Job ID = 2641130 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T12:30:44 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 : 10,133,073 reads read : 20,266,146 reads written : 20,266,146 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: 00:14:22 10133073 reads; of these: 10133073 (100.00%) were paired; of these: 3857542 (38.07%) aligned concordantly 0 times 5265752 (51.97%) aligned concordantly exactly 1 time 1009779 (9.97%) aligned concordantly >1 times ---- 3857542 pairs aligned concordantly 0 times; of these: 2665793 (69.11%) aligned discordantly 1 time ---- 1191749 pairs aligned 0 times concordantly or discordantly; of these: 2383498 mates make up the pairs; of these: 1203582 (50.50%) aligned 0 times 191680 (8.04%) aligned exactly 1 time 988236 (41.46%) aligned >1 times 94.06% overall alignment rate Time searching: 00:14:22 Overall time: 00:14:22 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] 434537 / 8939517 = 0.0486 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:10:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546567/SRX5546567.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546567/SRX5546567.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546567/SRX5546567.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546567/SRX5546567.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 22:10:36: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:10:36: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:10:46: 1000000 INFO @ Sat, 24 Aug 2019 22:10:55: 2000000 INFO @ Sat, 24 Aug 2019 22:11:03: 3000000 INFO @ Sat, 24 Aug 2019 22:11:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546567/SRX5546567.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546567/SRX5546567.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546567/SRX5546567.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546567/SRX5546567.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 22:11:05: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:11:05: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:11:12: 4000000 INFO @ Sat, 24 Aug 2019 22:11:19: 1000000 INFO @ Sat, 24 Aug 2019 22:11:20: 5000000 INFO @ Sat, 24 Aug 2019 22:11:29: 6000000 INFO @ Sat, 24 Aug 2019 22:11:32: 2000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:11:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546567/SRX5546567.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546567/SRX5546567.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546567/SRX5546567.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546567/SRX5546567.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 22:11:35: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:11:35: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:11:39: 7000000 INFO @ Sat, 24 Aug 2019 22:11:44: 3000000 INFO @ Sat, 24 Aug 2019 22:11:46: 1000000 INFO @ Sat, 24 Aug 2019 22:11:50: 8000000 INFO @ Sat, 24 Aug 2019 22:11:56: 2000000 INFO @ Sat, 24 Aug 2019 22:11:57: 4000000 INFO @ Sat, 24 Aug 2019 22:12:02: 9000000 INFO @ Sat, 24 Aug 2019 22:12:05: 3000000 INFO @ Sat, 24 Aug 2019 22:12:10: 5000000 INFO @ Sat, 24 Aug 2019 22:12:14: 10000000 INFO @ Sat, 24 Aug 2019 22:12:15: 4000000 INFO @ Sat, 24 Aug 2019 22:12:22: 6000000 INFO @ Sat, 24 Aug 2019 22:12:25: 11000000 INFO @ Sat, 24 Aug 2019 22:12:26: 5000000 INFO @ Sat, 24 Aug 2019 22:12:35: 7000000 INFO @ Sat, 24 Aug 2019 22:12:37: 12000000 INFO @ Sat, 24 Aug 2019 22:12:38: 6000000 INFO @ Sat, 24 Aug 2019 22:12:47: 8000000 INFO @ Sat, 24 Aug 2019 22:12:49: 13000000 INFO @ Sat, 24 Aug 2019 22:12:51: 7000000 INFO @ Sat, 24 Aug 2019 22:12:59: 9000000 INFO @ Sat, 24 Aug 2019 22:13:01: 14000000 INFO @ Sat, 24 Aug 2019 22:13:03: 8000000 INFO @ Sat, 24 Aug 2019 22:13:10: 10000000 INFO @ Sat, 24 Aug 2019 22:13:13: 15000000 INFO @ Sat, 24 Aug 2019 22:13:15: 9000000 INFO @ Sat, 24 Aug 2019 22:13:20: 11000000 INFO @ Sat, 24 Aug 2019 22:13:24: 16000000 INFO @ Sat, 24 Aug 2019 22:13:28: 10000000 INFO @ Sat, 24 Aug 2019 22:13:31: 12000000 INFO @ Sat, 24 Aug 2019 22:13:36: 17000000 INFO @ Sat, 24 Aug 2019 22:13:41: 13000000 INFO @ Sat, 24 Aug 2019 22:13:42: 11000000 INFO @ Sat, 24 Aug 2019 22:13:48: 18000000 INFO @ Sat, 24 Aug 2019 22:13:50: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:13:50: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:13:50: #1 total tags in treatment: 5957470 INFO @ Sat, 24 Aug 2019 22:13:50: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:13:50: #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 22:13:50: #1 tags after filtering in treatment: 4727222 INFO @ Sat, 24 Aug 2019 22:13:50: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 24 Aug 2019 22:13:50: #1 finished! INFO @ Sat, 24 Aug 2019 22:13:50: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:13:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:13:51: #2 number of paired peaks: 26 WARNING @ Sat, 24 Aug 2019 22:13:51: Too few paired peaks (26) 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 22:13:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546567/SRX5546567.05_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/SRX5546567/SRX5546567.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546567/SRX5546567.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546567/SRX5546567.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:13:51: 14000000 INFO @ Sat, 24 Aug 2019 22:13:55: 12000000 INFO @ Sat, 24 Aug 2019 22:14:01: 15000000 INFO @ Sat, 24 Aug 2019 22:14:06: 13000000 INFO @ Sat, 24 Aug 2019 22:14:11: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:14:20: 14000000 INFO @ Sat, 24 Aug 2019 22:14:21: 17000000 INFO @ Sat, 24 Aug 2019 22:14:31: 18000000 INFO @ Sat, 24 Aug 2019 22:14:33: 15000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 22:14:33: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:14:33: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:14:33: #1 total tags in treatment: 5957470 INFO @ Sat, 24 Aug 2019 22:14:33: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:14:33: #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 22:14:33: #1 tags after filtering in treatment: 4727222 INFO @ Sat, 24 Aug 2019 22:14:33: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 24 Aug 2019 22:14:33: #1 finished! INFO @ Sat, 24 Aug 2019 22:14:33: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:14:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:14:34: #2 number of paired peaks: 26 WARNING @ Sat, 24 Aug 2019 22:14:34: Too few paired peaks (26) 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 22:14:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546567/SRX5546567.10_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/SRX5546567/SRX5546567.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546567/SRX5546567.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546567/SRX5546567.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:14:45: 16000000 INFO @ Sat, 24 Aug 2019 22:14:58: 17000000 INFO @ Sat, 24 Aug 2019 22:15:10: 18000000 INFO @ Sat, 24 Aug 2019 22:15:12: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:15:12: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:15:12: #1 total tags in treatment: 5957470 INFO @ Sat, 24 Aug 2019 22:15:12: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:15:12: #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 22:15:12: #1 tags after filtering in treatment: 4727222 INFO @ Sat, 24 Aug 2019 22:15:12: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 24 Aug 2019 22:15:12: #1 finished! INFO @ Sat, 24 Aug 2019 22:15:12: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:15:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:15:13: #2 number of paired peaks: 26 WARNING @ Sat, 24 Aug 2019 22:15:13: Too few paired peaks (26) 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 22:15:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546567/SRX5546567.20_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/SRX5546567/SRX5546567.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546567/SRX5546567.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546567/SRX5546567.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling