Job ID = 1294586 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:05:23 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 ) 2019-06-03T00:05:23 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.27' from '172.19.7.67' 2019-06-03T00:05:23 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' (130.14.250.27) from '172.19.7.67' 2019-06-03T00:05:23 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/SRR869948' 2019-06-03T00:05:23 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 ) 2019-06-03T00:05:23 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.27' from '172.19.7.67' 2019-06-03T00:05:23 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' (130.14.250.27) from '172.19.7.67' 2019-06-03T00:05:23 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/SRR869948' 2019-06-03T00:05:32 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR869948' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T00:05:32 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR869948' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T00:05:32 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T00:05:32 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T00:10:32 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' 2019-06-03T00:10:32 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/sra12/SRR/000849/SRR869948' 2019-06-03T00:10:42 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR869948', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T00:10:46 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' 2019-06-03T00:10:46 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/sra12/SRR/000849/SRR869948' 2019-06-03T00:10:46 fasterq-dump.2.9.6 err: invalid accession 'SRR869948' 2019-06-03T00:11:44 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 ) 2019-06-03T00:11:44 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.27' from '172.19.7.67' 2019-06-03T00:11:44 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' (130.14.250.27) from '172.19.7.67' 2019-06-03T00:11:44 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/SRR869948' 2019-06-03T00:11:54 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR869948', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 9,902,142 reads read : 9,902,142 reads written : 9,902,142 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: 00:04:39 9902142 reads; of these: 9902142 (100.00%) were unpaired; of these: 575670 (5.81%) aligned 0 times 6136618 (61.97%) aligned exactly 1 time 3189854 (32.21%) aligned >1 times 94.19% overall alignment rate Time searching: 00:04:39 Overall time: 00:04:39 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_rmdupse_core] 1090150 / 9326472 = 0.1169 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 09:25:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.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 09:25:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:25:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:25:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.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 09:25:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:25:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:25:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.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 09:25:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:25:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:25:45: 1000000 INFO @ Mon, 03 Jun 2019 09:25:47: 1000000 INFO @ Mon, 03 Jun 2019 09:25:47: 1000000 INFO @ Mon, 03 Jun 2019 09:25:53: 2000000 INFO @ Mon, 03 Jun 2019 09:25:56: 2000000 INFO @ Mon, 03 Jun 2019 09:25:56: 2000000 INFO @ Mon, 03 Jun 2019 09:26:00: 3000000 INFO @ Mon, 03 Jun 2019 09:26:04: 3000000 INFO @ Mon, 03 Jun 2019 09:26:04: 3000000 INFO @ Mon, 03 Jun 2019 09:26:08: 4000000 INFO @ Mon, 03 Jun 2019 09:26:14: 4000000 INFO @ Mon, 03 Jun 2019 09:26:14: 4000000 INFO @ Mon, 03 Jun 2019 09:26:16: 5000000 INFO @ Mon, 03 Jun 2019 09:26:22: 5000000 INFO @ Mon, 03 Jun 2019 09:26:23: 5000000 INFO @ Mon, 03 Jun 2019 09:26:23: 6000000 INFO @ Mon, 03 Jun 2019 09:26:30: 7000000 INFO @ Mon, 03 Jun 2019 09:26:31: 6000000 INFO @ Mon, 03 Jun 2019 09:26:31: 6000000 INFO @ Mon, 03 Jun 2019 09:26:37: 8000000 INFO @ Mon, 03 Jun 2019 09:26:39: 7000000 INFO @ Mon, 03 Jun 2019 09:26:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:26:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:26:39: #1 total tags in treatment: 8236322 INFO @ Mon, 03 Jun 2019 09:26:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:26:39: #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 09:26:39: #1 tags after filtering in treatment: 8236322 INFO @ Mon, 03 Jun 2019 09:26:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:26:39: #1 finished! INFO @ Mon, 03 Jun 2019 09:26:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:26:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:26:40: 7000000 INFO @ Mon, 03 Jun 2019 09:26:40: #2 number of paired peaks: 574 WARNING @ Mon, 03 Jun 2019 09:26:40: Fewer paired peaks (574) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 574 pairs to build model! INFO @ Mon, 03 Jun 2019 09:26:40: start model_add_line... INFO @ Mon, 03 Jun 2019 09:26:40: start X-correlation... INFO @ Mon, 03 Jun 2019 09:26:40: end of X-cor INFO @ Mon, 03 Jun 2019 09:26:40: #2 finished! INFO @ Mon, 03 Jun 2019 09:26:40: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 09:26:40: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 09:26:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.10_model.r WARNING @ Mon, 03 Jun 2019 09:26:40: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:26:40: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 09:26:40: #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 09:26:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:26:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:26:47: 8000000 INFO @ Mon, 03 Jun 2019 09:26:48: 8000000 INFO @ Mon, 03 Jun 2019 09:26:49: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:26:49: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:26:49: #1 total tags in treatment: 8236322 INFO @ Mon, 03 Jun 2019 09:26:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:26:49: #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 09:26:50: #1 tags after filtering in treatment: 8236322 INFO @ Mon, 03 Jun 2019 09:26:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:26:50: #1 finished! INFO @ Mon, 03 Jun 2019 09:26:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:26:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:26:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:26:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:26:50: #1 total tags in treatment: 8236322 INFO @ Mon, 03 Jun 2019 09:26:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:26:50: #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 09:26:50: #1 tags after filtering in treatment: 8236322 INFO @ Mon, 03 Jun 2019 09:26:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:26:50: #1 finished! INFO @ Mon, 03 Jun 2019 09:26:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:26:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:26:50: #2 number of paired peaks: 574 WARNING @ Mon, 03 Jun 2019 09:26:50: Fewer paired peaks (574) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 574 pairs to build model! INFO @ Mon, 03 Jun 2019 09:26:50: start model_add_line... INFO @ Mon, 03 Jun 2019 09:26:50: start X-correlation... INFO @ Mon, 03 Jun 2019 09:26:50: end of X-cor INFO @ Mon, 03 Jun 2019 09:26:50: #2 finished! INFO @ Mon, 03 Jun 2019 09:26:50: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 09:26:50: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 09:26:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.20_model.r WARNING @ Mon, 03 Jun 2019 09:26:50: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:26:50: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 09:26:50: #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 09:26:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:26:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:26:51: #2 number of paired peaks: 574 WARNING @ Mon, 03 Jun 2019 09:26:51: Fewer paired peaks (574) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 574 pairs to build model! INFO @ Mon, 03 Jun 2019 09:26:51: start model_add_line... INFO @ Mon, 03 Jun 2019 09:26:51: start X-correlation... INFO @ Mon, 03 Jun 2019 09:26:51: end of X-cor INFO @ Mon, 03 Jun 2019 09:26:51: #2 finished! INFO @ Mon, 03 Jun 2019 09:26:51: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 09:26:51: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 09:26:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.05_model.r WARNING @ Mon, 03 Jun 2019 09:26:51: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:26:51: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 09:26:51: #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 09:26:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:26:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:27:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:27:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:27:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:27:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:27:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:27:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.10_summits.bed INFO @ Mon, 03 Jun 2019 09:27:15: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1651 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:27:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:27:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:27:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.20_summits.bed INFO @ Mon, 03 Jun 2019 09:27:26: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1216 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:27:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:27:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:27:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287759/SRX287759.05_summits.bed INFO @ Mon, 03 Jun 2019 09:27:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1971 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。