Job ID = 1306726 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T12:50:46 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' 2019-06-03T12:50:46 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/001184/SRR1213172' 2019-06-03T12:50:46 fasterq-dump.2.9.6 err: invalid accession 'SRR1213172' spots read : 3,216,665 reads read : 3,216,665 reads written : 3,216,665 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: 00:01:36 3216665 reads; of these: 3216665 (100.00%) were unpaired; of these: 192731 (5.99%) aligned 0 times 2117425 (65.83%) aligned exactly 1 time 906509 (28.18%) aligned >1 times 94.01% overall alignment rate Time searching: 00:01:36 Overall time: 00:01:36 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] 838816 / 3023934 = 0.2774 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 21:55:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.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 21:55:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:55:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:55:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.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 21:55:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:55:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:55:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.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 21:55:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:55:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:55:49: 1000000 INFO @ Mon, 03 Jun 2019 21:55:50: 1000000 INFO @ Mon, 03 Jun 2019 21:55:51: 1000000 INFO @ Mon, 03 Jun 2019 21:55:58: 2000000 INFO @ Mon, 03 Jun 2019 21:55:59: 2000000 INFO @ Mon, 03 Jun 2019 21:56:00: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:56:00: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:56:00: #1 total tags in treatment: 2185118 INFO @ Mon, 03 Jun 2019 21:56:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:56:00: #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 21:56:00: #1 tags after filtering in treatment: 2185118 INFO @ Mon, 03 Jun 2019 21:56:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:56:00: #1 finished! INFO @ Mon, 03 Jun 2019 21:56:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:56:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:56:00: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:56:00: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:56:00: #1 total tags in treatment: 2185118 INFO @ Mon, 03 Jun 2019 21:56:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:56:00: #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 21:56:00: #1 tags after filtering in treatment: 2185118 INFO @ Mon, 03 Jun 2019 21:56:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:56:00: #1 finished! INFO @ Mon, 03 Jun 2019 21:56:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:56:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:56:00: #2 number of paired peaks: 1446 INFO @ Mon, 03 Jun 2019 21:56:00: start model_add_line... INFO @ Mon, 03 Jun 2019 21:56:00: start X-correlation... INFO @ Mon, 03 Jun 2019 21:56:00: end of X-cor INFO @ Mon, 03 Jun 2019 21:56:00: #2 finished! INFO @ Mon, 03 Jun 2019 21:56:00: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 21:56:00: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 03 Jun 2019 21:56:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.05_model.r WARNING @ Mon, 03 Jun 2019 21:56:00: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 21:56:00: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 03 Jun 2019 21:56:00: #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 21:56:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:56:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:56:00: #2 number of paired peaks: 1446 INFO @ Mon, 03 Jun 2019 21:56:00: start model_add_line... INFO @ Mon, 03 Jun 2019 21:56:00: start X-correlation... INFO @ Mon, 03 Jun 2019 21:56:00: end of X-cor INFO @ Mon, 03 Jun 2019 21:56:00: #2 finished! INFO @ Mon, 03 Jun 2019 21:56:00: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 21:56:00: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 03 Jun 2019 21:56:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.10_model.r WARNING @ Mon, 03 Jun 2019 21:56:00: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 21:56:00: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 03 Jun 2019 21:56:00: #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 21:56:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:56:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:56:02: 2000000 INFO @ Mon, 03 Jun 2019 21:56:03: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:56:03: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:56:03: #1 total tags in treatment: 2185118 INFO @ Mon, 03 Jun 2019 21:56:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:56:03: #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 21:56:03: #1 tags after filtering in treatment: 2185118 INFO @ Mon, 03 Jun 2019 21:56:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:56:03: #1 finished! INFO @ Mon, 03 Jun 2019 21:56:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:56:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:56:04: #2 number of paired peaks: 1446 INFO @ Mon, 03 Jun 2019 21:56:04: start model_add_line... INFO @ Mon, 03 Jun 2019 21:56:04: start X-correlation... INFO @ Mon, 03 Jun 2019 21:56:04: end of X-cor INFO @ Mon, 03 Jun 2019 21:56:04: #2 finished! INFO @ Mon, 03 Jun 2019 21:56:04: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 21:56:04: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 03 Jun 2019 21:56:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.20_model.r WARNING @ Mon, 03 Jun 2019 21:56:04: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 21:56:04: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 03 Jun 2019 21:56:04: #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 21:56:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:56:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:56:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:56:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:56:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:56:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.05_peaks.xls INFO @ Mon, 03 Jun 2019 21:56:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:56:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.05_summits.bed INFO @ Mon, 03 Jun 2019 21:56:11: Done! INFO @ Mon, 03 Jun 2019 21:56:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.10_peaks.xls INFO @ Mon, 03 Jun 2019 21:56:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.10_peaks.narrowPeak pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1456 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:56:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.10_summits.bed INFO @ Mon, 03 Jun 2019 21:56:11: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (922 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:56:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.20_peaks.xls INFO @ Mon, 03 Jun 2019 21:56:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:56:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507385/SRX507385.20_summits.bed INFO @ Mon, 03 Jun 2019 21:56:14: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (447 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。