Job ID = 1294253 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T20:46:02 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' 2019-06-02T20:46:02 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/sra36/SRR/000616/SRR631788' 2019-06-02T20:46:02 fasterq-dump.2.9.6 err: invalid accession 'SRR631788' spots read : 8,270,656 reads read : 8,270,656 reads written : 8,270,656 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: 00:02:38 8270656 reads; of these: 8270656 (100.00%) were unpaired; of these: 411009 (4.97%) aligned 0 times 6034327 (72.96%) aligned exactly 1 time 1825320 (22.07%) aligned >1 times 95.03% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 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] 679885 / 7859647 = 0.0865 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 05:56:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.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 05:56:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:56:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:56:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.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 05:56:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:56:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:56:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.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 05:56:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:56:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:56:21: 1000000 INFO @ Mon, 03 Jun 2019 05:56:23: 1000000 INFO @ Mon, 03 Jun 2019 05:56:24: 1000000 INFO @ Mon, 03 Jun 2019 05:56:29: 2000000 INFO @ Mon, 03 Jun 2019 05:56:32: 2000000 INFO @ Mon, 03 Jun 2019 05:56:35: 2000000 INFO @ Mon, 03 Jun 2019 05:56:37: 3000000 INFO @ Mon, 03 Jun 2019 05:56:41: 3000000 INFO @ Mon, 03 Jun 2019 05:56:45: 4000000 INFO @ Mon, 03 Jun 2019 05:56:46: 3000000 INFO @ Mon, 03 Jun 2019 05:56:51: 4000000 INFO @ Mon, 03 Jun 2019 05:56:53: 5000000 INFO @ Mon, 03 Jun 2019 05:56:58: 4000000 INFO @ Mon, 03 Jun 2019 05:57:00: 5000000 INFO @ Mon, 03 Jun 2019 05:57:01: 6000000 INFO @ Mon, 03 Jun 2019 05:57:09: 5000000 INFO @ Mon, 03 Jun 2019 05:57:10: 6000000 INFO @ Mon, 03 Jun 2019 05:57:10: 7000000 INFO @ Mon, 03 Jun 2019 05:57:11: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:57:11: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:57:11: #1 total tags in treatment: 7179762 INFO @ Mon, 03 Jun 2019 05:57:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:57:11: #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 05:57:11: #1 tags after filtering in treatment: 7179762 INFO @ Mon, 03 Jun 2019 05:57:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:57:11: #1 finished! INFO @ Mon, 03 Jun 2019 05:57:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:57:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:57:12: #2 number of paired peaks: 102 WARNING @ Mon, 03 Jun 2019 05:57:12: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Mon, 03 Jun 2019 05:57:12: start model_add_line... INFO @ Mon, 03 Jun 2019 05:57:12: start X-correlation... INFO @ Mon, 03 Jun 2019 05:57:12: end of X-cor INFO @ Mon, 03 Jun 2019 05:57:12: #2 finished! INFO @ Mon, 03 Jun 2019 05:57:12: #2 predicted fragment length is 39 bps INFO @ Mon, 03 Jun 2019 05:57:12: #2 alternative fragment length(s) may be 39 bps INFO @ Mon, 03 Jun 2019 05:57:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.20_model.r WARNING @ Mon, 03 Jun 2019 05:57:12: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:57:12: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Mon, 03 Jun 2019 05:57:12: #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 05:57:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:57:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:57:19: 7000000 INFO @ Mon, 03 Jun 2019 05:57:20: 6000000 INFO @ Mon, 03 Jun 2019 05:57:21: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:57:21: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:57:21: #1 total tags in treatment: 7179762 INFO @ Mon, 03 Jun 2019 05:57:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:57:21: #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 05:57:21: #1 tags after filtering in treatment: 7179762 INFO @ Mon, 03 Jun 2019 05:57:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:57:21: #1 finished! INFO @ Mon, 03 Jun 2019 05:57:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:57:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:57:22: #2 number of paired peaks: 102 WARNING @ Mon, 03 Jun 2019 05:57:22: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Mon, 03 Jun 2019 05:57:22: start model_add_line... INFO @ Mon, 03 Jun 2019 05:57:22: start X-correlation... INFO @ Mon, 03 Jun 2019 05:57:22: end of X-cor INFO @ Mon, 03 Jun 2019 05:57:22: #2 finished! INFO @ Mon, 03 Jun 2019 05:57:22: #2 predicted fragment length is 39 bps INFO @ Mon, 03 Jun 2019 05:57:22: #2 alternative fragment length(s) may be 39 bps INFO @ Mon, 03 Jun 2019 05:57:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.10_model.r WARNING @ Mon, 03 Jun 2019 05:57:22: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:57:22: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Mon, 03 Jun 2019 05:57:22: #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 05:57:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:57:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:57:31: 7000000 INFO @ Mon, 03 Jun 2019 05:57:33: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:57:33: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:57:33: #1 total tags in treatment: 7179762 INFO @ Mon, 03 Jun 2019 05:57:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:57:33: #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 05:57:33: #1 tags after filtering in treatment: 7179762 INFO @ Mon, 03 Jun 2019 05:57:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:57:33: #1 finished! INFO @ Mon, 03 Jun 2019 05:57:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:57:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:57:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:57:34: #2 number of paired peaks: 102 WARNING @ Mon, 03 Jun 2019 05:57:34: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Mon, 03 Jun 2019 05:57:34: start model_add_line... INFO @ Mon, 03 Jun 2019 05:57:34: start X-correlation... INFO @ Mon, 03 Jun 2019 05:57:34: end of X-cor INFO @ Mon, 03 Jun 2019 05:57:34: #2 finished! INFO @ Mon, 03 Jun 2019 05:57:34: #2 predicted fragment length is 39 bps INFO @ Mon, 03 Jun 2019 05:57:34: #2 alternative fragment length(s) may be 39 bps INFO @ Mon, 03 Jun 2019 05:57:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.05_model.r WARNING @ Mon, 03 Jun 2019 05:57:34: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:57:34: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Mon, 03 Jun 2019 05:57:34: #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 05:57:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:57:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:57:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:57:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:57:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:57:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.20_summits.bed INFO @ Mon, 03 Jun 2019 05:57:44: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (248 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:57:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:57:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:57:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.10_summits.bed INFO @ Mon, 03 Jun 2019 05:57:53: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (564 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:57:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:58:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:58:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:58:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX209933/SRX209933.05_summits.bed INFO @ Mon, 03 Jun 2019 05:58:05: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (977 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。