Job ID = 1306932 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:00:29 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' 2019-06-03T13:00:29 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/sra18/SRR/001188/SRR1217235' 2019-06-03T13:00:38 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1217235' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T13:00:38 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T13:03:50 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 ) 2019-06-03T13:03:50 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 ) 2019-06-03T13:03:50 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 ) 2019-06-03T13:03:51 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 : 8,214,435 reads read : 8,214,435 reads written : 8,214,435 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: 00:04:14 8214435 reads; of these: 8214435 (100.00%) were unpaired; of these: 181508 (2.21%) aligned 0 times 5119822 (62.33%) aligned exactly 1 time 2913105 (35.46%) aligned >1 times 97.79% overall alignment rate Time searching: 00:04:14 Overall time: 00:04:14 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] 505998 / 8032927 = 0.0630 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 22:16:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.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 22:16:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:16:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:16:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.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 22:16:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:16:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:16:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.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 22:16:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:16:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:17:01: 1000000 INFO @ Mon, 03 Jun 2019 22:17:03: 1000000 INFO @ Mon, 03 Jun 2019 22:17:05: 1000000 INFO @ Mon, 03 Jun 2019 22:17:09: 2000000 INFO @ Mon, 03 Jun 2019 22:17:11: 2000000 INFO @ Mon, 03 Jun 2019 22:17:15: 2000000 INFO @ Mon, 03 Jun 2019 22:17:16: 3000000 INFO @ Mon, 03 Jun 2019 22:17:19: 3000000 INFO @ Mon, 03 Jun 2019 22:17:24: 4000000 INFO @ Mon, 03 Jun 2019 22:17:24: 3000000 INFO @ Mon, 03 Jun 2019 22:17:26: 4000000 INFO @ Mon, 03 Jun 2019 22:17:32: 5000000 INFO @ Mon, 03 Jun 2019 22:17:34: 4000000 INFO @ Mon, 03 Jun 2019 22:17:34: 5000000 INFO @ Mon, 03 Jun 2019 22:17:39: 6000000 INFO @ Mon, 03 Jun 2019 22:17:42: 6000000 INFO @ Mon, 03 Jun 2019 22:17:45: 5000000 INFO @ Mon, 03 Jun 2019 22:17:47: 7000000 INFO @ Mon, 03 Jun 2019 22:17:50: 7000000 INFO @ Mon, 03 Jun 2019 22:17:51: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:17:51: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:17:51: #1 total tags in treatment: 7526929 INFO @ Mon, 03 Jun 2019 22:17:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:17:51: #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 22:17:52: #1 tags after filtering in treatment: 7526929 INFO @ Mon, 03 Jun 2019 22:17:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:17:52: #1 finished! INFO @ Mon, 03 Jun 2019 22:17:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:17:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:17:52: #2 number of paired peaks: 1492 INFO @ Mon, 03 Jun 2019 22:17:52: start model_add_line... INFO @ Mon, 03 Jun 2019 22:17:52: start X-correlation... INFO @ Mon, 03 Jun 2019 22:17:52: end of X-cor INFO @ Mon, 03 Jun 2019 22:17:52: #2 finished! INFO @ Mon, 03 Jun 2019 22:17:52: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 22:17:52: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 22:17:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.10_model.r WARNING @ Mon, 03 Jun 2019 22:17:52: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:17:52: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 22:17:52: #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 22:17:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:17:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:17:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:17:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:17:55: #1 total tags in treatment: 7526929 INFO @ Mon, 03 Jun 2019 22:17:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:17:55: #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 22:17:55: #1 tags after filtering in treatment: 7526929 INFO @ Mon, 03 Jun 2019 22:17:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:17:55: #1 finished! INFO @ Mon, 03 Jun 2019 22:17:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:17:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:17:56: #2 number of paired peaks: 1492 INFO @ Mon, 03 Jun 2019 22:17:56: start model_add_line... INFO @ Mon, 03 Jun 2019 22:17:56: start X-correlation... INFO @ Mon, 03 Jun 2019 22:17:56: end of X-cor INFO @ Mon, 03 Jun 2019 22:17:56: #2 finished! INFO @ Mon, 03 Jun 2019 22:17:56: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 22:17:56: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 22:17:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.05_model.r WARNING @ Mon, 03 Jun 2019 22:17:56: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:17:56: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 22:17:56: #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 22:17:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:17:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:17:56: 6000000 INFO @ Mon, 03 Jun 2019 22:18:07: 7000000 INFO @ Mon, 03 Jun 2019 22:18:12: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:18:12: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:18:12: #1 total tags in treatment: 7526929 INFO @ Mon, 03 Jun 2019 22:18:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:18:12: #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 22:18:13: #1 tags after filtering in treatment: 7526929 INFO @ Mon, 03 Jun 2019 22:18:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:18:13: #1 finished! INFO @ Mon, 03 Jun 2019 22:18:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:18:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:18:13: #2 number of paired peaks: 1492 INFO @ Mon, 03 Jun 2019 22:18:13: start model_add_line... INFO @ Mon, 03 Jun 2019 22:18:14: start X-correlation... INFO @ Mon, 03 Jun 2019 22:18:14: end of X-cor INFO @ Mon, 03 Jun 2019 22:18:14: #2 finished! INFO @ Mon, 03 Jun 2019 22:18:14: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 22:18:14: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 22:18:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.20_model.r WARNING @ Mon, 03 Jun 2019 22:18:14: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:18:14: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 22:18:14: #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 22:18:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:18:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:18:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:18:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:18:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:18:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:18:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.10_summits.bed INFO @ Mon, 03 Jun 2019 22:18:27: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1844 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:18:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:18:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:18:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.05_summits.bed INFO @ Mon, 03 Jun 2019 22:18:29: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3087 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:18:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:18:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:18:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:18:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511130/SRX511130.20_summits.bed INFO @ Mon, 03 Jun 2019 22:18:47: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (891 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。