Job ID = 1294402 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T22:11:27 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' 2019-06-02T22:11:27 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/SRR869719' 2019-06-02T22:11:36 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR869719' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T22:11:36 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 13,358,141 reads read : 13,358,141 reads written : 13,358,141 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: 00:08:19 13358141 reads; of these: 13358141 (100.00%) were unpaired; of these: 617228 (4.62%) aligned 0 times 5816192 (43.54%) aligned exactly 1 time 6924721 (51.84%) aligned >1 times 95.38% overall alignment rate Time searching: 00:08:20 Overall time: 00:08:20 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 8 files... [bam_rmdupse_core] 1906136 / 12740913 = 0.1496 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 07:39:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.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 07:39:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:39:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:39:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.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 07:39:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:39:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:39:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.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 07:39:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:39:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:39:29: 1000000 INFO @ Mon, 03 Jun 2019 07:39:29: 1000000 INFO @ Mon, 03 Jun 2019 07:39:30: 1000000 INFO @ Mon, 03 Jun 2019 07:39:37: 2000000 INFO @ Mon, 03 Jun 2019 07:39:38: 2000000 INFO @ Mon, 03 Jun 2019 07:39:38: 2000000 INFO @ Mon, 03 Jun 2019 07:39:45: 3000000 INFO @ Mon, 03 Jun 2019 07:39:46: 3000000 INFO @ Mon, 03 Jun 2019 07:39:46: 3000000 INFO @ Mon, 03 Jun 2019 07:39:52: 4000000 INFO @ Mon, 03 Jun 2019 07:39:54: 4000000 INFO @ Mon, 03 Jun 2019 07:39:55: 4000000 INFO @ Mon, 03 Jun 2019 07:40:00: 5000000 INFO @ Mon, 03 Jun 2019 07:40:02: 5000000 INFO @ Mon, 03 Jun 2019 07:40:03: 5000000 INFO @ Mon, 03 Jun 2019 07:40:08: 6000000 INFO @ Mon, 03 Jun 2019 07:40:09: 6000000 INFO @ Mon, 03 Jun 2019 07:40:11: 6000000 INFO @ Mon, 03 Jun 2019 07:40:15: 7000000 INFO @ Mon, 03 Jun 2019 07:40:17: 7000000 INFO @ Mon, 03 Jun 2019 07:40:19: 7000000 INFO @ Mon, 03 Jun 2019 07:40:23: 8000000 INFO @ Mon, 03 Jun 2019 07:40:25: 8000000 INFO @ Mon, 03 Jun 2019 07:40:28: 8000000 INFO @ Mon, 03 Jun 2019 07:40:31: 9000000 INFO @ Mon, 03 Jun 2019 07:40:33: 9000000 INFO @ Mon, 03 Jun 2019 07:40:36: 9000000 INFO @ Mon, 03 Jun 2019 07:40:39: 10000000 INFO @ Mon, 03 Jun 2019 07:40:42: 10000000 INFO @ Mon, 03 Jun 2019 07:40:45: 10000000 INFO @ Mon, 03 Jun 2019 07:40:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:40:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:40:46: #1 total tags in treatment: 10834777 INFO @ Mon, 03 Jun 2019 07:40:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:40:46: #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 07:40:46: #1 tags after filtering in treatment: 10834777 INFO @ Mon, 03 Jun 2019 07:40:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:40:46: #1 finished! INFO @ Mon, 03 Jun 2019 07:40:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:40:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:40:47: #2 number of paired peaks: 589 WARNING @ Mon, 03 Jun 2019 07:40:47: Fewer paired peaks (589) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 589 pairs to build model! INFO @ Mon, 03 Jun 2019 07:40:47: start model_add_line... INFO @ Mon, 03 Jun 2019 07:40:47: start X-correlation... INFO @ Mon, 03 Jun 2019 07:40:47: end of X-cor INFO @ Mon, 03 Jun 2019 07:40:47: #2 finished! INFO @ Mon, 03 Jun 2019 07:40:47: #2 predicted fragment length is 57 bps INFO @ Mon, 03 Jun 2019 07:40:47: #2 alternative fragment length(s) may be 57 bps INFO @ Mon, 03 Jun 2019 07:40:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.05_model.r WARNING @ Mon, 03 Jun 2019 07:40:47: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:40:47: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Mon, 03 Jun 2019 07:40:47: #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 07:40:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:40:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:40:49: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:40:49: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:40:49: #1 total tags in treatment: 10834777 INFO @ Mon, 03 Jun 2019 07:40:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:40:49: #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 07:40:49: #1 tags after filtering in treatment: 10834777 INFO @ Mon, 03 Jun 2019 07:40:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:40:49: #1 finished! INFO @ Mon, 03 Jun 2019 07:40:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:40:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:40:50: #2 number of paired peaks: 589 WARNING @ Mon, 03 Jun 2019 07:40:50: Fewer paired peaks (589) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 589 pairs to build model! INFO @ Mon, 03 Jun 2019 07:40:50: start model_add_line... INFO @ Mon, 03 Jun 2019 07:40:51: start X-correlation... INFO @ Mon, 03 Jun 2019 07:40:51: end of X-cor INFO @ Mon, 03 Jun 2019 07:40:51: #2 finished! INFO @ Mon, 03 Jun 2019 07:40:51: #2 predicted fragment length is 57 bps INFO @ Mon, 03 Jun 2019 07:40:51: #2 alternative fragment length(s) may be 57 bps INFO @ Mon, 03 Jun 2019 07:40:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.10_model.r WARNING @ Mon, 03 Jun 2019 07:40:51: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:40:51: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Mon, 03 Jun 2019 07:40:51: #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 07:40:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:40:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:40:52: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:40:52: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:40:52: #1 total tags in treatment: 10834777 INFO @ Mon, 03 Jun 2019 07:40:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:40:52: #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 07:40:52: #1 tags after filtering in treatment: 10834777 INFO @ Mon, 03 Jun 2019 07:40:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:40:52: #1 finished! INFO @ Mon, 03 Jun 2019 07:40:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:40:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:40:53: #2 number of paired peaks: 589 WARNING @ Mon, 03 Jun 2019 07:40:53: Fewer paired peaks (589) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 589 pairs to build model! INFO @ Mon, 03 Jun 2019 07:40:53: start model_add_line... INFO @ Mon, 03 Jun 2019 07:40:53: start X-correlation... INFO @ Mon, 03 Jun 2019 07:40:53: end of X-cor INFO @ Mon, 03 Jun 2019 07:40:53: #2 finished! INFO @ Mon, 03 Jun 2019 07:40:53: #2 predicted fragment length is 57 bps INFO @ Mon, 03 Jun 2019 07:40:53: #2 alternative fragment length(s) may be 57 bps INFO @ Mon, 03 Jun 2019 07:40:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.20_model.r WARNING @ Mon, 03 Jun 2019 07:40:53: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:40:53: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Mon, 03 Jun 2019 07:40:53: #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 07:40:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:40:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:41:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:41:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:41:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:41:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.05_peaks.xls INFO @ Mon, 03 Jun 2019 07:41:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:41:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.05_summits.bed INFO @ Mon, 03 Jun 2019 07:41:35: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (5034 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:41:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:41:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:41:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.10_summits.bed INFO @ Mon, 03 Jun 2019 07:41:37: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2397 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:41:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:41:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:41:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287576/SRX287576.20_summits.bed INFO @ Mon, 03 Jun 2019 07:41:40: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1277 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。