Job ID = 4289242 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T05:10:02 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 ) 2019-12-10T05:14:50 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 ) 2019-12-10T05:14:50 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 : 85,176,113 reads read : 170,352,226 reads written : 85,176,113 reads 0-length : 85,176,113 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: 00:13:19 85176113 reads; of these: 85176113 (100.00%) were unpaired; of these: 6737554 (7.91%) aligned 0 times 51029165 (59.91%) aligned exactly 1 time 27409394 (32.18%) aligned >1 times 92.09% overall alignment rate Time searching: 00:13:19 Overall time: 00:13:19 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 32 files... [bam_rmdupse_core] 60624910 / 78438559 = 0.7729 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:44:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635426/SRX6635426.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635426/SRX6635426.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635426/SRX6635426.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635426/SRX6635426.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 @ Tue, 10 Dec 2019 14:44:58: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:44:58: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:45:05: 1000000 INFO @ Tue, 10 Dec 2019 14:45:12: 2000000 INFO @ Tue, 10 Dec 2019 14:45:19: 3000000 INFO @ Tue, 10 Dec 2019 14:45:27: 4000000 INFO @ Tue, 10 Dec 2019 14:45:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635426/SRX6635426.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635426/SRX6635426.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635426/SRX6635426.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635426/SRX6635426.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 @ Tue, 10 Dec 2019 14:45:28: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:45:28: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:45:34: 5000000 INFO @ Tue, 10 Dec 2019 14:45:37: 1000000 INFO @ Tue, 10 Dec 2019 14:45:42: 6000000 INFO @ Tue, 10 Dec 2019 14:45:46: 2000000 INFO @ Tue, 10 Dec 2019 14:45:50: 7000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:45:55: 3000000 INFO @ Tue, 10 Dec 2019 14:45:57: 8000000 INFO @ Tue, 10 Dec 2019 14:45:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635426/SRX6635426.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635426/SRX6635426.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635426/SRX6635426.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635426/SRX6635426.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 @ Tue, 10 Dec 2019 14:45:58: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:45:58: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:46:05: 4000000 INFO @ Tue, 10 Dec 2019 14:46:06: 9000000 INFO @ Tue, 10 Dec 2019 14:46:07: 1000000 INFO @ Tue, 10 Dec 2019 14:46:15: 5000000 INFO @ Tue, 10 Dec 2019 14:46:15: 10000000 INFO @ Tue, 10 Dec 2019 14:46:16: 2000000 INFO @ Tue, 10 Dec 2019 14:46:24: 11000000 INFO @ Tue, 10 Dec 2019 14:46:24: 6000000 INFO @ Tue, 10 Dec 2019 14:46:25: 3000000 INFO @ Tue, 10 Dec 2019 14:46:33: 12000000 INFO @ Tue, 10 Dec 2019 14:46:33: 4000000 INFO @ Tue, 10 Dec 2019 14:46:34: 7000000 INFO @ Tue, 10 Dec 2019 14:46:42: 13000000 INFO @ Tue, 10 Dec 2019 14:46:42: 5000000 INFO @ Tue, 10 Dec 2019 14:46:43: 8000000 INFO @ Tue, 10 Dec 2019 14:46:51: 14000000 INFO @ Tue, 10 Dec 2019 14:46:51: 6000000 INFO @ Tue, 10 Dec 2019 14:46:53: 9000000 INFO @ Tue, 10 Dec 2019 14:47:00: 15000000 INFO @ Tue, 10 Dec 2019 14:47:01: 7000000 INFO @ Tue, 10 Dec 2019 14:47:03: 10000000 INFO @ Tue, 10 Dec 2019 14:47:09: 16000000 INFO @ Tue, 10 Dec 2019 14:47:09: 8000000 INFO @ Tue, 10 Dec 2019 14:47:12: 11000000 INFO @ Tue, 10 Dec 2019 14:47:18: 17000000 INFO @ Tue, 10 Dec 2019 14:47:18: 9000000 INFO @ Tue, 10 Dec 2019 14:47:22: 12000000 INFO @ Tue, 10 Dec 2019 14:47:24: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:47:24: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:47:24: #1 total tags in treatment: 17813649 INFO @ Tue, 10 Dec 2019 14:47:24: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:47:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 14:47:25: #1 tags after filtering in treatment: 17813649 INFO @ Tue, 10 Dec 2019 14:47:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:47:25: #1 finished! INFO @ Tue, 10 Dec 2019 14:47:25: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:47:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:47:26: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:47:26: 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 @ Tue, 10 Dec 2019 14:47:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635426/SRX6635426.05_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/SRX6635426/SRX6635426.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635426/SRX6635426.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635426/SRX6635426.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:47:27: 10000000 INFO @ Tue, 10 Dec 2019 14:47:31: 13000000 INFO @ Tue, 10 Dec 2019 14:47:34: 11000000 INFO @ Tue, 10 Dec 2019 14:47:40: 14000000 INFO @ Tue, 10 Dec 2019 14:47:42: 12000000 INFO @ Tue, 10 Dec 2019 14:47:49: 13000000 INFO @ Tue, 10 Dec 2019 14:47:50: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 14:47:57: 14000000 INFO @ Tue, 10 Dec 2019 14:47:59: 16000000 BigWig に変換しました。 INFO @ Tue, 10 Dec 2019 14:48:04: 15000000 INFO @ Tue, 10 Dec 2019 14:48:08: 17000000 INFO @ Tue, 10 Dec 2019 14:48:12: 16000000 INFO @ Tue, 10 Dec 2019 14:48:15: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:48:15: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:48:15: #1 total tags in treatment: 17813649 INFO @ Tue, 10 Dec 2019 14:48:15: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:48:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 14:48:16: #1 tags after filtering in treatment: 17813649 INFO @ Tue, 10 Dec 2019 14:48:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:48:16: #1 finished! INFO @ Tue, 10 Dec 2019 14:48:16: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:48:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:48:17: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:48:17: 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 @ Tue, 10 Dec 2019 14:48:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635426/SRX6635426.10_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/SRX6635426/SRX6635426.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635426/SRX6635426.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635426/SRX6635426.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:48:20: 17000000 INFO @ Tue, 10 Dec 2019 14:48:25: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:48:25: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:48:25: #1 total tags in treatment: 17813649 INFO @ Tue, 10 Dec 2019 14:48:25: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:48:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 14:48:26: #1 tags after filtering in treatment: 17813649 INFO @ Tue, 10 Dec 2019 14:48:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:48:26: #1 finished! INFO @ Tue, 10 Dec 2019 14:48:26: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:48:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:48:27: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:48:27: 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 @ Tue, 10 Dec 2019 14:48:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635426/SRX6635426.20_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/SRX6635426/SRX6635426.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635426/SRX6635426.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635426/SRX6635426.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling