Job ID = 1294476 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:13:29 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 ) 2019-06-02T23:13:29 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.25' from '172.19.7.80' 2019-06-02T23:13:29 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 '172.19.7.80' 2019-06-02T23:13:29 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/sra12/SRR/000849/SRR869863' 2019-06-02T23:13:29 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 ) 2019-06-02T23:13:29 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.25' from '172.19.7.80' 2019-06-02T23:13:29 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 '172.19.7.80' 2019-06-02T23:13:29 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/sra12/SRR/000849/SRR869863' 2019-06-02T23:13:39 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR869863' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T23:13:39 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T23:13:39 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR869863' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T23:13:39 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T23:13:46 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 ) 2019-06-02T23:13:46 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 ) 2019-06-02T23:15:34 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 ) 2019-06-02T23:19:59 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 ) 2019-06-02T23:19:59 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 ) 2019-06-02T23:30:09 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 ) 2019-06-02T23:30:09 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 : 27,279,884 reads read : 27,279,884 reads written : 27,279,884 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: 00:26:53 27279884 reads; of these: 27279884 (100.00%) were unpaired; of these: 930261 (3.41%) aligned 0 times 5583374 (20.47%) aligned exactly 1 time 20766249 (76.12%) aligned >1 times 96.59% overall alignment rate Time searching: 00:26:53 Overall time: 00:26:53 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 12 files... [bam_rmdupse_core] 8776196 / 26349623 = 0.3331 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 09:16:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.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 09:16:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:16:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:16:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.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 09:16:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:16:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:16:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.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 09:16:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:16:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:16:35: 1000000 INFO @ Mon, 03 Jun 2019 09:16:36: 1000000 INFO @ Mon, 03 Jun 2019 09:16:36: 1000000 INFO @ Mon, 03 Jun 2019 09:16:43: 2000000 INFO @ Mon, 03 Jun 2019 09:16:44: 2000000 INFO @ Mon, 03 Jun 2019 09:16:44: 2000000 INFO @ Mon, 03 Jun 2019 09:16:51: 3000000 INFO @ Mon, 03 Jun 2019 09:16:52: 3000000 INFO @ Mon, 03 Jun 2019 09:16:52: 3000000 INFO @ Mon, 03 Jun 2019 09:16:59: 4000000 INFO @ Mon, 03 Jun 2019 09:17:00: 4000000 INFO @ Mon, 03 Jun 2019 09:17:01: 4000000 INFO @ Mon, 03 Jun 2019 09:17:06: 5000000 INFO @ Mon, 03 Jun 2019 09:17:09: 5000000 INFO @ Mon, 03 Jun 2019 09:17:09: 5000000 INFO @ Mon, 03 Jun 2019 09:17:14: 6000000 INFO @ Mon, 03 Jun 2019 09:17:17: 6000000 INFO @ Mon, 03 Jun 2019 09:17:17: 6000000 INFO @ Mon, 03 Jun 2019 09:17:23: 7000000 INFO @ Mon, 03 Jun 2019 09:17:25: 7000000 INFO @ Mon, 03 Jun 2019 09:17:25: 7000000 INFO @ Mon, 03 Jun 2019 09:17:31: 8000000 INFO @ Mon, 03 Jun 2019 09:17:33: 8000000 INFO @ Mon, 03 Jun 2019 09:17:33: 8000000 INFO @ Mon, 03 Jun 2019 09:17:40: 9000000 INFO @ Mon, 03 Jun 2019 09:17:41: 9000000 INFO @ Mon, 03 Jun 2019 09:17:42: 9000000 INFO @ Mon, 03 Jun 2019 09:17:48: 10000000 INFO @ Mon, 03 Jun 2019 09:17:49: 10000000 INFO @ Mon, 03 Jun 2019 09:17:50: 10000000 INFO @ Mon, 03 Jun 2019 09:17:56: 11000000 INFO @ Mon, 03 Jun 2019 09:17:56: 11000000 INFO @ Mon, 03 Jun 2019 09:17:58: 11000000 INFO @ Mon, 03 Jun 2019 09:18:04: 12000000 INFO @ Mon, 03 Jun 2019 09:18:04: 12000000 INFO @ Mon, 03 Jun 2019 09:18:07: 12000000 INFO @ Mon, 03 Jun 2019 09:18:12: 13000000 INFO @ Mon, 03 Jun 2019 09:18:13: 13000000 INFO @ Mon, 03 Jun 2019 09:18:15: 13000000 INFO @ Mon, 03 Jun 2019 09:18:20: 14000000 INFO @ Mon, 03 Jun 2019 09:18:22: 14000000 INFO @ Mon, 03 Jun 2019 09:18:24: 14000000 INFO @ Mon, 03 Jun 2019 09:18:27: 15000000 INFO @ Mon, 03 Jun 2019 09:18:30: 15000000 INFO @ Mon, 03 Jun 2019 09:18:32: 15000000 INFO @ Mon, 03 Jun 2019 09:18:34: 16000000 INFO @ Mon, 03 Jun 2019 09:18:38: 16000000 INFO @ Mon, 03 Jun 2019 09:18:40: 16000000 INFO @ Mon, 03 Jun 2019 09:18:42: 17000000 INFO @ Mon, 03 Jun 2019 09:18:46: 17000000 INFO @ Mon, 03 Jun 2019 09:18:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:18:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:18:47: #1 total tags in treatment: 17573427 INFO @ Mon, 03 Jun 2019 09:18:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:18:47: #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 09:18:47: #1 tags after filtering in treatment: 17573427 INFO @ Mon, 03 Jun 2019 