Job ID = 2591003 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T15:25:41 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 : 30,497,148 reads read : 30,497,148 reads written : 30,497,148 rm: cannot remove ‘[DSE]RR*’: 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: 00:10:01 30497148 reads; of these: 30497148 (100.00%) were unpaired; of these: 23158924 (75.94%) aligned 0 times 6130896 (20.10%) aligned exactly 1 time 1207328 (3.96%) aligned >1 times 24.06% overall alignment rate Time searching: 00:10:01 Overall time: 00:10:01 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] 5718389 / 7338224 = 0.7793 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 @ Tue, 13 Aug 2019 01:06:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.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 @ Tue, 13 Aug 2019 01:06:48: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:06:48: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:06:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.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 @ Tue, 13 Aug 2019 01:06:49: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:06:49: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:06:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.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 @ Tue, 13 Aug 2019 01:06:50: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:06:50: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:06:59: 1000000 INFO @ Tue, 13 Aug 2019 01:07:00: 1000000 INFO @ Tue, 13 Aug 2019 01:07:00: 1000000 INFO @ Tue, 13 Aug 2019 01:07:06: #1 tag size is determined as 100 bps INFO @ Tue, 13 Aug 2019 01:07:06: #1 tag size = 100 INFO @ Tue, 13 Aug 2019 01:07:06: #1 total tags in treatment: 1619835 INFO @ Tue, 13 Aug 2019 01:07:06: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:07:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 01:07:06: #1 tags after filtering in treatment: 1619835 INFO @ Tue, 13 Aug 2019 01:07:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 01:07:06: #1 finished! INFO @ Tue, 13 Aug 2019 01:07:06: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:07:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:07:07: #2 number of paired peaks: 2701 INFO @ Tue, 13 Aug 2019 01:07:07: start model_add_line... INFO @ Tue, 13 Aug 2019 01:07:07: start X-correlation... INFO @ Tue, 13 Aug 2019 01:07:07: end of X-cor INFO @ Tue, 13 Aug 2019 01:07:07: #2 finished! INFO @ Tue, 13 Aug 2019 01:07:07: #2 predicted fragment length is 95 bps INFO @ Tue, 13 Aug 2019 01:07:07: #2 alternative fragment length(s) may be 95 bps INFO @ Tue, 13 Aug 2019 01:07:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.05_model.r WARNING @ Tue, 13 Aug 2019 01:07:07: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 01:07:07: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Tue, 13 Aug 2019 01:07:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 01:07:07: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:07:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:07:07: #1 tag size is determined as 100 bps INFO @ Tue, 13 Aug 2019 01:07:07: #1 tag size = 100 INFO @ Tue, 13 Aug 2019 01:07:07: #1 total tags in treatment: 1619835 INFO @ Tue, 13 Aug 2019 01:07:07: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:07:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 01:07:07: #1 tags after filtering in treatment: 1619835 INFO @ Tue, 13 Aug 2019 01:07:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 01:07:07: #1 finished! INFO @ Tue, 13 Aug 2019 01:07:07: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:07:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:07:07: #2 number of paired peaks: 2701 INFO @ Tue, 13 Aug 2019 01:07:07: start model_add_line... INFO @ Tue, 13 Aug 2019 01:07:07: start X-correlation... INFO @ Tue, 13 Aug 2019 01:07:07: end of X-cor INFO @ Tue, 13 Aug 2019 01:07:07: #2 finished! INFO @ Tue, 13 Aug 2019 01:07:07: #2 predicted fragment length is 95 bps INFO @ Tue, 13 Aug 2019 01:07:07: #2 alternative fragment length(s) may be 95 bps INFO @ Tue, 13 Aug 2019 01:07:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.20_model.r WARNING @ Tue, 13 Aug 2019 01:07:07: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 01:07:07: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Tue, 13 Aug 2019 01:07:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 01:07:07: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:07:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:07:07: #1 tag size is determined as 100 bps INFO @ Tue, 13 Aug 2019 01:07:07: #1 tag size = 100 INFO @ Tue, 13 Aug 2019 01:07:07: #1 total tags in treatment: 1619835 INFO @ Tue, 13 Aug 2019 01:07:07: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:07:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 01:07:07: #1 tags after filtering in treatment: 1619835 INFO @ Tue, 13 Aug 2019 01:07:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 01:07:07: #1 finished! INFO @ Tue, 13 Aug 2019 01:07:07: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:07:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:07:08: #2 number of paired peaks: 2701 INFO @ Tue, 13 Aug 2019 01:07:08: start model_add_line... INFO @ Tue, 13 Aug 2019 01:07:08: start X-correlation... INFO @ Tue, 13 Aug 2019 01:07:08: end of X-cor INFO @ Tue, 13 Aug 2019 01:07:08: #2 finished! INFO @ Tue, 13 Aug 2019 01:07:08: #2 predicted fragment length is 95 bps INFO @ Tue, 13 Aug 2019 01:07:08: #2 alternative fragment length(s) may be 95 bps INFO @ Tue, 13 Aug 2019 01:07:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.10_model.r WARNING @ Tue, 13 Aug 2019 01:07:08: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 01:07:08: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Tue, 13 Aug 2019 01:07:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 01:07:08: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:07:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:07:12: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:07:12: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:07:13: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:07:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.05_peaks.xls INFO @ Tue, 13 Aug 2019 01:07:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:07:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.05_summits.bed INFO @ Tue, 13 Aug 2019 01:07:14: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1254 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 01:07:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.20_peaks.xls INFO @ Tue, 13 Aug 2019 01:07:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:07:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.20_summits.bed INFO @ Tue, 13 Aug 2019 01:07:15: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (453 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 01:07:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.10_peaks.xls INFO @ Tue, 13 Aug 2019 01:07:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:07:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645131/SRX645131.10_summits.bed INFO @ Tue, 13 Aug 2019 01:07:15: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (706 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。