Job ID = 2007835 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:32:06 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 ) 2019-07-05T07:32:06 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.10' 2019-07-05T07:32:06 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 '172.19.7.10' 2019-07-05T07:32:06 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/ERR496966/ERR496966.1' 2019-07-05T07:32:06 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR496966' ) -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-07-05T07:32:06 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 ) 2019-07-05T07:32:06 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.10' 2019-07-05T07:32:06 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 '172.19.7.10' 2019-07-05T07:32:06 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/ERR496966/ERR496966.1' 2019-07-05T07:32:06 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR496966' ) -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-07-05T07:32:06 fasterq-dump.2.9.6 err: perform_fastq_split_file_join().make_fastq_csra_iter() -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-07-05T07:32:06 fasterq-dump.2.9.6 err: perform_fastq_split_file_join().make_fastq_csra_iter() -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-07-05T07:32:06 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 ) 2019-07-05T07:32:06 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.10' 2019-07-05T07:32:06 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 '172.19.7.10' 2019-07-05T07:32:06 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/ERR496966/ERR496966.1' 2019-07-05T07:32:06 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR496966' ) -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-07-05T07:32:06 fasterq-dump.2.9.6 err: perform_fastq_split_file_join().make_fastq_csra_iter() -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-07-05T07:32:06 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 ) 2019-07-05T07:32:06 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.10' 2019-07-05T07:32:06 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 '172.19.7.10' 2019-07-05T07:32:06 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/ERR496966/ERR496966.1' 2019-07-05T07:32:06 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR496966' ) -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-07-05T07:32:06 fasterq-dump.2.9.6 err: perform_fastq_split_file_join().make_fastq_csra_iter() -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) spots read : 181,527 reads read : 363,054 reads written : 363,054 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: 00:00:08 181527 reads; of these: 181527 (100.00%) were paired; of these: 20099 (11.07%) aligned concordantly 0 times 146357 (80.63%) aligned concordantly exactly 1 time 15071 (8.30%) aligned concordantly >1 times ---- 20099 pairs aligned concordantly 0 times; of these: 2927 (14.56%) aligned discordantly 1 time ---- 17172 pairs aligned 0 times concordantly or discordantly; of these: 34344 mates make up the pairs; of these: 32060 (93.35%) aligned 0 times 1355 (3.95%) aligned exactly 1 time 929 (2.70%) aligned >1 times 91.17% overall alignment rate Time searching: 00:00:08 Overall time: 00:00:08 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] 2606 / 163927 = 0.0159 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 16:36:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.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 16:36:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:36:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:36:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.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 16:36:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:36:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:36:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.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 16:36:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:36:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:36:19: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:36:19: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:36:19: #1 total tags in treatment: 158861 INFO @ Fri, 05 Jul 2019 16:36:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:36:19: #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 16:36:19: #1 tags after filtering in treatment: 157896 INFO @ Fri, 05 Jul 2019 16:36:19: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:36:19: #1 finished! INFO @ Fri, 05 Jul 2019 16:36:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:36:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:36:19: #2 number of paired peaks: 140 WARNING @ Fri, 05 Jul 2019 16:36:19: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Fri, 05 Jul 2019 16:36:19: start model_add_line... INFO @ Fri, 05 Jul 2019 16:36:19: start X-correlation... INFO @ Fri, 05 Jul 2019 16:36:19: end of X-cor INFO @ Fri, 05 Jul 2019 16:36:19: #2 finished! INFO @ Fri, 05 Jul 2019 16:36:19: #2 predicted fragment length is 287 bps INFO @ Fri, 05 Jul 2019 16:36:19: #2 alternative fragment length(s) may be 64,94,115,135,174,212,234,268,287,302,328,361,378,421,445,504,572 bps INFO @ Fri, 05 Jul 2019 16:36:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.05_model.r INFO @ Fri, 05 Jul 2019 16:36:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:36:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:36:20: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:36:20: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:36:20: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:36:20: #1 total tags in treatment: 158861 INFO @ Fri, 05 Jul 2019 16:36:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:36:20: #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 16:36:20: #1 tags after filtering in treatment: 157896 INFO @ Fri, 05 Jul 2019 16:36:20: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:36:20: #1 finished! INFO @ Fri, 05 Jul 2019 16:36:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:36:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:36:20: #2 number of paired peaks: 140 WARNING @ Fri, 05 Jul 2019 16:36:20: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Fri, 05 Jul 2019 16:36:20: start model_add_line... INFO @ Fri, 05 Jul 2019 16:36:20: start X-correlation... INFO @ Fri, 05 Jul 2019 16:36:20: end of X-cor INFO @ Fri, 05 Jul 2019 16:36:20: #2 finished! INFO @ Fri, 05 Jul 2019 16:36:20: #2 predicted fragment length is 287 bps INFO @ Fri, 05 Jul 2019 16:36:20: #2 alternative fragment length(s) may be 64,94,115,135,174,212,234,268,287,302,328,361,378,421,445,504,572 bps INFO @ Fri, 05 Jul 2019 16:36:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.10_model.r INFO @ Fri, 05 Jul 2019 16:36:20: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:36:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:36:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:36:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:36:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.05_summits.bed INFO @ Fri, 05 Jul 2019 16:36:20: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (2 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:36:21: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:36:21: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:36:21: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:36:21: #1 total tags in treatment: 158861 INFO @ Fri, 05 Jul 2019 16:36:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:36:21: #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 16:36:21: #1 tags after filtering in treatment: 157896 INFO @ Fri, 05 Jul 2019 16:36:21: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:36:21: #1 finished! INFO @ Fri, 05 Jul 2019 16:36:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:36:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:36:21: #2 number of paired peaks: 140 WARNING @ Fri, 05 Jul 2019 16:36:21: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Fri, 05 Jul 2019 16:36:21: start model_add_line... INFO @ Fri, 05 Jul 2019 16:36:21: start X-correlation... INFO @ Fri, 05 Jul 2019 16:36:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:36:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:36:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.10_summits.bed INFO @ Fri, 05 Jul 2019 16:36:21: Done! INFO @ Fri, 05 Jul 2019 16:36:21: end of X-cor INFO @ Fri, 05 Jul 2019 16:36:21: #2 finished! INFO @ Fri, 05 Jul 2019 16:36:21: #2 predicted fragment length is 287 bps INFO @ Fri, 05 Jul 2019 16:36:21: #2 alternative fragment length(s) may be 64,94,115,135,174,212,234,268,287,302,328,361,378,421,445,504,572 bps INFO @ Fri, 05 Jul 2019 16:36:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.20_model.r INFO @ Fri, 05 Jul 2019 16:36:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:36:21: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 16:36:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:36:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:36:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:36:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462382/ERX462382.20_summits.bed INFO @ Fri, 05 Jul 2019 16:36:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 CompletedMACS2peakCalling