Job ID = 2007921 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:40:37 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T07:40:37 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-2/ERR506359/ERR506359.1' 2019-07-05T07:40:37 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'ERR506359', 'SEQUENCE', 'CMP_READ' ).VDBManagerOpenDBRead() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:41 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T07:40:41 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-2/ERR506359/ERR506359.1' 2019-07-05T07:40:41 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506359' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:46 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T07:40:46 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-2/ERR506359/ERR506359.1' 2019-07-05T07:40:46 fasterq-dump.2.9.6 err: invalid accession 'ERR506359' 2019-07-05T07:41:01 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T07:41:01 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-2/ERR506359/ERR506359.1' 2019-07-05T07:41:01 fasterq-dump.2.9.6 err: invalid accession 'ERR506359' 2019-07-05T07:41:16 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T07:41:16 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/sos/sra-pub-run-2/ERR506359/ERR506359.1' 2019-07-05T07:41:16 fasterq-dump.2.9.6 err: invalid accession 'ERR506359' 2019-07-05T07:43:44 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 ) 2019-07-05T07:43:44 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.65' 2019-07-05T07:43:44 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 '172.19.7.65' 2019-07-05T07:43:44 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/ERR506359/ERR506359.1' 2019-07-05T07:43:44 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506359' ) -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-07-05T07:43:44 fasterq-dump.2.9.6 err: sorter.c run_producer_pool() : processed lookup rows: 2231156 of 3346731 2019-07-05T07:43:44 fasterq-dump.2.9.6 err: sorter.c execute_lookup_production() -> RC(rcVDB,rcNoTarg,rcConstructing,rcSize,rcInvalid) 2019-07-05T07:43:44 fasterq-dump.2.9.6 err: fasterq-dump.c produce_lookup_files() -> RC(rcVDB,rcNoTarg,rcConstructing,rcSize,rcInvalid) spots read : 1,785,774 reads read : 3,571,548 reads written : 3,571,548 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: 00:01:55 1785774 reads; of these: 1785774 (100.00%) were paired; of these: 280736 (15.72%) aligned concordantly 0 times 1400118 (78.40%) aligned concordantly exactly 1 time 104920 (5.88%) aligned concordantly >1 times ---- 280736 pairs aligned concordantly 0 times; of these: 137970 (49.15%) aligned discordantly 1 time ---- 142766 pairs aligned 0 times concordantly or discordantly; of these: 285532 mates make up the pairs; of these: 229046 (80.22%) aligned 0 times 31821 (11.14%) aligned exactly 1 time 24665 (8.64%) aligned >1 times 93.59% overall alignment rate Time searching: 00:01:55 Overall time: 00:01:55 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] 75763 / 1628549 = 0.0465 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 16:55:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471716/ERX471716.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471716/ERX471716.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471716/ERX471716.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471716/ERX471716.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 16:55:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:55:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:55:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471716/ERX471716.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471716/ERX471716.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471716/ERX471716.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471716/ERX471716.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 16:55:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:55:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:55:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471716/ERX471716.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471716/ERX471716.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471716/ERX471716.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471716/ERX471716.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 16:55:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:55:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:55:36: 1000000 INFO @ Fri, 05 Jul 2019 16:55:37: 1000000 INFO @ Fri, 05 Jul 2019 16:55:37: 1000000 INFO @ Fri, 05 Jul 2019 16:55:46: 2000000 INFO @ Fri, 05 Jul 2019 16:55:47: 2000000 INFO @ Fri, 05 Jul 2019 16:55:49: 2000000 INFO @ Fri, 05 Jul 2019 16:55:56: 3000000 INFO @ Fri, 05 Jul 2019 16:55:57: 3000000 INFO @ Fri, 05 Jul 2019 16:55:58: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:55:58: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:55:58: #1 total tags in treatment: 1433133 INFO @ Fri, 05 Jul 2019 16:55:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:55:58: #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 16:55:58: #1 tags after filtering in treatment: 1331701 INFO @ Fri, 05 Jul 2019 16:55:58: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 16:55:58: #1 finished! INFO @ Fri, 05 Jul 2019 16:55:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:55:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:55:58: #2 number of paired peaks: 60 WARNING @ Fri, 05 Jul 2019 16:55:58: Too few paired peaks (60) 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 16:55:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471716/ERX471716.10_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/ERX471716/ERX471716.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471716/ERX471716.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471716/ERX471716.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:55:58: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:55:58: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:55:58: #1 total tags in treatment: 1433133 INFO @ Fri, 05 Jul 2019 16:55:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:55:58: #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 16:55:58: #1 tags after filtering in treatment: 1331701 INFO @ Fri, 05 Jul 2019 16:55:58: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 16:55:58: #1 finished! INFO @ Fri, 05 Jul 2019 16:55:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:55:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:55:59: #2 number of paired peaks: 60 WARNING @ Fri, 05 Jul 2019 16:55:59: Too few paired peaks (60) 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 16:55:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471716/ERX471716.20_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/ERX471716/ERX471716.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471716/ERX471716.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471716/ERX471716.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:56:00: 3000000 INFO @ Fri, 05 Jul 2019 16:56:02: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:56:02: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:56:02: #1 total tags in treatment: 1433133 INFO @ Fri, 05 Jul 2019 16:56:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:56:02: #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 16:56:02: #1 tags after filtering in treatment: 1331701 INFO @ Fri, 05 Jul 2019 16:56:02: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 16:56:02: #1 finished! INFO @ Fri, 05 Jul 2019 16:56:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:56:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:56:02: #2 number of paired peaks: 60 WARNING @ Fri, 05 Jul 2019 16:56:02: Too few paired peaks (60) 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 16:56:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471716/ERX471716.05_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/ERX471716/ERX471716.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471716/ERX471716.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471716/ERX471716.05_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。