Job ID = 4289289 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T04:59:27 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 ) 2019-12-10T05:01:04 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 ) 2019-12-10T05:06:43 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 ) 2019-12-10T05:08:35 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 : 35,463,489 reads read : 70,926,978 reads written : 35,463,489 reads 0-length : 35,463,489 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: 00:07:42 35463489 reads; of these: 35463489 (100.00%) were unpaired; of these: 1296356 (3.66%) aligned 0 times 26895574 (75.84%) aligned exactly 1 time 7271559 (20.50%) aligned >1 times 96.34% overall alignment rate Time searching: 00:07:42 Overall time: 00:07:42 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 16 files... [bam_rmdupse_core] 22142769 / 34167133 = 0.6481 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:26:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635438/SRX6635438.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635438/SRX6635438.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635438/SRX6635438.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635438/SRX6635438.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 14:26:50: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:26:50: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:26:57: 1000000 INFO @ Tue, 10 Dec 2019 14:27:05: 2000000 INFO @ Tue, 10 Dec 2019 14:27:13: 3000000 INFO @ Tue, 10 Dec 2019 14:27:20: 4000000 INFO @ Tue, 10 Dec 2019 14:27:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635438/SRX6635438.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635438/SRX6635438.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635438/SRX6635438.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635438/SRX6635438.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 14:27:20: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:27:20: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:27:27: 5000000 INFO @ Tue, 10 Dec 2019 14:27:31: 1000000 INFO @ Tue, 10 Dec 2019 14:27:34: 6000000 INFO @ Tue, 10 Dec 2019 14:27:41: 2000000 INFO @ Tue, 10 Dec 2019 14:27:41: 7000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:27:48: 8000000 INFO @ Tue, 10 Dec 2019 14:27:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635438/SRX6635438.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635438/SRX6635438.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635438/SRX6635438.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635438/SRX6635438.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 14:27:50: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:27:50: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:27:51: 3000000 INFO @ Tue, 10 Dec 2019 14:27:55: 9000000 INFO @ Tue, 10 Dec 2019 14:27:59: 1000000 INFO @ Tue, 10 Dec 2019 14:28:02: 4000000 INFO @ Tue, 10 Dec 2019 14:28:03: 10000000 INFO @ Tue, 10 Dec 2019 14:28:07: 2000000 INFO @ Tue, 10 Dec 2019 14:28:10: 11000000 INFO @ Tue, 10 Dec 2019 14:28:13: 5000000 INFO @ Tue, 10 Dec 2019 14:28:15: 3000000 INFO @ Tue, 10 Dec 2019 14:28:17: 12000000 INFO @ Tue, 10 Dec 2019 14:28:18: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:28:18: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:28:18: #1 total tags in treatment: 12024364 INFO @ Tue, 10 Dec 2019 14:28:18: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:28:18: #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 14:28:18: #1 tags after filtering in treatment: 12024364 INFO @ Tue, 10 Dec 2019 14:28:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:28:18: #1 finished! INFO @ Tue, 10 Dec 2019 14:28:18: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:28:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:28:19: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:28:19: 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 14:28:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635438/SRX6635438.05_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/SRX6635438/SRX6635438.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635438/SRX6635438.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635438/SRX6635438.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:28:23: 6000000 INFO @ Tue, 10 Dec 2019 14:28:24: 4000000 INFO @ Tue, 10 Dec 2019 14:28:31: 5000000 INFO @ Tue, 10 Dec 2019 14:28:33: 7000000 INFO @ Tue, 10 Dec 2019 14:28:39: 6000000 INFO @ Tue, 10 Dec 2019 14:28:43: 8000000 INFO @ Tue, 10 Dec 2019 14:28:47: 7000000 INFO @ Tue, 10 Dec 2019 14:28:52: 9000000 INFO @ Tue, 10 Dec 2019 14:28:55: 8000000 INFO @ Tue, 10 Dec 2019 14:29:02: 10000000 INFO @ Tue, 10 Dec 2019 14:29:02: 9000000 INFO @ Tue, 10 Dec 2019 14:29:10: 10000000 INFO @ Tue, 10 Dec 2019 14:29:12: 11000000 INFO @ Tue, 10 Dec 2019 14:29:17: 11000000 INFO @ Tue, 10 Dec 2019 14:29:21: 12000000 INFO @ Tue, 10 Dec 2019 14:29:21: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:29:21: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:29:21: #1 total tags in treatment: 12024364 INFO @ Tue, 10 Dec 2019 14:29:21: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:29:21: #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 14:29:21: #1 tags after filtering in treatment: 12024364 INFO @ Tue, 10 Dec 2019 14:29:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:29:21: #1 finished! INFO @ Tue, 10 Dec 2019 14:29:21: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:29:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:29:22: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:29:22: 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 14:29:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635438/SRX6635438.10_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/SRX6635438/SRX6635438.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635438/SRX6635438.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635438/SRX6635438.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:29:24: 12000000 INFO @ Tue, 10 Dec 2019 14:29:25: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:29:25: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:29:25: #1 total tags in treatment: 12024364 INFO @ Tue, 10 Dec 2019 14:29:25: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:29:25: #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 14:29:25: #1 tags after filtering in treatment: 12024364 INFO @ Tue, 10 Dec 2019 14:29:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:29:25: #1 finished! INFO @ Tue, 10 Dec 2019 14:29:25: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:29:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:29:26: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:29:26: 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 14:29:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635438/SRX6635438.20_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/SRX6635438/SRX6635438.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635438/SRX6635438.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635438/SRX6635438.20_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。