Job ID = 1294028 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T19:11:51 fasterq-dump.2.9.6 sys: timeout exhausted while creating file within network system module - Failed to Make Connection in KClientHttpOpen to 'www.ncbi.nlm.nih.gov:443' 2019-06-02T19:11:51 fasterq-dump.2.9.6 err: invalid accession 'SRR3503065' spots read : 4,878,566 reads read : 9,757,132 reads written : 4,878,566 reads 0-length : 4,878,566 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: 00:09:25 4878566 reads; of these: 4878566 (100.00%) were unpaired; of these: 1251005 (25.64%) aligned 0 times 1869155 (38.31%) aligned exactly 1 time 1758406 (36.04%) aligned >1 times 74.36% overall alignment rate Time searching: 00:09:25 Overall time: 00:09:25 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] 194993 / 3627561 = 0.0538 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 04:30:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.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 04:30:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:30:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:30:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.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 04:30:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:30:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:30:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.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 04:30:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:30:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:31:08: 1000000 INFO @ Mon, 03 Jun 2019 04:31:08: 1000000 INFO @ Mon, 03 Jun 2019 04:31:09: 1000000 INFO @ Mon, 03 Jun 2019 04:31:22: 2000000 INFO @ Mon, 03 Jun 2019 04:31:22: 2000000 INFO @ Mon, 03 Jun 2019 04:31:26: 2000000 INFO @ Mon, 03 Jun 2019 04:31:35: 3000000 INFO @ Mon, 03 Jun 2019 04:31:37: 3000000 INFO @ Mon, 03 Jun 2019 04:31:41: #1 tag size is determined as 151 bps INFO @ Mon, 03 Jun 2019 04:31:41: #1 tag size = 151 INFO @ Mon, 03 Jun 2019 04:31:41: #1 total tags in treatment: 3432568 INFO @ Mon, 03 Jun 2019 04:31:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:31:41: #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 04:31:41: #1 tags after filtering in treatment: 3432568 INFO @ Mon, 03 Jun 2019 04:31:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:31:41: #1 finished! INFO @ Mon, 03 Jun 2019 04:31:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:31:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:31:41: #2 number of paired peaks: 1144 INFO @ Mon, 03 Jun 2019 04:31:41: start model_add_line... INFO @ Mon, 03 Jun 2019 04:31:41: start X-correlation... INFO @ Mon, 03 Jun 2019 04:31:41: end of X-cor INFO @ Mon, 03 Jun 2019 04:31:41: #2 finished! INFO @ Mon, 03 Jun 2019 04:31:41: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 04:31:41: #2 alternative fragment length(s) may be 136 bps INFO @ Mon, 03 Jun 2019 04:31:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.05_model.r WARNING @ Mon, 03 Jun 2019 04:31:41: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:31:41: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Mon, 03 Jun 2019 04:31:41: #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 04:31:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:31:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:31:43: 3000000 INFO @ Mon, 03 Jun 2019 04:31:43: #1 tag size is determined as 151 bps INFO @ Mon, 03 Jun 2019 04:31:43: #1 tag size = 151 INFO @ Mon, 03 Jun 2019 04:31:43: #1 total tags in treatment: 3432568 INFO @ Mon, 03 Jun 2019 04:31:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:31:43: #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 04:31:43: #1 tags after filtering in treatment: 3432568 INFO @ Mon, 03 Jun 2019 04:31:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:31:43: #1 finished! INFO @ Mon, 03 Jun 2019 04:31:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:31:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:31:44: #2 number of paired peaks: 1144 INFO @ Mon, 03 Jun 2019 04:31:44: start model_add_line... INFO @ Mon, 03 Jun 2019 04:31:44: start X-correlation... INFO @ Mon, 03 Jun 2019 04:31:44: end of X-cor INFO @ Mon, 03 Jun 2019 04:31:44: #2 finished! INFO @ Mon, 03 Jun 2019 04:31:44: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 04:31:44: #2 alternative fragment length(s) may be 136 bps INFO @ Mon, 03 Jun 2019 04:31:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.10_model.r WARNING @ Mon, 03 Jun 2019 04:31:44: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:31:44: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Mon, 03 Jun 2019 04:31:44: #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 04:31:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:31:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:31:49: #1 tag size is determined as 151 bps INFO @ Mon, 03 Jun 2019 04:31:49: #1 tag size = 151 INFO @ Mon, 03 Jun 2019 04:31:49: #1 total tags in treatment: 3432568 INFO @ Mon, 03 Jun 2019 04:31:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:31:49: #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 04:31:49: #1 tags after filtering in treatment: 3432568 INFO @ Mon, 03 Jun 2019 04:31:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:31:49: #1 finished! INFO @ Mon, 03 Jun 2019 04:31:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:31:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:31:50: #2 number of paired peaks: 1144 INFO @ Mon, 03 Jun 2019 04:31:50: start model_add_line... INFO @ Mon, 03 Jun 2019 04:31:50: start X-correlation... INFO @ Mon, 03 Jun 2019 04:31:50: end of X-cor INFO @ Mon, 03 Jun 2019 04:31:50: #2 finished! INFO @ Mon, 03 Jun 2019 04:31:50: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 04:31:50: #2 alternative fragment length(s) may be 136 bps INFO @ Mon, 03 Jun 2019 04:31:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.20_model.r WARNING @ Mon, 03 Jun 2019 04:31:50: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:31:50: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Mon, 03 Jun 2019 04:31:50: #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 04:31:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:31:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:31:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:31:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:31:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:31:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:31:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.05_summits.bed INFO @ Mon, 03 Jun 2019 04:31:59: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2637 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:32:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:32:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:32:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.10_summits.bed INFO @ Mon, 03 Jun 2019 04:32:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1153 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:32:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:32:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:32:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:32:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1760704/SRX1760704.20_summits.bed INFO @ Mon, 03 Jun 2019 04:32:06: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (414 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。