Job ID = 1300313 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:10:47 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 ) 2019-06-03T10:10:47 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.25' from '172.19.7.70' 2019-06-03T10:10:47 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 '172.19.7.70' 2019-06-03T10:10:47 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/sra17/SRR/001154/SRR1182705' 2019-06-03T10:10:47 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 ) 2019-06-03T10:10:47 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.25' from '172.19.7.70' 2019-06-03T10:10:47 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 '172.19.7.70' 2019-06-03T10:10:47 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/sra17/SRR/001154/SRR1182705' 2019-06-03T10:10:47 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 ) 2019-06-03T10:10:47 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.25' from '172.19.7.70' 2019-06-03T10:10:47 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 '172.19.7.70' 2019-06-03T10:10:47 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/sra17/SRR/001154/SRR1182705' 2019-06-03T10:10:52 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-03T10:10:52 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/sra17/SRR/001154/SRR1182705' 2019-06-03T10:10:52 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1182705' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T10:10:52 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T10:10:57 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1182705' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T10:10:57 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1182705' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T10:10:57 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T10:10:57 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T10:14:01 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 ) spots read : 17,582,721 reads read : 17,582,721 reads written : 17,582,721 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: 00:06:28 17582721 reads; of these: 17582721 (100.00%) were unpaired; of these: 761263 (4.33%) aligned 0 times 13349287 (75.92%) aligned exactly 1 time 3472171 (19.75%) aligned >1 times 95.67% overall alignment rate Time searching: 00:06:28 Overall time: 00:06:28 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] 3670691 / 16821458 = 0.2182 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 19:43:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.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 19:43:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:43:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:43:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.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 19:43:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:43:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:43:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.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 19:43:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:43:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:43:58: 1000000 INFO @ Mon, 03 Jun 2019 19:43:59: 1000000 INFO @ Mon, 03 Jun 2019 19:43:59: 1000000 INFO @ Mon, 03 Jun 2019 19:44:06: 2000000 INFO @ Mon, 03 Jun 2019 19:44:08: 2000000 INFO @ Mon, 03 Jun 2019 19:44:09: 2000000 INFO @ Mon, 03 Jun 2019 19:44:14: 3000000 INFO @ Mon, 03 Jun 2019 19:44:17: 3000000 INFO @ Mon, 03 Jun 2019 19:44:18: 3000000 INFO @ Mon, 03 Jun 2019 19:44:22: 4000000 INFO @ Mon, 03 Jun 2019 19:44:26: 4000000 INFO @ Mon, 03 Jun 2019 19:44:27: 4000000 INFO @ Mon, 03 Jun 2019 19:44:31: 5000000 INFO @ Mon, 03 Jun 2019 19:44:35: 5000000 INFO @ Mon, 03 Jun 2019 19:44:36: 5000000 INFO @ Mon, 03 Jun 2019 19:44:39: 6000000 INFO @ Mon, 03 Jun 2019 19:44:43: 6000000 INFO @ Mon, 03 Jun 2019 19:44:45: 6000000 INFO @ Mon, 03 Jun 2019 19:44:47: 7000000 INFO @ Mon, 03 Jun 2019 19:44:52: 7000000 INFO @ Mon, 03 Jun 2019 19:44:54: 7000000 INFO @ Mon, 03 Jun 2019 19:44:56: 8000000 INFO @ Mon, 03 Jun 2019 19:45:01: 8000000 INFO @ Mon, 03 Jun 2019 19:45:03: 8000000 INFO @ Mon, 03 Jun 2019 19:45:04: 9000000 INFO @ Mon, 03 Jun 2019 19:45:10: 9000000 INFO @ Mon, 03 Jun 2019 19:45:12: 9000000 INFO @ Mon, 03 Jun 2019 19:45:13: 10000000 INFO @ Mon, 03 Jun 2019 19:45:19: 10000000 INFO @ Mon, 03 Jun 2019 19:45:21: 11000000 INFO @ Mon, 03 Jun 2019 19:45:22: 10000000 INFO @ Mon, 03 Jun 2019 19:45:28: 11000000 INFO @ Mon, 03 Jun 2019 19:45:30: 12000000 INFO @ Mon, 03 Jun 2019 19:45:31: 11000000 INFO @ Mon, 03 Jun 2019 19:45:37: 12000000 INFO @ Mon, 03 Jun 2019 19:45:38: 13000000 INFO @ Mon, 03 Jun 2019 19:45:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:45:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:45:39: #1 total tags in treatment: 13150767 INFO @ Mon, 03 Jun 2019 19:45:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:45:39: #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 19:45:40: #1 tags after filtering in treatment: 13150767 INFO @ Mon, 03 Jun 2019 19:45:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:45:40: #1 finished! INFO @ Mon, 03 Jun 2019 19:45:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:45:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:45:40: 12000000 INFO @ Mon, 03 Jun 2019 19:45:42: #2 number of paired peaks: 4587 INFO @ Mon, 03 Jun 2019 19:45:42: start model_add_line... INFO @ Mon, 03 Jun 2019 19:45:42: start X-correlation... INFO @ Mon, 03 Jun 2019 19:45:42: end of X-cor INFO @ Mon, 03 Jun 2019 19:45:42: #2 finished! INFO @ Mon, 03 Jun 2019 19:45:42: #2 predicted fragment length is 188 bps INFO @ Mon, 03 Jun 2019 19:45:42: #2 alternative fragment length(s) may be 188 bps INFO @ Mon, 03 Jun 2019 19:45:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.05_model.r INFO @ Mon, 03 Jun 2019 19:45:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:45:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:45:46: 13000000 INFO @ Mon, 03 Jun 2019 19:45:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:45:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:45:47: #1 total tags in treatment: 13150767 INFO @ Mon, 03 Jun 2019 19:45:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:45:47: #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 19:45:48: #1 tags after filtering in treatment: 13150767 INFO @ Mon, 03 Jun 2019 19:45:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:45:48: #1 finished! INFO @ Mon, 03 Jun 2019 19:45:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:45:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:45:49: 13000000 INFO @ Mon, 03 Jun 2019 19:45:50: #2 number of paired peaks: 4587 INFO @ Mon, 03 Jun 2019 19:45:50: start model_add_line... INFO @ Mon, 03 Jun 2019 19:45:50: start X-correlation... INFO @ Mon, 03 Jun 2019 19:45:50: end of X-cor INFO @ Mon, 03 Jun 2019 19:45:50: #2 finished! INFO @ Mon, 03 Jun 2019 19:45:50: #2 predicted fragment length is 188 bps INFO @ Mon, 03 Jun 2019 19:45:50: #2 alternative fragment length(s) may be 188 bps INFO @ Mon, 03 Jun 2019 19:45:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.10_model.r INFO @ Mon, 03 Jun 2019 19:45:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:45:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:45:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:45:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:45:50: #1 total tags in treatment: 13150767 INFO @ Mon, 03 Jun 2019 19:45:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:45:50: #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 19:45:51: #1 tags after filtering in treatment: 13150767 INFO @ Mon, 03 Jun 2019 19:45:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:45:51: #1 finished! INFO @ Mon, 03 Jun 2019 19:45:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:45:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:45:53: #2 number of paired peaks: 4587 INFO @ Mon, 03 Jun 2019 19:45:53: start model_add_line... INFO @ Mon, 03 Jun 2019 19:45:53: start X-correlation... INFO @ Mon, 03 Jun 2019 19:45:53: end of X-cor INFO @ Mon, 03 Jun 2019 19:45:53: #2 finished! INFO @ Mon, 03 Jun 2019 19:45:53: #2 predicted fragment length is 188 bps INFO @ Mon, 03 Jun 2019 19:45:53: #2 alternative fragment length(s) may be 188 bps INFO @ Mon, 03 Jun 2019 19:45:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.20_model.r INFO @ Mon, 03 Jun 2019 19:45:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:45:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:46:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:46:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:46:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:46:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:46:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:46:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.05_summits.bed INFO @ Mon, 03 Jun 2019 19:46:46: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (8613 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:46:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:46:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:46:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.10_summits.bed INFO @ Mon, 03 Jun 2019 19:46:52: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7662 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:46:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:46:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:46:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX481094/SRX481094.20_summits.bed INFO @ Mon, 03 Jun 2019 19:46:57: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6168 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。