Job ID = 4289358 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T05:18:27 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 ) 2019-12-10T05:18:27 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.25' from '172.19.7.60' 2019-12-10T05:18:27 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' (130.14.250.25) from '172.19.7.60' 2019-12-10T05:18:27 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/sra57/SRR/009696/SRR9929305' 2019-12-10T05:18:37 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR9929305' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-12-10T05:18:37 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-12-10T05:26:09 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 : 24,304,250 reads read : 24,304,250 reads written : 24,304,250 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR9929305.sra.cache’: 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: 00:05:00 24304250 reads; of these: 24304250 (100.00%) were unpaired; of these: 836333 (3.44%) aligned 0 times 21401271 (88.06%) aligned exactly 1 time 2066646 (8.50%) aligned >1 times 96.56% overall alignment rate Time searching: 00:05:01 Overall time: 00:05:01 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] 11861620 / 23467917 = 0.5054 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:47:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678252/SRX6678252.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678252/SRX6678252.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678252/SRX6678252.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678252/SRX6678252.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 14:47:59: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:47:59: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:48:06: 1000000 INFO @ Tue, 10 Dec 2019 14:48:13: 2000000 INFO @ Tue, 10 Dec 2019 14:48:20: 3000000 INFO @ Tue, 10 Dec 2019 14:48:28: 4000000 INFO @ Tue, 10 Dec 2019 14:48:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678252/SRX6678252.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678252/SRX6678252.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678252/SRX6678252.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678252/SRX6678252.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 14:48:29: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:48:29: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:48:35: 5000000 INFO @ Tue, 10 Dec 2019 14:48:37: 1000000 INFO @ Tue, 10 Dec 2019 14:48:42: 6000000 INFO @ Tue, 10 Dec 2019 14:48:46: 2000000 INFO @ Tue, 10 Dec 2019 14:48:50: 7000000 INFO @ Tue, 10 Dec 2019 14:48:55: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:48:57: 8000000 INFO @ Tue, 10 Dec 2019 14:48:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6678252/SRX6678252.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6678252/SRX6678252.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6678252/SRX6678252.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6678252/SRX6678252.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 14:48:59: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:48:59: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:49:04: 4000000 INFO @ Tue, 10 Dec 2019 14:49:05: 9000000 INFO @ Tue, 10 Dec 2019 14:49:06: 1000000 INFO @ Tue, 10 Dec 2019 14:49:12: 10000000 INFO @ Tue, 10 Dec 2019 14:49:12: 5000000 INFO @ Tue, 10 Dec 2019 14:49:13: 2000000 INFO @ Tue, 10 Dec 2019 14:49:19: 11000000 INFO @ Tue, 10 Dec 2019 14:49:20: 3000000 INFO @ Tue, 10 Dec 2019 14:49:21: 6000000 INFO @ Tue, 10 Dec 2019 14:49:23: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:49:23: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:49:23: #1 total tags in treatment: 11606297 INFO @ Tue, 10 Dec 2019 14:49:23: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:49:23: #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 14:49:24: #1 tags after filtering in treatment: 11606297 INFO @ Tue, 10 Dec 2019 14:49:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:49:24: #1 finished! INFO @ Tue, 10 Dec 2019 14:49:24: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:49:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:49:24: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:49:24: 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 14:49:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678252/SRX6678252.05_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/SRX6678252/SRX6678252.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678252/SRX6678252.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678252/SRX6678252.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:49:27: 4000000 INFO @ Tue, 10 Dec 2019 14:49:30: 7000000 INFO @ Tue, 10 Dec 2019 14:49:33: 5000000 INFO @ Tue, 10 Dec 2019 14:49:39: 8000000 INFO @ Tue, 10 Dec 2019 14:49:40: 6000000 INFO @ Tue, 10 Dec 2019 14:49:47: 7000000 INFO @ Tue, 10 Dec 2019 14:49:47: 9000000 INFO @ Tue, 10 Dec 2019 14:49:54: 8000000 INFO @ Tue, 10 Dec 2019 14:49:56: 10000000 INFO @ Tue, 10 Dec 2019 14:50:01: 9000000 INFO @ Tue, 10 Dec 2019 14:50:04: 11000000 INFO @ Tue, 10 Dec 2019 14:50:07: 10000000 INFO @ Tue, 10 Dec 2019 14:50:09: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:50:09: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:50:09: #1 total tags in treatment: 11606297 INFO @ Tue, 10 Dec 2019 14:50:09: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:50:09: #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 14:50:09: #1 tags after filtering in treatment: 11606297 INFO @ Tue, 10 Dec 2019 14:50:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:50:09: #1 finished! INFO @ Tue, 10 Dec 2019 14:50:09: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:50:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:50:10: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:50:10: 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 14:50:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678252/SRX6678252.10_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/SRX6678252/SRX6678252.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678252/SRX6678252.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678252/SRX6678252.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:50:14: 11000000 INFO @ Tue, 10 Dec 2019 14:50:18: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 14:50:18: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 14:50:18: #1 total tags in treatment: 11606297 INFO @ Tue, 10 Dec 2019 14:50:18: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:50:18: #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 14:50:18: #1 tags after filtering in treatment: 11606297 INFO @ Tue, 10 Dec 2019 14:50:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:50:18: #1 finished! INFO @ Tue, 10 Dec 2019 14:50:18: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:50:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:50:19: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:50:19: 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 14:50:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6678252/SRX6678252.20_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/SRX6678252/SRX6678252.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678252/SRX6678252.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6678252/SRX6678252.20_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。