Job ID = 1294519 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:37:22 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 ) 2019-06-02T23:37:22 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.25' from '172.19.7.66' 2019-06-02T23:37:22 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 '172.19.7.66' 2019-06-02T23:37:22 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/sra12/SRR/000849/SRR869904' 2019-06-02T23:37:22 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 ) 2019-06-02T23:37:22 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.25' from '172.19.7.66' 2019-06-02T23:37:22 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 '172.19.7.66' 2019-06-02T23:37:22 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/sra12/SRR/000849/SRR869904' 2019-06-02T23:37:31 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR869904' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T23:37:31 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T23:37:31 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR869904' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T23:37:31 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T23:39:38 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 ) 2019-06-02T23:40:01 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 ) 2019-06-02T23:40:40 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 ) 2019-06-02T23:40:40 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 ) 2019-06-02T23:43:18 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 ) 2019-06-02T23:46:08 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 ) 2019-06-02T23:46:26 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 ) 2019-06-02T23:49:13 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 ) 2019-06-02T23:49:13 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 : 16,318,298 reads read : 16,318,298 reads written : 16,318,298 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:04:13 16318298 reads; of these: 16318298 (100.00%) were unpaired; of these: 1096346 (6.72%) aligned 0 times 13543028 (82.99%) aligned exactly 1 time 1678924 (10.29%) aligned >1 times 93.28% overall alignment rate Time searching: 00:04:13 Overall time: 00:04:13 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 849596 / 15221952 = 0.0558 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 03 Jun 2019 09:07:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287716/SRX287716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287716/SRX287716.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287716/SRX287716.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287716/SRX287716.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 09:07:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287716/SRX287716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287716/SRX287716.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287716/SRX287716.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287716/SRX287716.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 09:07:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:07:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:07:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:07:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:07:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287716/SRX287716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287716/SRX287716.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287716/SRX287716.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287716/SRX287716.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 09:07:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:07:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:07:27: 1000000 INFO @ Mon, 03 Jun 2019 09:07:27: 1000000 INFO @ Mon, 03 Jun 2019 09:07:27: 1000000 INFO @ Mon, 03 Jun 2019 09:07:35: 2000000 INFO @ Mon, 03 Jun 2019 09:07:35: 2000000 INFO @ Mon, 03 Jun 2019 09:07:35: 2000000 INFO @ Mon, 03 Jun 2019 09:07:43: 3000000 INFO @ Mon, 03 Jun 2019 09:07:43: 3000000 INFO @ Mon, 03 Jun 2019 09:07:44: 3000000 INFO @ Mon, 03 Jun 2019 09:07:51: 4000000 INFO @ Mon, 03 Jun 2019 09:07:51: 4000000 INFO @ Mon, 03 Jun 2019 09:07:52: 4000000 INFO @ Mon, 03 Jun 2019 09:07:59: 5000000 INFO @ Mon, 03 Jun 2019 09:07:59: 5000000 INFO @ Mon, 03 Jun 2019 09:08:00: 5000000 INFO @ Mon, 03 Jun 2019 09:08:07: 6000000 INFO @ Mon, 03 Jun 2019 09:08:07: 6000000 INFO @ Mon, 03 Jun 2019 09:08:08: 6000000 INFO @ Mon, 03 Jun 2019 09:08:15: 7000000 INFO @ Mon, 03 Jun 2019 09:08:15: 7000000 INFO @ Mon, 03 Jun 2019 09:08:17: 7000000 INFO @ Mon, 03 Jun 2019 09:08:23: 8000000 INFO @ Mon, 03 Jun 2019 09:08:23: 8000000 INFO @ Mon, 03 Jun 2019 09:08:25: 8000000 INFO @ Mon, 03 Jun 2019 09:08:31: 9000000 INFO @ Mon, 03 Jun 2019 09:08:31: 9000000 INFO @ Mon, 03 Jun 2019 09:08:33: 9000000 INFO @ Mon, 03 Jun 2019 09:08:39: 10000000 INFO @ Mon, 03 Jun 2019 09:08:39: 10000000 INFO @ Mon, 03 Jun 2019 09:08:41: 10000000 INFO @ Mon, 03 Jun 2019 09:08:47: 11000000 INFO @ Mon, 03 Jun 2019 09:08:47: 11000000 INFO @ Mon, 03 Jun 2019 09:08:49: 11000000 INFO @ Mon, 03 Jun 2019 09:08:55: 12000000 INFO @ Mon, 03 Jun 2019 09:08:55: 12000000 INFO @ Mon, 03 Jun 2019 09:08:58: 12000000 INFO @ Mon, 03 Jun 2019 09:09:03: 13000000 INFO @ Mon, 03 Jun 2019 09:09:03: 13000000 INFO @ Mon, 03 Jun 2019 09:09:06: 13000000 INFO @ Mon, 03 Jun 2019 09:09:11: 14000000 INFO @ Mon, 03 Jun 2019 09:09:11: 14000000 INFO @ Mon, 03 Jun 2019 09:09:14: 14000000 INFO @ Mon, 03 Jun 2019 09:09:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:09:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:09:14: #1 total tags in treatment: 14372356 INFO @ Mon, 03 Jun 2019 09:09:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:09:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 09:09:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:09:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:09:14: #1 total tags in treatment: 14372356 INFO @ Mon, 03 Jun 2019 09:09:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:09:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 09:09:14: #1 tags after filtering in treatment: 14372356 INFO @ Mon, 03 Jun 2019 09:09:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:09:14: #1 finished! INFO @ Mon, 03 Jun 2019 09:09:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:09:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:09:14: #1 tags after filtering in treatment: 14372356 INFO @ Mon, 03 Jun 2019 09:09:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:09:14: #1 finished! INFO @ Mon, 03 Jun 2019 09:09:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:09:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:09:15: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 09:09:15: 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 @ Mon, 03 Jun 2019 09:09:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX287716/SRX287716.20_peaks.narrowPeak: No such file or directory INFO @ Mon, 03 Jun 2019 09:09:15: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 09:09:15: 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 @ Mon, 03 Jun 2019 09:09:15: Process for pairing-model is terminated! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287716/SRX287716.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287716/SRX287716.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287716/SRX287716.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling cut: /home/okishinya/chipatlas/results/dm3/SRX287716/SRX287716.05_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/dm3/SRX287716/SRX287716.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287716/SRX287716.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287716/SRX287716.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:09:17: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:09:17: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:09:17: #1 total tags in treatment: 14372356 INFO @ Mon, 03 Jun 2019 09:09:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:09:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 09:09:17: #1 tags after filtering in treatment: 14372356 INFO @ Mon, 03 Jun 2019 09:09:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:09:17: #1 finished! INFO @ Mon, 03 Jun 2019 09:09:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:09:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:09:18: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 09:09:18: 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 @ Mon, 03 Jun 2019 09:09:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX287716/SRX287716.10_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/dm3/SRX287716/SRX287716.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287716/SRX287716.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287716/SRX287716.10_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。