Job ID = 4289216 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T04:55:35 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 ) 2019-12-10T04:55:35 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 ) 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 ) 2019-12-10T05:06:43 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 ) 2019-12-10T05:07:55 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 ) 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 ) spots read : 82,052,699 reads read : 164,105,398 reads written : 82,052,699 reads 0-length : 82,052,699 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: 00:13:44 82052699 reads; of these: 82052699 (100.00%) were unpaired; of these: 2528449 (3.08%) aligned 0 times 63716610 (77.65%) aligned exactly 1 time 15807640 (19.27%) aligned >1 times 96.92% overall alignment rate Time searching: 00:13:44 Overall time: 00:13:44 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 36 files... [bam_rmdupse_core] 58646825 / 79524250 = 0.7375 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:39:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635421/SRX6635421.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635421/SRX6635421.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635421/SRX6635421.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635421/SRX6635421.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 14:39:46: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:39:46: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:39:55: 1000000 INFO @ Tue, 10 Dec 2019 14:40:03: 2000000 INFO @ Tue, 10 Dec 2019 14:40:11: 3000000 INFO @ Tue, 10 Dec 2019 14:40:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635421/SRX6635421.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635421/SRX6635421.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635421/SRX6635421.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635421/SRX6635421.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 14:40:16: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:40:16: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:40:18: 4000000 INFO @ Tue, 10 Dec 2019 14:40:24: 1000000 INFO @ Tue, 10 Dec 2019 14:40:26: 5000000 INFO @ Tue, 10 Dec 2019 14:40:32: 2000000 INFO @ Tue, 10 Dec 2019 14:40:34: 6000000 INFO @ Tue, 10 Dec 2019 14:40:41: 3000000 INFO @ Tue, 10 Dec 2019 14:40:42: 7000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:40:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6635421/SRX6635421.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6635421/SRX6635421.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6635421/SRX6635421.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6635421/SRX6635421.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 14:40:46: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:40:46: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:40:50: 8000000 INFO @ Tue, 10 Dec 2019 14:40:50: 4000000 INFO @ Tue, 10 Dec 2019 14:40:53: 1000000 INFO @ Tue, 10 Dec 2019 14:40:57: 9000000 INFO @ Tue, 10 Dec 2019 14:40:58: 5000000 INFO @ Tue, 10 Dec 2019 14:41:02: 2000000 INFO @ Tue, 10 Dec 2019 14:41:05: 10000000 INFO @ Tue, 10 Dec 2019 14:41:07: 6000000 INFO @ Tue, 10 Dec 2019 14:41:10: 3000000 INFO @ Tue, 10 Dec 2019 14:41:12: 11000000 INFO @ Tue, 10 Dec 2019 14:41:16: 7000000 INFO @ Tue, 10 Dec 2019 14:41:18: 4000000 INFO @ Tue, 10 Dec 2019 14:41:19: 12000000 INFO @ Tue, 10 Dec 2019 14:41:24: 8000000 INFO @ Tue, 10 Dec 2019 14:41:26: 13000000 INFO @ Tue, 10 Dec 2019 14:41:26: 5000000 INFO @ Tue, 10 Dec 2019 14:41:33: 14000000 INFO @ Tue, 10 Dec 2019 14:41:34: 9000000 INFO @ Tue, 10 Dec 2019 14:41:35: 6000000 INFO @ Tue, 10 Dec 2019 14:41:40: 15000000 INFO @ Tue, 10 Dec 2019 14:41:43: 10000000 INFO @ Tue, 10 Dec 2019 14:41:43: 7000000 INFO @ Tue, 10 Dec 2019 14:41:47: 16000000 INFO @ Tue, 10 Dec 2019 14:41:51: 8000000 INFO @ Tue, 10 Dec 2019 14:41:51: 11000000 INFO @ Tue, 10 Dec 2019 14:41:54: 17000000 INFO @ Tue, 10 Dec 2019 14:41:59: 9000000 INFO @ Tue, 10 Dec 2019 14:42:00: 12000000 INFO @ Tue, 10 Dec 2019 14:42:01: 18000000 INFO @ Tue, 10 Dec 2019 14:42:08: 10000000 INFO @ Tue, 10 Dec 2019 14:42:08: 13000000 INFO @ Tue, 10 Dec 2019 14:42:08: 19000000 INFO @ Tue, 10 Dec 2019 14:42:15: 20000000 INFO @ Tue, 10 Dec 2019 14:42:16: 11000000 INFO @ Tue, 10 Dec 2019 14:42:16: 14000000 INFO @ Tue, 10 Dec 2019 14:42:21: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:42:21: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:42:21: #1 total tags in treatment: 20877425 INFO @ Tue, 10 Dec 2019 14:42:21: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:42:21: #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 14:42:22: #1 tags after filtering in treatment: 20877425 INFO @ Tue, 10 Dec 2019 14:42:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:42:22: #1 finished! INFO @ Tue, 10 Dec 2019 14:42:22: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:42:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:42:23: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:42:23: 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 14:42:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635421/SRX6635421.05_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/SRX6635421/SRX6635421.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635421/SRX6635421.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635421/SRX6635421.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:42:24: 12000000 INFO @ Tue, 10 Dec 2019 14:42:25: 15000000 INFO @ Tue, 10 Dec 2019 14:42:32: 13000000 INFO @ Tue, 10 Dec 2019 14:42:33: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 14:42:41: 14000000 INFO @ Tue, 10 Dec 2019 14:42:41: 17000000 BigWig に変換しました。 INFO @ Tue, 10 Dec 2019 14:42:49: 15000000 INFO @ Tue, 10 Dec 2019 14:42:49: 18000000 INFO @ Tue, 10 Dec 2019 14:42:57: 16000000 INFO @ Tue, 10 Dec 2019 14:42:58: 19000000 INFO @ Tue, 10 Dec 2019 14:43:05: 17000000 INFO @ Tue, 10 Dec 2019 14:43:07: 20000000 INFO @ Tue, 10 Dec 2019 14:43:13: 18000000 INFO @ Tue, 10 Dec 2019 14:43:14: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:43:14: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:43:14: #1 total tags in treatment: 20877425 INFO @ Tue, 10 Dec 2019 14:43:14: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:43:14: #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 14:43:15: #1 tags after filtering in treatment: 20877425 INFO @ Tue, 10 Dec 2019 14:43:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:43:15: #1 finished! INFO @ Tue, 10 Dec 2019 14:43:15: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:43:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:43:16: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:43:16: 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 14:43:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635421/SRX6635421.10_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/SRX6635421/SRX6635421.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635421/SRX6635421.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635421/SRX6635421.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:43:21: 19000000 INFO @ Tue, 10 Dec 2019 14:43:29: 20000000 INFO @ Tue, 10 Dec 2019 14:43:37: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:43:37: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:43:37: #1 total tags in treatment: 20877425 INFO @ Tue, 10 Dec 2019 14:43:37: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:43:37: #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 14:43:37: #1 tags after filtering in treatment: 20877425 INFO @ Tue, 10 Dec 2019 14:43:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:43:37: #1 finished! INFO @ Tue, 10 Dec 2019 14:43:37: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:43:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:43:39: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:43:39: 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 14:43:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6635421/SRX6635421.20_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/SRX6635421/SRX6635421.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635421/SRX6635421.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6635421/SRX6635421.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling