Job ID = 2007755 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:26:52 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 ) 2019-07-05T07:26:52 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.96' 2019-07-05T07:26:52 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' (130.14.250.26) from '172.19.7.96' 2019-07-05T07:26:52 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/sos/sra-pub-run-2/ERR467462/ERR467462.1' 2019-07-05T07:26:52 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR467462' ) -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-07-05T07:26:52 fasterq-dump.2.9.6 err: perform_fastq_split_file_join().make_fastq_csra_iter() -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-07-05T07:26:52 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 ) 2019-07-05T07:26:52 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.96' 2019-07-05T07:26:52 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' (130.14.250.26) from '172.19.7.96' 2019-07-05T07:26:52 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/sos/sra-pub-run-2/ERR467462/ERR467462.1' 2019-07-05T07:26:52 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR467462' ) -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-07-05T07:26:52 fasterq-dump.2.9.6 err: perform_fastq_split_file_join().make_fastq_csra_iter() -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-07-05T07:26:52 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 ) 2019-07-05T07:26:52 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.96' 2019-07-05T07:26:52 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' (130.14.250.26) from '172.19.7.96' 2019-07-05T07:26:52 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/sos/sra-pub-run-2/ERR467462/ERR467462.1' 2019-07-05T07:26:52 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR467462' ) -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-07-05T07:26:52 fasterq-dump.2.9.6 err: perform_fastq_split_file_join().make_fastq_csra_iter() -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) spots read : 566,565 reads read : 1,133,130 reads written : 1,133,130 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: 00:00:18 566565 reads; of these: 566565 (100.00%) were paired; of these: 79353 (14.01%) aligned concordantly 0 times 448046 (79.08%) aligned concordantly exactly 1 time 39166 (6.91%) aligned concordantly >1 times ---- 79353 pairs aligned concordantly 0 times; of these: 46999 (59.23%) aligned discordantly 1 time ---- 32354 pairs aligned 0 times concordantly or discordantly; of these: 64708 mates make up the pairs; of these: 45990 (71.07%) aligned 0 times 9311 (14.39%) aligned exactly 1 time 9407 (14.54%) aligned >1 times 95.94% overall alignment rate Time searching: 00:00:18 Overall time: 00:00:18 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 559 / 532650 = 0.0010 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 @ Fri, 05 Jul 2019 16:31:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433697/ERX433697.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433697/ERX433697.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433697/ERX433697.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433697/ERX433697.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 @ Fri, 05 Jul 2019 16:31:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:31:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:31:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433697/ERX433697.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433697/ERX433697.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433697/ERX433697.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433697/ERX433697.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 @ Fri, 05 Jul 2019 16:31:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:31:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:31:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433697/ERX433697.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433697/ERX433697.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433697/ERX433697.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433697/ERX433697.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 @ Fri, 05 Jul 2019 16:31:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:31:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:31:54: 1000000 INFO @ Fri, 05 Jul 2019 16:31:54: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:31:54: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:31:54: #1 total tags in treatment: 486672 INFO @ Fri, 05 Jul 2019 16:31:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:31:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:31:54: #1 tags after filtering in treatment: 480979 INFO @ Fri, 05 Jul 2019 16:31:54: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:31:54: #1 finished! INFO @ Fri, 05 Jul 2019 16:31:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:31:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:31:54: #2 number of paired peaks: 19 WARNING @ Fri, 05 Jul 2019 16:31:54: Too few paired peaks (19) 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 @ Fri, 05 Jul 2019 16:31:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX433697/ERX433697.05_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/ERX433697/ERX433697.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX433697/ERX433697.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX433697/ERX433697.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:31:55: 1000000 INFO @ Fri, 05 Jul 2019 16:31:55: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:31:55: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:31:55: #1 total tags in treatment: 486672 INFO @ Fri, 05 Jul 2019 16:31:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:31:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:31:55: #1 tags after filtering in treatment: 480979 INFO @ Fri, 05 Jul 2019 16:31:55: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:31:55: #1 finished! INFO @ Fri, 05 Jul 2019 16:31:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:31:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:31:55: #2 number of paired peaks: 19 WARNING @ Fri, 05 Jul 2019 16:31:55: Too few paired peaks (19) 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 @ Fri, 05 Jul 2019 16:31:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX433697/ERX433697.10_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/ERX433697/ERX433697.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX433697/ERX433697.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX433697/ERX433697.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:31:55: 1000000 INFO @ Fri, 05 Jul 2019 16:31:56: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:31:56: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:31:56: #1 total tags in treatment: 486672 INFO @ Fri, 05 Jul 2019 16:31:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:31:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:31:56: #1 tags after filtering in treatment: 480979 INFO @ Fri, 05 Jul 2019 16:31:56: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:31:56: #1 finished! INFO @ Fri, 05 Jul 2019 16:31:56: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:31:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:31:56: #2 number of paired peaks: 19 WARNING @ Fri, 05 Jul 2019 16:31:56: Too few paired peaks (19) 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 @ Fri, 05 Jul 2019 16:31:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX433697/ERX433697.20_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/ERX433697/ERX433697.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX433697/ERX433697.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX433697/ERX433697.20_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。