Job ID = 1293917 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T18:16:17 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' 2019-06-02T18:16:17 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/refseq/NC_000081.5' 2019-06-02T18:18:08 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 ) 2019-06-02T18:20:18 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 ) 2019-06-02T18:31:57 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 : 65,367,367 reads read : 65,367,367 reads written : 65,367,367 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: 00:08:52 65367367 reads; of these: 65367367 (100.00%) were unpaired; of these: 60752894 (92.94%) aligned 0 times 2940898 (4.50%) aligned exactly 1 time 1673575 (2.56%) aligned >1 times 7.06% overall alignment rate Time searching: 00:08:52 Overall time: 00:08:52 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_rmdupse_core] 645785 / 4614473 = 0.1399 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 03:55:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.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 03:55:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:55:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:55:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.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 03:55:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:55:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:55:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.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 03:55:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:55:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:56:03: 1000000 INFO @ Mon, 03 Jun 2019 03:56:03: 1000000 INFO @ Mon, 03 Jun 2019 03:56:04: 1000000 INFO @ Mon, 03 Jun 2019 03:56:12: 2000000 INFO @ Mon, 03 Jun 2019 03:56:14: 2000000 INFO @ Mon, 03 Jun 2019 03:56:14: 2000000 INFO @ Mon, 03 Jun 2019 03:56:22: 3000000 INFO @ Mon, 03 Jun 2019 03:56:24: 3000000 INFO @ Mon, 03 Jun 2019 03:56:25: 3000000 INFO @ Mon, 03 Jun 2019 03:56:30: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:56:30: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:56:30: #1 total tags in treatment: 3968688 INFO @ Mon, 03 Jun 2019 03:56:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:56:30: #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 03:56:30: #1 tags after filtering in treatment: 3968688 INFO @ Mon, 03 Jun 2019 03:56:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:56:30: #1 finished! INFO @ Mon, 03 Jun 2019 03:56:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:56:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:56:31: #2 number of paired peaks: 820 WARNING @ Mon, 03 Jun 2019 03:56:31: Fewer paired peaks (820) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 820 pairs to build model! INFO @ Mon, 03 Jun 2019 03:56:31: start model_add_line... INFO @ Mon, 03 Jun 2019 03:56:31: start X-correlation... INFO @ Mon, 03 Jun 2019 03:56:31: end of X-cor INFO @ Mon, 03 Jun 2019 03:56:31: #2 finished! INFO @ Mon, 03 Jun 2019 03:56:31: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 03:56:31: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 03:56:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.05_model.r WARNING @ Mon, 03 Jun 2019 03:56:31: #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 03:56:31: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 03:56:31: #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 03:56:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:56:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:56:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:56:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:56:34: #1 total tags in treatment: 3968688 INFO @ Mon, 03 Jun 2019 03:56:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:56:34: #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 03:56:34: #1 tags after filtering in treatment: 3968688 INFO @ Mon, 03 Jun 2019 03:56:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:56:34: #1 finished! INFO @ Mon, 03 Jun 2019 03:56:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:56:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:56:34: #2 number of paired peaks: 820 WARNING @ Mon, 03 Jun 2019 03:56:34: Fewer paired peaks (820) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 820 pairs to build model! INFO @ Mon, 03 Jun 2019 03:56:34: start model_add_line... INFO @ Mon, 03 Jun 2019 03:56:34: start X-correlation... INFO @ Mon, 03 Jun 2019 03:56:34: end of X-cor INFO @ Mon, 03 Jun 2019 03:56:34: #2 finished! INFO @ Mon, 03 Jun 2019 03:56:34: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 03:56:34: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 03:56:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.10_model.r WARNING @ Mon, 03 Jun 2019 03:56:34: #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 03:56:34: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 03:56:34: #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 03:56:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:56:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:56:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:56:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:56:34: #1 total tags in treatment: 3968688 INFO @ Mon, 03 Jun 2019 03:56:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:56:34: #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 03:56:35: #1 tags after filtering in treatment: 3968688 INFO @ Mon, 03 Jun 2019 03:56:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:56:35: #1 finished! INFO @ Mon, 03 Jun 2019 03:56:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:56:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:56:35: #2 number of paired peaks: 820 WARNING @ Mon, 03 Jun 2019 03:56:35: Fewer paired peaks (820) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 820 pairs to build model! INFO @ Mon, 03 Jun 2019 03:56:35: start model_add_line... INFO @ Mon, 03 Jun 2019 03:56:35: start X-correlation... INFO @ Mon, 03 Jun 2019 03:56:35: end of X-cor INFO @ Mon, 03 Jun 2019 03:56:35: #2 finished! INFO @ Mon, 03 Jun 2019 03:56:35: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 03:56:35: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 03:56:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.20_model.r WARNING @ Mon, 03 Jun 2019 03:56:35: #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 03:56:35: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 03:56:35: #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 03:56:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:56:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:56:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:56:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:56:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:56:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:56:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:56:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.05_summits.bed INFO @ Mon, 03 Jun 2019 03:56:49: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1793 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:56:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:56:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:56:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.10_summits.bed INFO @ Mon, 03 Jun 2019 03:56:52: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (988 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:56:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:56:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:56:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1473021/SRX1473021.20_summits.bed INFO @ Mon, 03 Jun 2019 03:56:53: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (352 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。