Job ID = 1293378 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T14:10:58 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' 2019-06-02T14:10:58 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/era18/ERR/ERR1912/ERR1912872' 2019-06-02T14:10:58 fasterq-dump.2.9.6 err: invalid accession 'ERR1912872' spots read : 2,533,492 reads read : 5,066,984 reads written : 5,066,984 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: 00:06:52 2533492 reads; of these: 2533492 (100.00%) were paired; of these: 339700 (13.41%) aligned concordantly 0 times 1558613 (61.52%) aligned concordantly exactly 1 time 635179 (25.07%) aligned concordantly >1 times ---- 339700 pairs aligned concordantly 0 times; of these: 71226 (20.97%) aligned discordantly 1 time ---- 268474 pairs aligned 0 times concordantly or discordantly; of these: 536948 mates make up the pairs; of these: 449048 (83.63%) aligned 0 times 32993 (6.14%) aligned exactly 1 time 54907 (10.23%) aligned >1 times 91.14% overall alignment rate Time searching: 00:06:52 Overall time: 00:06:52 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 15700 / 2253421 = 0.0070 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 23:24:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.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 @ Sun, 02 Jun 2019 23:24:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:24:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:24:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.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 @ Sun, 02 Jun 2019 23:24:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:24:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:24:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.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 @ Sun, 02 Jun 2019 23:24:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:24:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:24:15: 1000000 INFO @ Sun, 02 Jun 2019 23:24:15: 1000000 INFO @ Sun, 02 Jun 2019 23:24:16: 1000000 INFO @ Sun, 02 Jun 2019 23:24:24: 2000000 INFO @ Sun, 02 Jun 2019 23:24:24: 2000000 INFO @ Sun, 02 Jun 2019 23:24:26: 2000000 INFO @ Sun, 02 Jun 2019 23:24:33: 3000000 INFO @ Sun, 02 Jun 2019 23:24:33: 3000000 INFO @ Sun, 02 Jun 2019 23:24:37: 3000000 INFO @ Sun, 02 Jun 2019 23:24:42: 4000000 INFO @ Sun, 02 Jun 2019 23:24:42: 4000000 INFO @ Sun, 02 Jun 2019 23:24:47: 4000000 INFO @ Sun, 02 Jun 2019 23:24:47: #1 tag size is determined as 82 bps INFO @ Sun, 02 Jun 2019 23:24:47: #1 tag size = 82 INFO @ Sun, 02 Jun 2019 23:24:47: #1 total tags in treatment: 2178133 INFO @ Sun, 02 Jun 2019 23:24:47: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:24:47: #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 23:24:48: #1 tags after filtering in treatment: 2099326 INFO @ Sun, 02 Jun 2019 23:24:48: #1 Redundant rate of treatment: 0.04 INFO @ Sun, 02 Jun 2019 23:24:48: #1 finished! INFO @ Sun, 02 Jun 2019 23:24:48: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:24:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:24:48: #1 tag size is determined as 82 bps INFO @ Sun, 02 Jun 2019 23:24:48: #1 tag size = 82 INFO @ Sun, 02 Jun 2019 23:24:48: #1 total tags in treatment: 2178133 INFO @ Sun, 02 Jun 2019 23:24:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:24:48: #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 23:24:48: #1 tags after filtering in treatment: 2099326 INFO @ Sun, 02 Jun 2019 23:24:48: #1 Redundant rate of treatment: 0.04 INFO @ Sun, 02 Jun 2019 23:24:48: #1 finished! INFO @ Sun, 02 Jun 2019 23:24:48: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:24:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:24:48: #2 number of paired peaks: 128 WARNING @ Sun, 02 Jun 2019 23:24:48: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sun, 02 Jun 2019 23:24:48: start model_add_line... INFO @ Sun, 02 Jun 2019 23:24:48: start X-correlation... INFO @ Sun, 02 Jun 2019 23:24:48: end of X-cor INFO @ Sun, 02 Jun 2019 23:24:48: #2 finished! INFO @ Sun, 02 Jun 2019 23:24:48: #2 predicted fragment length is 100 bps INFO @ Sun, 02 Jun 2019 23:24:48: #2 alternative fragment length(s) may be 100 bps INFO @ Sun, 02 Jun 2019 23:24:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.05_model.r WARNING @ Sun, 02 Jun 2019 23:24:48: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:24:48: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Sun, 02 Jun 2019 23:24:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:24:48: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:24:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:24:48: #2 number of paired peaks: 128 WARNING @ Sun, 02 Jun 2019 23:24:48: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sun, 02 Jun 2019 23:24:48: start model_add_line... INFO @ Sun, 02 Jun 2019 23:24:48: start X-correlation... INFO @ Sun, 02 Jun 2019 23:24:48: end of X-cor INFO @ Sun, 02 Jun 2019 23:24:48: #2 finished! INFO @ Sun, 02 Jun 2019 23:24:48: #2 predicted fragment length is 100 bps INFO @ Sun, 02 Jun 2019 23:24:48: #2 alternative fragment length(s) may be 100 bps INFO @ Sun, 02 Jun 2019 23:24:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.10_model.r WARNING @ Sun, 02 Jun 2019 23:24:48: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:24:48: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Sun, 02 Jun 2019 23:24:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:24:48: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:24:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:24:53: #1 tag size is determined as 82 bps INFO @ Sun, 02 Jun 2019 23:24:53: #1 tag size = 82 INFO @ Sun, 02 Jun 2019 23:24:53: #1 total tags in treatment: 2178133 INFO @ Sun, 02 Jun 2019 23:24:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:24:53: #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 23:24:53: #1 tags after filtering in treatment: 2099326 INFO @ Sun, 02 Jun 2019 23:24:53: #1 Redundant rate of treatment: 0.04 INFO @ Sun, 02 Jun 2019 23:24:53: #1 finished! INFO @ Sun, 02 Jun 2019 23:24:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:24:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:24:53: #2 number of paired peaks: 128 WARNING @ Sun, 02 Jun 2019 23:24:53: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sun, 02 Jun 2019 23:24:53: start model_add_line... INFO @ Sun, 02 Jun 2019 23:24:53: start X-correlation... INFO @ Sun, 02 Jun 2019 23:24:53: end of X-cor INFO @ Sun, 02 Jun 2019 23:24:53: #2 finished! INFO @ Sun, 02 Jun 2019 23:24:53: #2 predicted fragment length is 100 bps INFO @ Sun, 02 Jun 2019 23:24:53: #2 alternative fragment length(s) may be 100 bps INFO @ Sun, 02 Jun 2019 23:24:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.20_model.r WARNING @ Sun, 02 Jun 2019 23:24:53: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:24:53: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Sun, 02 Jun 2019 23:24:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:24:53: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:24:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:24:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:24:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:24:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:24:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:24:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.05_summits.bed INFO @ Sun, 02 Jun 2019 23:24:58: Done! INFO @ Sun, 02 Jun 2019 23:24:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:24:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:24:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.10_summits.bed pass1 - making usageList (11 chroms): 1 millis INFO @ Sun, 02 Jun 2019 23:24:58: Done! pass2 - checking and writing primary data (281 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (147 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:24:59: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:25:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:25:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:25:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1973295/ERX1973295.20_summits.bed INFO @ Sun, 02 Jun 2019 23:25:02: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (76 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。