Job ID = 1292592 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T10:35:33 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' 2019-06-02T10:35:33 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/sra17/SRR/001170/SRR1198375' 2019-06-02T10:35:42 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1198375' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T10:37:24 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 ) 2019-06-02T10:37:24 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 : 15,611,842 reads read : 15,611,842 reads written : 15,611,842 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: 00:03:24 15611842 reads; of these: 15611842 (100.00%) were unpaired; of these: 956500 (6.13%) aligned 0 times 9800653 (62.78%) aligned exactly 1 time 4854689 (31.10%) aligned >1 times 93.87% overall alignment rate Time searching: 00:03:24 Overall time: 00:03:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 6904749 / 14655342 = 0.4711 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 @ Sun, 02 Jun 2019 19:55:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 19:55:36: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:55:36: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:55:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 19:55:36: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:55:36: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:55:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 19:55:36: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:55:36: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:55:45: 1000000 INFO @ Sun, 02 Jun 2019 19:55:47: 1000000 INFO @ Sun, 02 Jun 2019 19:55:47: 1000000 INFO @ Sun, 02 Jun 2019 19:55:54: 2000000 INFO @ Sun, 02 Jun 2019 19:55:57: 2000000 INFO @ Sun, 02 Jun 2019 19:55:57: 2000000 INFO @ Sun, 02 Jun 2019 19:56:02: 3000000 INFO @ Sun, 02 Jun 2019 19:56:08: 3000000 INFO @ Sun, 02 Jun 2019 19:56:08: 3000000 INFO @ Sun, 02 Jun 2019 19:56:10: 4000000 INFO @ Sun, 02 Jun 2019 19:56:18: 4000000 INFO @ Sun, 02 Jun 2019 19:56:18: 4000000 INFO @ Sun, 02 Jun 2019 19:56:19: 5000000 INFO @ Sun, 02 Jun 2019 19:56:27: 6000000 INFO @ Sun, 02 Jun 2019 19:56:29: 5000000 INFO @ Sun, 02 Jun 2019 19:56:29: 5000000 INFO @ Sun, 02 Jun 2019 19:56:35: 7000000 INFO @ Sun, 02 Jun 2019 19:56:40: 6000000 INFO @ Sun, 02 Jun 2019 19:56:40: 6000000 INFO @ Sun, 02 Jun 2019 19:56:42: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:56:42: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:56:42: #1 total tags in treatment: 7750593 INFO @ Sun, 02 Jun 2019 19:56:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:56:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:56:42: #1 tags after filtering in treatment: 7750593 INFO @ Sun, 02 Jun 2019 19:56:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:56:42: #1 finished! INFO @ Sun, 02 Jun 2019 19:56:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:56:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:56:43: #2 number of paired peaks: 5939 INFO @ Sun, 02 Jun 2019 19:56:43: start model_add_line... INFO @ Sun, 02 Jun 2019 19:56:44: start X-correlation... INFO @ Sun, 02 Jun 2019 19:56:44: end of X-cor INFO @ Sun, 02 Jun 2019 19:56:44: #2 finished! INFO @ Sun, 02 Jun 2019 19:56:44: #2 predicted fragment length is 216 bps INFO @ Sun, 02 Jun 2019 19:56:44: #2 alternative fragment length(s) may be 3,202,216 bps INFO @ Sun, 02 Jun 2019 19:56:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.05_model.r INFO @ Sun, 02 Jun 2019 19:56:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:56:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:56:50: 7000000 INFO @ Sun, 02 Jun 2019 19:56:50: 7000000 INFO @ Sun, 02 Jun 2019 19:56:57: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:56:57: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:56:57: #1 total tags in treatment: 7750593 INFO @ Sun, 02 Jun 2019 19:56:57: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:56:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:56:57: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:56:57: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:56:57: #1 total tags in treatment: 7750593 INFO @ Sun, 02 Jun 2019 19:56:57: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:56:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:56:57: #1 tags after filtering in treatment: 7750593 INFO @ Sun, 02 Jun 2019 19:56:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:56:57: #1 finished! INFO @ Sun, 02 Jun 2019 19:56:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:56:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:56:57: #1 tags after filtering in treatment: 7750593 INFO @ Sun, 02 Jun 2019 19:56:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:56:57: #1 finished! INFO @ Sun, 02 Jun 2019 19:56:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:56:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:56:59: #2 number of paired peaks: 5939 INFO @ Sun, 02 Jun 2019 19:56:59: start model_add_line... INFO @ Sun, 02 Jun 2019 19:56:59: #2 number of paired peaks: 5939 INFO @ Sun, 02 Jun 2019 19:56:59: start model_add_line... INFO @ Sun, 02 Jun 2019 19:56:59: start X-correlation... INFO @ Sun, 02 Jun 2019 19:56:59: end of X-cor INFO @ Sun, 02 Jun 2019 19:56:59: #2 finished! INFO @ Sun, 02 Jun 2019 19:56:59: #2 predicted fragment length is 216 bps INFO @ Sun, 02 Jun 2019 19:56:59: #2 alternative fragment length(s) may be 3,202,216 bps INFO @ Sun, 02 Jun 2019 19:56:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.10_model.r INFO @ Sun, 02 Jun 2019 19:56:59: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:56:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:56:59: start X-correlation... INFO @ Sun, 02 Jun 2019 19:56:59: end of X-cor INFO @ Sun, 02 Jun 2019 19:56:59: #2 finished! INFO @ Sun, 02 Jun 2019 19:56:59: #2 predicted fragment length is 216 bps INFO @ Sun, 02 Jun 2019 19:56:59: #2 alternative fragment length(s) may be 3,202,216 bps INFO @ Sun, 02 Jun 2019 19:56:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.20_model.r INFO @ Sun, 02 Jun 2019 19:56:59: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:56:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:57:19: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:57:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:57:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:57:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.05_summits.bed INFO @ Sun, 02 Jun 2019 19:57:30: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3495 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:57:35: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:57:35: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 02 Jun 2019 19:57:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:57:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:57:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.20_summits.bed INFO @ Sun, 02 Jun 2019 19:57:46: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (782 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:57:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:57:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:57:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494843/SRX494843.10_summits.bed INFO @ Sun, 02 Jun 2019 19:57:46: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1990 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。