Job ID = 4289435 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T05:25:34 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 ) 2019-12-10T05:25:34 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.28' from '172.19.7.60' 2019-12-10T05:25:34 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 '172.19.7.60' 2019-12-10T05:25:34 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/sra25/SRR/009696/SRR9929315' 2019-12-10T05:25:43 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR9929315', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-12-10T05:42:10 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 21,918,962 reads read : 21,918,962 reads written : 21,918,962 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: 00:04:00 21918962 reads; of these: 21918962 (100.00%) were unpaired; of these: 1451037 (6.62%) aligned 0 times 18625052 (84.97%) aligned exactly 1 time 1842873 (8.41%) aligned >1 times 93.38% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 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 12 files... [bam_rmdupse_core] 12321786 / 20467925 = 0.6020 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:53:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678262/SRX6678262.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678262/SRX6678262.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678262/SRX6678262.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678262/SRX6678262.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 14:53:02: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:53:02: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:53:10: 1000000 INFO @ Tue, 10 Dec 2019 14:53:18: 2000000 INFO @ Tue, 10 Dec 2019 14:53:26: 3000000 INFO @ Tue, 10 Dec 2019 14:53:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678262/SRX6678262.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678262/SRX6678262.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678262/SRX6678262.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678262/SRX6678262.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 14:53:32: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:53:32: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:53:34: 4000000 INFO @ Tue, 10 Dec 2019 14:53:41: 1000000 INFO @ Tue, 10 Dec 2019 14:53:42: 5000000 INFO @ Tue, 10 Dec 2019 14:53:49: 2000000 INFO @ Tue, 10 Dec 2019 14:53:50: 6000000 INFO @ Tue, 10 Dec 2019 14:53:57: 3000000 INFO @ Tue, 10 Dec 2019 14:53:58: 7000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:54:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678262/SRX6678262.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678262/SRX6678262.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678262/SRX6678262.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678262/SRX6678262.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 14:54:02: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:54:02: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:54:06: 4000000 INFO @ Tue, 10 Dec 2019 14:54:06: 8000000 INFO @ Tue, 10 Dec 2019 14:54:07: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:54:07: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:54:07: #1 total tags in treatment: 8146139 INFO @ Tue, 10 Dec 2019 14:54:07: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:54:07: #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 14:54:08: #1 tags after filtering in treatment: 8146139 INFO @ Tue, 10 Dec 2019 14:54:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:54:08: #1 finished! INFO @ Tue, 10 Dec 2019 14:54:08: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:54:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:54:08: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:54:08: 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 14:54:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678262/SRX6678262.05_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/SRX6678262/SRX6678262.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678262/SRX6678262.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678262/SRX6678262.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:54:10: 1000000 INFO @ Tue, 10 Dec 2019 14:54:14: 5000000 INFO @ Tue, 10 Dec 2019 14:54:18: 2000000 INFO @ Tue, 10 Dec 2019 14:54:22: 6000000 INFO @ Tue, 10 Dec 2019 14:54:26: 3000000 INFO @ Tue, 10 Dec 2019 14:54:30: 7000000 INFO @ Tue, 10 Dec 2019 14:54:34: 4000000 INFO @ Tue, 10 Dec 2019 14:54:38: 8000000 INFO @ Tue, 10 Dec 2019 14:54:39: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:54:39: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:54:39: #1 total tags in treatment: 8146139 INFO @ Tue, 10 Dec 2019 14:54:39: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:54:39: #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 14:54:40: #1 tags after filtering in treatment: 8146139 INFO @ Tue, 10 Dec 2019 14:54:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:54:40: #1 finished! INFO @ Tue, 10 Dec 2019 14:54:40: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:54:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:54:40: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:54:40: 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 14:54:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678262/SRX6678262.10_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/SRX6678262/SRX6678262.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678262/SRX6678262.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678262/SRX6678262.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:54:42: 5000000 INFO @ Tue, 10 Dec 2019 14:54:50: 6000000 INFO @ Tue, 10 Dec 2019 14:54:58: 7000000 INFO @ Tue, 10 Dec 2019 14:55:06: 8000000 INFO @ Tue, 10 Dec 2019 14:55:07: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:55:07: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:55:07: #1 total tags in treatment: 8146139 INFO @ Tue, 10 Dec 2019 14:55:07: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:55:07: #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 14:55:07: #1 tags after filtering in treatment: 8146139 INFO @ Tue, 10 Dec 2019 14:55:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:55:07: #1 finished! INFO @ Tue, 10 Dec 2019 14:55:07: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:55:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:55:07: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:55:07: 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 14:55:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678262/SRX6678262.20_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/SRX6678262/SRX6678262.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678262/SRX6678262.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678262/SRX6678262.20_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。