Job ID = 2640476 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:07:33 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 ) 2019-08-24T08:07:33 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 ) 2019-08-24T08:07:33 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.56' 2019-08-24T08:07:33 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.56' 2019-08-24T08:07:33 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 '172.19.7.56' 2019-08-24T08:07:33 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 '172.19.7.56' 2019-08-24T08:07:33 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/sra77/SRR/008373/SRR8574044' 2019-08-24T08:07:33 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/sra77/SRR/008373/SRR8574044' 2019-08-24T08:07:33 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 ) 2019-08-24T08:07:33 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.56' 2019-08-24T08:07:33 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 '172.19.7.56' 2019-08-24T08:07:33 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/sra77/SRR/008373/SRR8574044' 2019-08-24T08:07:33 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR8574044' ) -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-08-24T08:07:33 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR8574044' ) -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-08-24T08:07:33 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR8574044' ) -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-08-24T08:07:33 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-08-24T08:07:33 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-08-24T08:07:33 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2019-08-24T08:18:32 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 ) 2019-08-24T08:21:09 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 ) 2019-08-24T08:21:09 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 : 17,392,682 reads read : 34,785,364 reads written : 17,392,682 reads 0-length : 17,392,682 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: 00:12:13 17392682 reads; of these: 17392682 (100.00%) were unpaired; of these: 931261 (5.35%) aligned 0 times 14213675 (81.72%) aligned exactly 1 time 2247746 (12.92%) aligned >1 times 94.65% overall alignment rate Time searching: 00:12:16 Overall time: 00:12:16 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 8 files... [bam_rmdupse_core] 2850953 / 16461421 = 0.1732 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:39:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.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 17:39:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:39:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:39:22: 1000000 INFO @ Sat, 24 Aug 2019 17:39:29: 2000000 INFO @ Sat, 24 Aug 2019 17:39:37: 3000000 INFO @ Sat, 24 Aug 2019 17:39:45: 4000000 INFO @ Sat, 24 Aug 2019 17:39:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.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 17:39:46: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:39:46: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:39:55: 5000000 INFO @ Sat, 24 Aug 2019 17:39:56: 1000000 INFO @ Sat, 24 Aug 2019 17:40:02: 6000000 INFO @ Sat, 24 Aug 2019 17:40:03: 2000000 INFO @ Sat, 24 Aug 2019 17:40:08: 7000000 INFO @ Sat, 24 Aug 2019 17:40:11: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:40:15: 8000000 INFO @ Sat, 24 Aug 2019 17:40:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.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 17:40:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:40:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:40:18: 4000000 INFO @ Sat, 24 Aug 2019 17:40:22: 9000000 INFO @ Sat, 24 Aug 2019 17:40:23: 1000000 INFO @ Sat, 24 Aug 2019 17:40:25: 5000000 INFO @ Sat, 24 Aug 2019 17:40:28: 10000000 INFO @ Sat, 24 Aug 2019 17:40:31: 2000000 INFO @ Sat, 24 Aug 2019 17:40:33: 6000000 INFO @ Sat, 24 Aug 2019 17:40:35: 11000000 INFO @ Sat, 24 Aug 2019 17:40:39: 3000000 INFO @ Sat, 24 Aug 2019 17:40:41: 7000000 INFO @ Sat, 24 Aug 2019 17:40:42: 12000000 INFO @ Sat, 24 Aug 2019 17:40:47: 4000000 INFO @ Sat, 24 Aug 2019 17:40:49: 13000000 INFO @ Sat, 24 Aug 2019 17:40:50: 8000000 INFO @ Sat, 24 Aug 2019 17:40:53: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:40:53: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:40:53: #1 total tags in treatment: 13610468 INFO @ Sat, 24 Aug 2019 17:40:53: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:40:53: #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 17:40:53: #1 tags after filtering in treatment: 13610226 INFO @ Sat, 24 Aug 2019 17:40:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:40:53: #1 finished! INFO @ Sat, 24 Aug 2019 17:40:53: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:40:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:40:54: 5000000 INFO @ Sat, 24 Aug 2019 17:40:58: #2 number of paired peaks: 84370 INFO @ Sat, 24 Aug 2019 17:40:58: