Job ID = 4306408 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-12T13:26:57 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -76 ( NET - Reading information from the socket failed ) 2019-12-12T13:26:57 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.28' from '172.19.7.70' 2019-12-12T13:26:57 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (130.14.250.28) from '172.19.7.70' 2019-12-12T13:26:57 fasterq-dump.2.9.6 err: connection failed while opening file within cryptographic module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra53/SRR/006039/SRR6184435' 2019-12-12T13:26:57 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR6184435', 'SEQUENCE', 'NAME' ).VDBManagerOpenDBRead() -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) spots read : 15,229,454 reads read : 30,458,908 reads written : 15,229,454 reads 0-length : 15,229,454 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: 00:03:02 15229454 reads; of these: 15229454 (100.00%) were unpaired; of these: 683680 (4.49%) aligned 0 times 12577613 (82.59%) aligned exactly 1 time 1968161 (12.92%) aligned >1 times 95.51% overall alignment rate Time searching: 00:03:02 Overall time: 00:03:02 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_rmdupse_core] 7007004 / 14545774 = 0.4817 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 22:40:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3294583/SRX3294583.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3294583/SRX3294583.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3294583/SRX3294583.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3294583/SRX3294583.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 @ Thu, 12 Dec 2019 22:40:00: #1 read tag files... INFO @ Thu, 12 Dec 2019 22:40:00: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 22:40:11: 1000000 INFO @ Thu, 12 Dec 2019 22:40:22: 2000000 INFO @ Thu, 12 Dec 2019 22:40:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3294583/SRX3294583.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3294583/SRX3294583.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3294583/SRX3294583.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3294583/SRX3294583.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 @ Thu, 12 Dec 2019 22:40:30: #1 read tag files... INFO @ Thu, 12 Dec 2019 22:40:30: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 22:40:32: 3000000 INFO @ Thu, 12 Dec 2019 22:40:42: 1000000 INFO @ Thu, 12 Dec 2019 22:40:43: 4000000 INFO @ Thu, 12 Dec 2019 22:40:54: 5000000 INFO @ Thu, 12 Dec 2019 22:40:54: 2000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 22:41:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3294583/SRX3294583.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3294583/SRX3294583.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3294583/SRX3294583.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3294583/SRX3294583.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 @ Thu, 12 Dec 2019 22:41:00: #1 read tag files... INFO @ Thu, 12 Dec 2019 22:41:00: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 22:41:04: 6000000 INFO @ Thu, 12 Dec 2019 22:41:05: 3000000 INFO @ Thu, 12 Dec 2019 22:41:08: 1000000 INFO @ Thu, 12 Dec 2019 22:41:14: 7000000 INFO @ Thu, 12 Dec 2019 22:41:15: 4000000 INFO @ Thu, 12 Dec 2019 22:41:17: 2000000 INFO @ Thu, 12 Dec 2019 22:41:20: #1 tag size is determined as 51 bps INFO @ Thu, 12 Dec 2019 22:41:20: #1 tag size = 51 INFO @ Thu, 12 Dec 2019 22:41:20: #1 total tags in treatment: 7538770 INFO @ Thu, 12 Dec 2019 22:41:20: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 22:41:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 22:41:20: #1 tags after filtering in treatment: 7538770 INFO @ Thu, 12 Dec 2019 22:41:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 22:41:20: #1 finished! INFO @ Thu, 12 Dec 2019 22:41:20: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 22:41:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 22:41:21: #2 number of paired peaks: 0 WARNING @ Thu, 12 Dec 2019 22:41:21: 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 @ Thu, 12 Dec 2019 22:41:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3294583/SRX3294583.05_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/SRX3294583/SRX3294583.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294583/SRX3294583.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294583/SRX3294583.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 22:41:25: 3000000 INFO @ Thu, 12 Dec 2019 22:41:26: 5000000 INFO @ Thu, 12 Dec 2019 22:41:33: 4000000 INFO @ Thu, 12 Dec 2019 22:41:36: 6000000 INFO @ Thu, 12 Dec 2019 22:41:41: 5000000 INFO @ Thu, 12 Dec 2019 22:41:46: 7000000 INFO @ Thu, 12 Dec 2019 22:41:49: 6000000 INFO @ Thu, 12 Dec 2019 22:41:51: #1 tag size is determined as 51 bps INFO @ Thu, 12 Dec 2019 22:41:51: #1 tag size = 51 INFO @ Thu, 12 Dec 2019 22:41:51: #1 total tags in treatment: 7538770 INFO @ Thu, 12 Dec 2019 22:41:51: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 22:41:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 22:41:51: #1 tags after filtering in treatment: 7538770 INFO @ Thu, 12 Dec 2019 22:41:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 22:41:51: #1 finished! INFO @ Thu, 12 Dec 2019 22:41:51: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 22:41:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 22:41:52: #2 number of paired peaks: 0 WARNING @ Thu, 12 Dec 2019 22:41:52: 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 @ Thu, 12 Dec 2019 22:41:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3294583/SRX3294583.10_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/SRX3294583/SRX3294583.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294583/SRX3294583.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294583/SRX3294583.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 22:41:57: 7000000 INFO @ Thu, 12 Dec 2019 22:42:01: #1 tag size is determined as 51 bps INFO @ Thu, 12 Dec 2019 22:42:01: #1 tag size = 51 INFO @ Thu, 12 Dec 2019 22:42:01: #1 total tags in treatment: 7538770 INFO @ Thu, 12 Dec 2019 22:42:01: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 22:42:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 22:42:01: #1 tags after filtering in treatment: 7538770 INFO @ Thu, 12 Dec 2019 22:42:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 22:42:01: #1 finished! INFO @ Thu, 12 Dec 2019 22:42:01: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 22:42:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 22:42:02: #2 number of paired peaks: 0 WARNING @ Thu, 12 Dec 2019 22:42:02: 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 @ Thu, 12 Dec 2019 22:42:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3294583/SRX3294583.20_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/SRX3294583/SRX3294583.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294583/SRX3294583.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3294583/SRX3294583.20_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。