Job ID = 1294229 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T20:36:04 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' 2019-06-02T20:36:04 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/sra21/SRR/000595/SRR610264' 2019-06-02T20:36:13 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR610264' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T20:36:13 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T20:40:00 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 ) 2019-06-02T20:40:00 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 ) 2019-06-02T20:40:07 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 ) 2019-06-02T20:41:07 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' 2019-06-02T20:41:07 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/sra21/SRR/000595/SRR610264' 2019-06-02T20:41:16 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR610264' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T20:41:16 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 10,881,660 reads read : 10,881,660 reads written : 10,881,660 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:50 10881660 reads; of these: 10881660 (100.00%) were unpaired; of these: 6236867 (57.32%) aligned 0 times 3460062 (31.80%) aligned exactly 1 time 1184731 (10.89%) aligned >1 times 42.68% overall alignment rate Time searching: 00:01:51 Overall time: 00:01:51 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] 1670268 / 4644793 = 0.3596 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 05:48:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.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 05:48:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:48:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:48:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.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 05:48:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:48:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:48:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.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 05:48:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:48:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:48:26: 1000000 INFO @ Mon, 03 Jun 2019 05:48:26: 1000000 INFO @ Mon, 03 Jun 2019 05:48:26: 1000000 INFO @ Mon, 03 Jun 2019 05:48:35: 2000000 INFO @ Mon, 03 Jun 2019 05:48:36: 2000000 INFO @ Mon, 03 Jun 2019 05:48:36: 2000000 INFO @ Mon, 03 Jun 2019 05:48:44: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:48:44: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:48:44: #1 total tags in treatment: 2974525 INFO @ Mon, 03 Jun 2019 05:48:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:48:44: #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 05:48:45: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:48:45: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:48:45: #1 total tags in treatment: 2974525 INFO @ Mon, 03 Jun 2019 05:48:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:48:45: #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 05:48:45: #1 tags after filtering in treatment: 2974525 INFO @ Mon, 03 Jun 2019 05:48:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:48:45: #1 finished! INFO @ Mon, 03 Jun 2019 05:48:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:48:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:48:45: #1 tags after filtering in treatment: 2974525 INFO @ Mon, 03 Jun 2019 05:48:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:48:45: #1 finished! INFO @ Mon, 03 Jun 2019 05:48:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:48:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:48:45: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:48:45: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:48:45: #1 total tags in treatment: 2974525 INFO @ Mon, 03 Jun 2019 05:48:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:48:45: #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 05:48:45: #1 tags after filtering in treatment: 2974525 INFO @ Mon, 03 Jun 2019 05:48:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:48:45: #1 finished! INFO @ Mon, 03 Jun 2019 05:48:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:48:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:48:45: #2 number of paired peaks: 1668 INFO @ Mon, 03 Jun 2019 05:48:45: start model_add_line... INFO @ Mon, 03 Jun 2019 05:48:45: start X-correlation... INFO @ Mon, 03 Jun 2019 05:48:45: end of X-cor INFO @ Mon, 03 Jun 2019 05:48:45: #2 finished! INFO @ Mon, 03 Jun 2019 05:48:45: #2 predicted fragment length is 84 bps INFO @ Mon, 03 Jun 2019 05:48:45: #2 number of paired peaks: 1668 INFO @ Mon, 03 Jun 2019 05:48:45: #2 alternative fragment length(s) may be 84 bps INFO @ Mon, 03 Jun 2019 05:48:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.20_model.r INFO @ Mon, 03 Jun 2019 05:48:45: start model_add_line... INFO @ Mon, 03 Jun 2019 05:48:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:48:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:48:45: start X-correlation... INFO @ Mon, 03 Jun 2019 05:48:45: end of X-cor INFO @ Mon, 03 Jun 2019 05:48:45: #2 finished! INFO @ Mon, 03 Jun 2019 05:48:45: #2 predicted fragment length is 84 bps INFO @ Mon, 03 Jun 2019 05:48:45: #2 alternative fragment length(s) may be 84 bps INFO @ Mon, 03 Jun 2019 05:48:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.10_model.r INFO @ Mon, 03 Jun 2019 05:48:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:48:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:48:45: #2 number of paired peaks: 1668 INFO @ Mon, 03 Jun 2019 05:48:45: start model_add_line... INFO @ Mon, 03 Jun 2019 05:48:45: start X-correlation... INFO @ Mon, 03 Jun 2019 05:48:45: end of X-cor INFO @ Mon, 03 Jun 2019 05:48:45: #2 finished! INFO @ Mon, 03 Jun 2019 05:48:45: #2 predicted fragment length is 84 bps INFO @ Mon, 03 Jun 2019 05:48:45: #2 alternative fragment length(s) may be 84 bps INFO @ Mon, 03 Jun 2019 05:48:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.05_model.r INFO @ Mon, 03 Jun 2019 05:48:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:48:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:48:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:48:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:48:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:48:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:48:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:48:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.10_summits.bed INFO @ Mon, 03 Jun 2019 05:48:59: Done! INFO @ Mon, 03 Jun 2019 05:48:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:48:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:48:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.20_summits.bed INFO @ Mon, 03 Jun 2019 05:48:59: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2185 records, 4 fields): 7 millis CompletedMACS2peakCalling pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (616 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:48:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:48:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:48:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX202118/SRX202118.05_summits.bed INFO @ Mon, 03 Jun 2019 05:48:59: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4602 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。