start model_add_line... INFO @ Sat, 24 Aug 2019 17:40:58: start X-correlation... INFO @ Sat, 24 Aug 2019 17:40:58: end of X-cor INFO @ Sat, 24 Aug 2019 17:40:58: #2 finished! INFO @ Sat, 24 Aug 2019 17:40:58: #2 predicted fragment length is 159 bps INFO @ Sat, 24 Aug 2019 17:40:58: #2 alternative fragment length(s) may be 159 bps INFO @ Sat, 24 Aug 2019 17:40:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.05_model.r INFO @ Sat, 24 Aug 2019 17:40:58: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:40:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:40:59: 9000000 INFO @ Sat, 24 Aug 2019 17:41:01: 6000000 INFO @ Sat, 24 Aug 2019 17:41:08: 7000000 INFO @ Sat, 24 Aug 2019 17:41:08: 10000000 INFO @ Sat, 24 Aug 2019 17:41:15: 8000000 INFO @ Sat, 24 Aug 2019 17:41:17: 11000000 INFO @ Sat, 24 Aug 2019 17:41:22: 9000000 INFO @ Sat, 24 Aug 2019 17:41:26: 12000000 INFO @ Sat, 24 Aug 2019 17:41:30: 10000000 INFO @ Sat, 24 Aug 2019 17:41:34: 13000000 INFO @ Sat, 24 Aug 2019 17:41:37: 11000000 INFO @ Sat, 24 Aug 2019 17:41:39: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:41:39: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:41:39: #1 total tags in treatment: 13610468 INFO @ Sat, 24 Aug 2019 17:41:39: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:41:39: #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 17:41:40: #1 tags after filtering in treatment: 13610226 INFO @ Sat, 24 Aug 2019 17:41:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:41:40: #1 finished! INFO @ Sat, 24 Aug 2019 17:41:40: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:41:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:41:43: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:41:44: 12000000 INFO @ Sat, 24 Aug 2019 17:41:44: #2 number of paired peaks: 84370 INFO @ Sat, 24 Aug 2019 17:41:44: start model_add_line... INFO @ Sat, 24 Aug 2019 17:41:45: start X-correlation... INFO @ Sat, 24 Aug 2019 17:41:45: end of X-cor INFO @ Sat, 24 Aug 2019 17:41:45: #2 finished! INFO @ Sat, 24 Aug 2019 17:41:45: #2 predicted fragment length is 159 bps INFO @ Sat, 24 Aug 2019 17:41:45: #2 alternative fragment length(s) may be 159 bps INFO @ Sat, 24 Aug 2019 17:41:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.10_model.r INFO @ Sat, 24 Aug 2019 17:41:45: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:41:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:41:51: 13000000 INFO @ Sat, 24 Aug 2019 17:41:56: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:41:56: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:41:56: #1 total tags in treatment: 13610468 INFO @ Sat, 24 Aug 2019 17:41:56: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:41:56: #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 17:41:56: #1 tags after filtering in treatment: 13610226 INFO @ Sat, 24 Aug 2019 17:41:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:41:56: #1 finished! INFO @ Sat, 24 Aug 2019 17:41:56: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:41:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:42:01: #2 number of paired peaks: 84370 INFO @ Sat, 24 Aug 2019 17:42:01: start model_add_line... INFO @ Sat, 24 Aug 2019 17:42:01: start X-correlation... INFO @ Sat, 24 Aug 2019 17:42:01: end of X-cor INFO @ Sat, 24 Aug 2019 17:42:01: #2 finished! INFO @ Sat, 24 Aug 2019 17:42:01: #2 predicted fragment length is 159 bps INFO @ Sat, 24 Aug 2019 17:42:01: #2 alternative fragment length(s) may be 159 bps INFO @ Sat, 24 Aug 2019 17:42:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.20_model.r INFO @ Sat, 24 Aug 2019 17:42:01: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:42:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:42:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:42:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:42:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.05_summits.bed INFO @ Sat, 24 Aug 2019 17:42:07: Done! pass1 - making usageList (120 chroms): 11 millis pass2 - checking and writing primary data (37418 records, 4 fields): 51 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:42:30: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:42:46: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:42:53: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:42:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:42:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.10_summits.bed INFO @ Sat, 24 Aug 2019 17:42:54: Done! pass1 - making usageList (102 chroms): 7 millis pass2 - checking and writing primary data (24165 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:43:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:43:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:43:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374989/SRX5374989.20_summits.bed INFO @ Sat, 24 Aug 2019 17:43:09: Done! pass1 - making usageList (74 chroms): 3 millis pass2 - checking and writing primary data (11959 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。