Job ID = 2590649 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T13:56:45 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 ) 2019-08-12T13:56:45 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 : 16,173,126 reads read : 16,173,126 reads written : 16,173,126 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: 00:07:38 16173126 reads; of these: 16173126 (100.00%) were unpaired; of these: 7277225 (45.00%) aligned 0 times 2564090 (15.85%) aligned exactly 1 time 6331811 (39.15%) aligned >1 times 55.00% overall alignment rate Time searching: 00:07:38 Overall time: 00:07:38 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] 3962069 / 8895901 = 0.4454 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, 12 Aug 2019 23:12:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.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, 12 Aug 2019 23:12:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:12:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:12:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.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, 12 Aug 2019 23:12:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:12:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:12:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.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, 12 Aug 2019 23:12:19: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:12:19: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:12:25: 1000000 INFO @ Mon, 12 Aug 2019 23:12:25: 1000000 INFO @ Mon, 12 Aug 2019 23:12:26: 1000000 INFO @ Mon, 12 Aug 2019 23:12:32: 2000000 INFO @ Mon, 12 Aug 2019 23:12:32: 2000000 INFO @ Mon, 12 Aug 2019 23:12:34: 2000000 INFO @ Mon, 12 Aug 2019 23:12:39: 3000000 INFO @ Mon, 12 Aug 2019 23:12:40: 3000000 INFO @ Mon, 12 Aug 2019 23:12:45: 3000000 INFO @ Mon, 12 Aug 2019 23:12:45: 4000000 INFO @ Mon, 12 Aug 2019 23:12:47: 4000000 INFO @ Mon, 12 Aug 2019 23:12:51: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:12:51: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:12:51: #1 total tags in treatment: 4933832 INFO @ Mon, 12 Aug 2019 23:12:51: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:12:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:12:52: #1 tags after filtering in treatment: 4933832 INFO @ Mon, 12 Aug 2019 23:12:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:12:52: #1 finished! INFO @ Mon, 12 Aug 2019 23:12:52: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:12:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:12:52: #2 number of paired peaks: 1708 INFO @ Mon, 12 Aug 2019 23:12:52: start model_add_line... INFO @ Mon, 12 Aug 2019 23:12:52: start X-correlation... INFO @ Mon, 12 Aug 2019 23:12:52: end of X-cor INFO @ Mon, 12 Aug 2019 23:12:52: #2 finished! INFO @ Mon, 12 Aug 2019 23:12:52: #2 predicted fragment length is 52 bps INFO @ Mon, 12 Aug 2019 23:12:52: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 12 Aug 2019 23:12:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.10_model.r WARNING @ Mon, 12 Aug 2019 23:12:52: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:12:52: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 12 Aug 2019 23:12:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:12:52: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:12:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:12:54: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:12:54: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:12:54: #1 total tags in treatment: 4933832 INFO @ Mon, 12 Aug 2019 23:12:54: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:12:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:12:54: #1 tags after filtering in treatment: 4933832 INFO @ Mon, 12 Aug 2019 23:12:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:12:54: #1 finished! INFO @ Mon, 12 Aug 2019 23:12:54: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:12:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:12:55: 4000000 INFO @ Mon, 12 Aug 2019 23:12:55: #2 number of paired peaks: 1708 INFO @ Mon, 12 Aug 2019 23:12:55: start model_add_line... INFO @ Mon, 12 Aug 2019 23:12:55: start X-correlation... INFO @ Mon, 12 Aug 2019 23:12:55: end of X-cor INFO @ Mon, 12 Aug 2019 23:12:55: #2 finished! INFO @ Mon, 12 Aug 2019 23:12:55: #2 predicted fragment length is 52 bps INFO @ Mon, 12 Aug 2019 23:12:55: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 12 Aug 2019 23:12:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.05_model.r WARNING @ Mon, 12 Aug 2019 23:12:55: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:12:55: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 12 Aug 2019 23:12:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:12:55: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:12:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:13:04: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:13:04: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:13:04: #1 total tags in treatment: 4933832 INFO @ Mon, 12 Aug 2019 23:13:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:13:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:13:04: #1 tags after filtering in treatment: 4933832 INFO @ Mon, 12 Aug 2019 23:13:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:13:04: #1 finished! INFO @ Mon, 12 Aug 2019 23:13:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:13:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:13:04: #2 number of paired peaks: 1708 INFO @ Mon, 12 Aug 2019 23:13:04: start model_add_line... INFO @ Mon, 12 Aug 2019 23:13:04: start X-correlation... INFO @ Mon, 12 Aug 2019 23:13:04: end of X-cor INFO @ Mon, 12 Aug 2019 23:13:04: #2 finished! INFO @ Mon, 12 Aug 2019 23:13:04: #2 predicted fragment length is 52 bps INFO @ Mon, 12 Aug 2019 23:13:04: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 12 Aug 2019 23:13:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.20_model.r WARNING @ Mon, 12 Aug 2019 23:13:05: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:13:05: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 12 Aug 2019 23:13:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:13:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:13:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:13:07: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:13:10: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:13:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:13:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:13:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.10_summits.bed INFO @ Mon, 12 Aug 2019 23:13:14: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1189 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:13:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:13:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:13:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.05_summits.bed INFO @ Mon, 12 Aug 2019 23:13:17: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2589 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:13:20: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:13:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:13:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:13:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495787/SRX495787.20_summits.bed INFO @ Mon, 12 Aug 2019 23:13:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (633 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。