732441/ERX2732441.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732441/ERX2732441.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732441/ERX2732441.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732441/ERX2732441.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 19:12:16: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:12:16: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:12:23: 1000000 INFO @ Sat, 24 Aug 2019 19:12:30: 2000000 INFO @ Sat, 24 Aug 2019 19:12:36: 3000000 INFO @ Sat, 24 Aug 2019 19:12:43: 4000000 INFO @ Sat, 24 Aug 2019 19:12:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732441/ERX2732441.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732441/ERX2732441.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732441/ERX2732441.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732441/ERX2732441.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 19:12:46: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:12:46: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:12:50: 5000000 INFO @ Sat, 24 Aug 2019 19:12:53: 1000000 INFO @ Sat, 24 Aug 2019 19:12:57: 6000000 INFO @ Sat, 24 Aug 2019 19:13:00: 2000000 INFO @ Sat, 24 Aug 2019 19:13:04: 7000000 INFO @ Sat, 24 Aug 2019 19:13:07: 3000000 INFO @ Sat, 24 Aug 2019 19:13:11: 8000000 INFO @ Sat, 24 Aug 2019 19:13:14: 4000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:13:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732441/ERX2732441.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732441/ERX2732441.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732441/ERX2732441.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732441/ERX2732441.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 19:13:16: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:13:16: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:13:18: 9000000 INFO @ Sat, 24 Aug 2019 19:13:21: 5000000 INFO @ Sat, 24 Aug 2019 19:13:24: 1000000 INFO @ Sat, 24 Aug 2019 19:13:25: 10000000 INFO @ Sat, 24 Aug 2019 19:13:28: 6000000 INFO @ Sat, 24 Aug 2019 19:13:31: 2000000 INFO @ Sat, 24 Aug 2019 19:13:31: 11000000 INFO @ Sat, 24 Aug 2019 19:13:34: 7000000 INFO @ Sat, 24 Aug 2019 19:13:38: 3000000 INFO @ Sat, 24 Aug 2019 19:13:38: 12000000 INFO @ Sat, 24 Aug 2019 19:13:41: 8000000 INFO @ Sat, 24 Aug 2019 19:13:45: 4000000 INFO @ Sat, 24 Aug 2019 19:13:45: 13000000 INFO @ Sat, 24 Aug 2019 19:13:48: 9000000 INFO @ Sat, 24 Aug 2019 19:13:51: 5000000 INFO @ Sat, 24 Aug 2019 19:13:52: 14000000 INFO @ Sat, 24 Aug 2019 19:13:55: 10000000 INFO @ Sat, 24 Aug 2019 19:13:58: 6000000 INFO @ Sat, 24 Aug 2019 19:13:59: 15000000 INFO @ Sat, 24 Aug 2019 19:14:02: 11000000 INFO @ Sat, 24 Aug 2019 19:14:06: 7000000 INFO @ Sat, 24 Aug 2019 19:14:06: 16000000 INFO @ Sat, 24 Aug 2019 19:14:09: 12000000 INFO @ Sat, 24 Aug 2019 19:14:13: 17000000 INFO @ Sat, 24 Aug 2019 19:14:14: 8000000 INFO @ Sat, 24 Aug 2019 19:14:16: 13000000 INFO @ Sat, 24 Aug 2019 19:14:20: 18000000 INFO @ Sat, 24 Aug 2019 19:14:21: 9000000 INFO @ Sat, 24 Aug 2019 19:14:22: 14000000 INFO @ Sat, 24 Aug 2019 19:14:27: 19000000 INFO @ Sat, 24 Aug 2019 19:14:28: 10000000 INFO @ Sat, 24 Aug 2019 19:14:29: 15000000 INFO @ Sat, 24 Aug 2019 19:14:34: 20000000 INFO @ Sat, 24 Aug 2019 19:14:35: 11000000 INFO @ Sat, 24 Aug 2019 19:14:36: 16000000 INFO @ Sat, 24 Aug 2019 19:14:40: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 19:14:40: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 19:14:40: #1 total tags in treatment: 10283294 INFO @ Sat, 24 Aug 2019 19:14:40: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:14:40: #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 19:14:40: #1 tags after filtering in treatment: 7845503 INFO @ Sat, 24 Aug 2019 19:14:40: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 24 Aug 2019 19:14:40: #1 finished! INFO @ Sat, 24 Aug 2019 19:14:40: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:14:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:14:41: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:14:41: 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 19:14:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732441/ERX2732441.05_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/ERX2732441/ERX2732441.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732441/ERX2732441.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732441/ERX2732441.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:14:42: 12000000 INFO @ Sat, 24 Aug 2019 19:14:43: 17000000 INFO @ Sat, 24 Aug 2019 19:14:48: 13000000 INFO @ Sat, 24 Aug 2019 19:14:49: 18000000 INFO @ Sat, 24 Aug 2019 19:14:55: 14000000 INFO @ Sat, 24 Aug 2019 19:14:56: 19000000 INFO @ Sat, 24 Aug 2019 19:15:02: 15000000 INFO @ Sat, 24 Aug 2019 19:15:03: 20000000 INFO @ Sat, 24 Aug 2019 19:15:09: 16000000 INFO @ Sat, 24 Aug 2019 19:15:09: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 19:15:09: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 19:15:09: #1 total tags in treatment: 10283294 INFO @ Sat, 24 Aug 2019 19:15:09: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:15:09: #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 19:15:09: #1 tags after filtering in treatment: 7845503 INFO @ Sat, 24 Aug 2019 19:15:09: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 24 Aug 2019 19:15:09: #1 finished! INFO @ Sat, 24 Aug 2019 19:15:09: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:15:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:15:10: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:15:10: 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 @ Sat, 24 Aug 2019 19:15:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732441/ERX2732441.10_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/ERX2732441/ERX2732441.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732441/ERX2732441.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732441/ERX2732441.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:15:15: 17000000 INFO @ Sat, 24 Aug 2019 19:15:22: 18000000 INFO @ Sat, 24 Aug 2019 19:15:28: 19000000 INFO @ Sat, 24 Aug 2019 19:15:35: 20000000 INFO @ Sat, 24 Aug 2019 19:15:41: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 19:15:41: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 19:15:41: #1 total tags in treatment: 10283294 INFO @ Sat, 24 Aug 2019 19:15:41: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:15:41: #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 19:15:41: #1 tags after filtering in treatment: 7845503 INFO @ Sat, 24 Aug 2019 19:15:41: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 24 Aug 2019 19:15:41: #1 finished! INFO @ Sat, 24 Aug 2019 19:15:41: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:15:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:15:42: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:15:42: 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 @ Sat, 24 Aug 2019 19:15:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732441/ERX2732441.20_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/ERX2732441/ERX2732441.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732441/ERX2732441.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732441/ERX2732441.20_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。