09:18:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:18:47: #1 finished! INFO @ Mon, 03 Jun 2019 09:18:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:18:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:18:48: 17000000 INFO @ Mon, 03 Jun 2019 09:18:49: #2 number of paired peaks: 734 WARNING @ Mon, 03 Jun 2019 09:18:49: Fewer paired peaks (734) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 734 pairs to build model! INFO @ Mon, 03 Jun 2019 09:18:49: start model_add_line... INFO @ Mon, 03 Jun 2019 09:18:49: start X-correlation... INFO @ Mon, 03 Jun 2019 09:18:49: end of X-cor INFO @ Mon, 03 Jun 2019 09:18:49: #2 finished! INFO @ Mon, 03 Jun 2019 09:18:49: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 09:18:49: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 09:18:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.20_model.r WARNING @ Mon, 03 Jun 2019 09:18:49: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:18:49: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 09:18:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 09:18:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:18:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:18:51: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:18:51: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:18:51: #1 total tags in treatment: 17573427 INFO @ Mon, 03 Jun 2019 09:18:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:18:51: #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 09:18:51: #1 tags after filtering in treatment: 17573427 INFO @ Mon, 03 Jun 2019 09:18:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:18:51: #1 finished! INFO @ Mon, 03 Jun 2019 09:18:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:18:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:18:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:18:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:18:53: #1 total tags in treatment: 17573427 INFO @ Mon, 03 Jun 2019 09:18:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:18:53: #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 09:18:53: #2 number of paired peaks: 734 WARNING @ Mon, 03 Jun 2019 09:18:53: Fewer paired peaks (734) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 734 pairs to build model! INFO @ Mon, 03 Jun 2019 09:18:53: start model_add_line... INFO @ Mon, 03 Jun 2019 09:18:53: #1 tags after filtering in treatment: 17573427 INFO @ Mon, 03 Jun 2019 09:18:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:18:53: #1 finished! INFO @ Mon, 03 Jun 2019 09:18:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:18:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:18:53: start X-correlation... INFO @ Mon, 03 Jun 2019 09:18:53: end of X-cor INFO @ Mon, 03 Jun 2019 09:18:53: #2 finished! INFO @ Mon, 03 Jun 2019 09:18:53: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 09:18:53: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 09:18:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.10_model.r WARNING @ Mon, 03 Jun 2019 09:18:53: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:18:53: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 09:18:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 09:18:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:18:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:18:55: #2 number of paired peaks: 734 WARNING @ Mon, 03 Jun 2019 09:18:55: Fewer paired peaks (734) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 734 pairs to build model! INFO @ Mon, 03 Jun 2019 09:18:55: start model_add_line... INFO @ Mon, 03 Jun 2019 09:18:55: start X-correlation... INFO @ Mon, 03 Jun 2019 09:18:55: end of X-cor INFO @ Mon, 03 Jun 2019 09:18:55: #2 finished! INFO @ Mon, 03 Jun 2019 09:18:55: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 09:18:55: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 09:18:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.05_model.r WARNING @ Mon, 03 Jun 2019 09:18:55: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:18:55: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 09:18:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 09:18:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:18:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:19:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:19:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:19:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:19:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:19:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:19:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.20_summits.bed INFO @ Mon, 03 Jun 2019 09:19:55: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1188 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:19:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:19:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:19:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.10_summits.bed INFO @ Mon, 03 Jun 2019 09:19:59: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2342 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:20:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:20:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:20:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287675/SRX287675.05_summits.bed INFO @ Mon, 03 Jun 2019 09:20:01: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9745 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。