Job ID = 2591027 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T15:44:48 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 ) 2019-08-12T15:44:48 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 : 16,501,235 reads read : 16,501,235 reads written : 16,501,235 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: 00:08:46 16501235 reads; of these: 16501235 (100.00%) were unpaired; of these: 1083214 (6.56%) aligned 0 times 14044615 (85.11%) aligned exactly 1 time 1373406 (8.32%) aligned >1 times 93.44% overall alignment rate Time searching: 00:08:46 Overall time: 00:08:46 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_sort_core] merging from 8 files... [bam_rmdupse_core] 13755032 / 15418021 = 0.8921 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 01:08:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.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 01:08:32: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:08:32: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:08:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.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 01:08:33: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:08:33: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:08:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.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 01:08:34: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:08:34: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:08:42: 1000000 INFO @ Tue, 13 Aug 2019 01:08:43: 1000000 INFO @ Tue, 13 Aug 2019 01:08:45: 1000000 INFO @ Tue, 13 Aug 2019 01:08:49: #1 tag size is determined as 100 bps INFO @ Tue, 13 Aug 2019 01:08:49: #1 tag size = 100 INFO @ Tue, 13 Aug 2019 01:08:49: #1 total tags in treatment: 1662989 INFO @ Tue, 13 Aug 2019 01:08:49: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:08:49: #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 01:08:49: #1 tags after filtering in treatment: 1662989 INFO @ Tue, 13 Aug 2019 01:08:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 01:08:49: #1 finished! INFO @ Tue, 13 Aug 2019 01:08:49: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:08:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:08:49: #2 number of paired peaks: 1946 INFO @ Tue, 13 Aug 2019 01:08:49: start model_add_line... INFO @ Tue, 13 Aug 2019 01:08:50: start X-correlation... INFO @ Tue, 13 Aug 2019 01:08:50: end of X-cor INFO @ Tue, 13 Aug 2019 01:08:50: #2 finished! INFO @ Tue, 13 Aug 2019 01:08:50: #2 predicted fragment length is 126 bps INFO @ Tue, 13 Aug 2019 01:08:50: #2 alternative fragment length(s) may be 126 bps INFO @ Tue, 13 Aug 2019 01:08:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.05_model.r WARNING @ Tue, 13 Aug 2019 01:08:50: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 01:08:50: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Tue, 13 Aug 2019 01:08:50: #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 01:08:50: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:08:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:08:50: #1 tag size is determined as 100 bps INFO @ Tue, 13 Aug 2019 01:08:50: #1 tag size = 100 INFO @ Tue, 13 Aug 2019 01:08:50: #1 total tags in treatment: 1662989 INFO @ Tue, 13 Aug 2019 01:08:50: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:08:50: #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 01:08:50: #1 tags after filtering in treatment: 1662989 INFO @ Tue, 13 Aug 2019 01:08:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 01:08:50: #1 finished! INFO @ Tue, 13 Aug 2019 01:08:50: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:08:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:08:51: #2 number of paired peaks: 1946 INFO @ Tue, 13 Aug 2019 01:08:51: start model_add_line... INFO @ Tue, 13 Aug 2019 01:08:51: start X-correlation... INFO @ Tue, 13 Aug 2019 01:08:51: end of X-cor INFO @ Tue, 13 Aug 2019 01:08:51: #2 finished! INFO @ Tue, 13 Aug 2019 01:08:51: #2 predicted fragment length is 126 bps INFO @ Tue, 13 Aug 2019 01:08:51: #2 alternative fragment length(s) may be 126 bps INFO @ Tue, 13 Aug 2019 01:08:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.10_model.r WARNING @ Tue, 13 Aug 2019 01:08:51: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 01:08:51: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Tue, 13 Aug 2019 01:08:51: #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 01:08:51: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:08:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:08:54: #1 tag size is determined as 100 bps INFO @ Tue, 13 Aug 2019 01:08:54: #1 tag size = 100 INFO @ Tue, 13 Aug 2019 01:08:54: #1 total tags in treatment: 1662989 INFO @ Tue, 13 Aug 2019 01:08:54: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:08:54: #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 01:08:54: #1 tags after filtering in treatment: 1662989 INFO @ Tue, 13 Aug 2019 01:08:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 01:08:54: #1 finished! INFO @ Tue, 13 Aug 2019 01:08:54: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:08:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:08:54: #2 number of paired peaks: 1946 INFO @ Tue, 13 Aug 2019 01:08:54: start model_add_line... INFO @ Tue, 13 Aug 2019 01:08:54: start X-correlation... INFO @ Tue, 13 Aug 2019 01:08:54: end of X-cor INFO @ Tue, 13 Aug 2019 01:08:54: #2 finished! INFO @ Tue, 13 Aug 2019 01:08:54: #2 predicted fragment length is 126 bps INFO @ Tue, 13 Aug 2019 01:08:54: #2 alternative fragment length(s) may be 126 bps INFO @ Tue, 13 Aug 2019 01:08:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.20_model.r WARNING @ Tue, 13 Aug 2019 01:08:54: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 01:08:54: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Tue, 13 Aug 2019 01:08:54: #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 01:08:54: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:08:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:08:55: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:08:56: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:08:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.05_peaks.xls INFO @ Tue, 13 Aug 2019 01:08:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:08:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.05_summits.bed INFO @ Tue, 13 Aug 2019 01:08:57: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1759 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 01:08:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.10_peaks.xls INFO @ Tue, 13 Aug 2019 01:08:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:08:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.10_summits.bed INFO @ Tue, 13 Aug 2019 01:08:58: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (690 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 01:08:59: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:09:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.20_peaks.xls INFO @ Tue, 13 Aug 2019 01:09:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:09:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX666356/SRX666356.20_summits.bed INFO @ Tue, 13 Aug 2019 01:09:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (332 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。