Job ID = 2640457 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:54:51 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 ) 2019-08-24T07:54:51 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.80' 2019-08-24T07:54:51 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 '172.19.7.80' 2019-08-24T07:54:51 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/sra74/SRR/008086/SRR8280065' 2019-08-24T07:54:51 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_table_names( 'SRR8280065' ).VDBManagerOpenDBRead() -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-08-24T07:56:12 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 ) 2019-08-24T07:56:12 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 ) 2019-08-24T07:56:12 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 ) 2019-08-24T08:02:29 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 ) 2019-08-24T08:02:29 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 ) 2019-08-24T08:03:20 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 ) 2019-08-24T08:03:20 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 ) 2019-08-24T08:04:08 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 ) 2019-08-24T08:04:08 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 ) 2019-08-24T08:28:15 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 ) 2019-08-24T08:35:31 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 ) 2019-08-24T08:35:31 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 ) 2019-08-24T08:42:42 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 ) 2019-08-24T08:51:02 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 ) 2019-08-24T09:06:11 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 ) 2019-08-24T09:12:56 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 : 418,394,862 reads read : 836,789,724 reads written : 418,394,862 reads 0-length : 418,394,862 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:07:46 418394862 reads; of these: 418394862 (100.00%) were unpaired; of these: 360724784 (86.22%) aligned 0 times 32028500 (7.66%) aligned exactly 1 time 25641578 (6.13%) aligned >1 times 13.78% overall alignment rate Time searching: 01:07:49 Overall time: 01:07:49 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 45576639 / 57670078 = 0.7903 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:38:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 19:38:18: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:38:18: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:38:26: 1000000 INFO @ Sat, 24 Aug 2019 19:38:34: 2000000 INFO @ Sat, 24 Aug 2019 19:38:41: 3000000 INFO @ Sat, 24 Aug 2019 19:38:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 19:38:48: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:38:48: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:38:48: 4000000 INFO @ Sat, 24 Aug 2019 19:38:55: 5000000 INFO @ Sat, 24 Aug 2019 19:38:56: 1000000 INFO @ Sat, 24 Aug 2019 19:39:02: 6000000 INFO @ Sat, 24 Aug 2019 19:39:04: 2000000 INFO @ Sat, 24 Aug 2019 19:39:09: 7000000 INFO @ Sat, 24 Aug 2019 19:39:12: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:39:17: 8000000 INFO @ Sat, 24 Aug 2019 19:39:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 19:39:18: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:39:18: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:39:21: 4000000 INFO @ Sat, 24 Aug 2019 19:39:24: 9000000 INFO @ Sat, 24 Aug 2019 19:39:27: 1000000 INFO @ Sat, 24 Aug 2019 19:39:28: 5000000 INFO @ Sat, 24 Aug 2019 19:39:31: 10000000 INFO @ Sat, 24 Aug 2019 19:39:35: 2000000 INFO @ Sat, 24 Aug 2019 19:39:37: 6000000 INFO @ Sat, 24 Aug 2019 19:39:39: 11000000 INFO @ Sat, 24 Aug 2019 19:39:44: 3000000 INFO @ Sat, 24 Aug 2019 19:39:44: 7000000 INFO @ Sat, 24 Aug 2019 19:39:46: 12000000 INFO @ Sat, 24 Aug 2019 19:39:47: #1 tag size is determined as 26 bps INFO @ Sat, 24 Aug 2019 19:39:47: #1 tag size = 26 INFO @ Sat, 24 Aug 2019 19:39:47: #1 total tags in treatment: 12093439 INFO @ Sat, 24 Aug 2019 19:39:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:39:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:39:47: #1 tags after filtering in treatment: 12093300 INFO @ Sat, 24 Aug 2019 19:39:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:39:47: #1 finished! INFO @ Sat, 24 Aug 2019 19:39:47: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:39:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:39:50: #2 number of paired peaks: 7865 INFO @ Sat, 24 Aug 2019 19:39:50: start model_add_line... INFO @ Sat, 24 Aug 2019 19:39:50: start X-correlation... INFO @ Sat, 24 Aug 2019 19:39:50: end of X-cor INFO @ Sat, 24 Aug 2019 19:39:50: #2 finished! INFO @ Sat, 24 Aug 2019 19:39:50: #2 predicted fragment length is 102 bps INFO @ Sat, 24 Aug 2019 19:39:50: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 24 Aug 2019 19:39:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.05_model.r INFO @ Sat, 24 Aug 2019 19:39:50: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:39:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:39:52: 8000000 INFO @ Sat, 24 Aug 2019 19:39:53: 4000000 INFO @ Sat, 24 Aug 2019 19:40:00: 9000000 INFO @ Sat, 24 Aug 2019 19:40:01: 5000000 INFO @ Sat, 24 Aug 2019 19:40:08: 10000000 INFO @ Sat, 24 Aug 2019 19:40:10: 6000000 INFO @ Sat, 24 Aug 2019 19:40:15: 11000000 INFO @ Sat, 24 Aug 2019 19:40:18: 7000000 INFO @ Sat, 24 Aug 2019 19:40:23: 12000000 INFO @ Sat, 24 Aug 2019 19:40:24: #1 tag size is determined as 26 bps INFO @ Sat, 24 Aug 2019 19:40:24: #1 tag size = 26 INFO @ Sat, 24 Aug 2019 19:40:24: #1 total tags in treatment: 12093439 INFO @ Sat, 24 Aug 2019 19:40:24: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:40:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:40:24: #1 tags after filtering in treatment: 12093300 INFO @ Sat, 24 Aug 2019 19:40:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:40:24: #1 finished! INFO @ Sat, 24 Aug 2019 19:40:24: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:40:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:40:27: #2 number of paired peaks: 7865 INFO @ Sat, 24 Aug 2019 19:40:27: start model_add_line... INFO @ Sat, 24 Aug 2019 19:40:27: start X-correlation... INFO @ Sat, 24 Aug 2019 19:40:27: end of X-cor INFO @ Sat, 24 Aug 2019 19:40:27: #2 finished! INFO @ Sat, 24 Aug 2019 19:40:27: #2 predicted fragment length is 102 bps INFO @ Sat, 24 Aug 2019 19:40:27: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 24 Aug 2019 19:40:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.10_model.r INFO @ Sat, 24 Aug 2019 19:40:27: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:40:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:40:27: 8000000 INFO @ Sat, 24 Aug 2019 19:40:28: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:40:35: 9000000 INFO @ Sat, 24 Aug 2019 19:40:43: 10000000 INFO @ Sat, 24 Aug 2019 19:40:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.05_peaks.xls INFO @ Sat, 24 Aug 2019 19:40:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:40:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.05_summits.bed INFO @ Sat, 24 Aug 2019 19:40:48: Done! pass1 - making usageList (23 chroms): 3 millis pass2 - checking and writing primary data (990 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:40:51: 11000000 INFO @ Sat, 24 Aug 2019 19:40:59: 12000000 INFO @ Sat, 24 Aug 2019 19:41:00: #1 tag size is determined as 26 bps INFO @ Sat, 24 Aug 2019 19:41:00: #1 tag size = 26 INFO @ Sat, 24 Aug 2019 19:41:00: #1 total tags in treatment: 12093439 INFO @ Sat, 24 Aug 2019 19:41:00: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:41:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:41:00: #1 tags after filtering in treatment: 12093300 INFO @ Sat, 24 Aug 2019 19:41:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:41:00: #1 finished! INFO @ Sat, 24 Aug 2019 19:41:00: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:41:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:41:03: #2 number of paired peaks: 7865 INFO @ Sat, 24 Aug 2019 19:41:03: start model_add_line... INFO @ Sat, 24 Aug 2019 19:41:03: start X-correlation... INFO @ Sat, 24 Aug 2019 19:41:03: end of X-cor INFO @ Sat, 24 Aug 2019 19:41:03: #2 finished! INFO @ Sat, 24 Aug 2019 19:41:03: #2 predicted fragment length is 102 bps INFO @ Sat, 24 Aug 2019 19:41:03: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 24 Aug 2019 19:41:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.20_model.r INFO @ Sat, 24 Aug 2019 19:41:03: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:41:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:41:05: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:41:25: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.10_peaks.xls INFO @ Sat, 24 Aug 2019 19:41:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:41:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.10_summits.bed INFO @ Sat, 24 Aug 2019 19:41:25: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (24 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:41:41: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:42:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.20_peaks.xls INFO @ Sat, 24 Aug 2019 19:42:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:42:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5094898/SRX5094898.20_summits.bed INFO @ Sat, 24 Aug 2019 19:42:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。