Job ID = 1295040 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T02:22:52 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 : 4,394,369 reads read : 8,788,738 reads written : 4,394,369 reads 0-length : 4,394,369 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: 00:03:16 4394369 reads; of these: 4394369 (100.00%) were unpaired; of these: 265365 (6.04%) aligned 0 times 3362198 (76.51%) aligned exactly 1 time 766806 (17.45%) aligned >1 times 93.96% overall alignment rate Time searching: 00:03:16 Overall time: 00:03:16 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] 965884 / 4129004 = 0.2339 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 11:31:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.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 11:31:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:31:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:31:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.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 11:31:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:31:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:31:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.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 11:31:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:31:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:31:14: 1000000 INFO @ Mon, 03 Jun 2019 11:31:16: 1000000 INFO @ Mon, 03 Jun 2019 11:31:16: 1000000 INFO @ Mon, 03 Jun 2019 11:31:25: 2000000 INFO @ Mon, 03 Jun 2019 11:31:28: 2000000 INFO @ Mon, 03 Jun 2019 11:31:29: 2000000 INFO @ Mon, 03 Jun 2019 11:31:36: 3000000 INFO @ Mon, 03 Jun 2019 11:31:38: #1 tag size is determined as 151 bps INFO @ Mon, 03 Jun 2019 11:31:38: #1 tag size = 151 INFO @ Mon, 03 Jun 2019 11:31:38: #1 total tags in treatment: 3163120 INFO @ Mon, 03 Jun 2019 11:31:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:31:38: #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 11:31:38: #1 tags after filtering in treatment: 3163120 INFO @ Mon, 03 Jun 2019 11:31:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:31:38: #1 finished! INFO @ Mon, 03 Jun 2019 11:31:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:31:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:31:38: #2 number of paired peaks: 4872 INFO @ Mon, 03 Jun 2019 11:31:38: start model_add_line... INFO @ Mon, 03 Jun 2019 11:31:38: start X-correlation... INFO @ Mon, 03 Jun 2019 11:31:38: end of X-cor INFO @ Mon, 03 Jun 2019 11:31:38: #2 finished! INFO @ Mon, 03 Jun 2019 11:31:38: #2 predicted fragment length is 210 bps INFO @ Mon, 03 Jun 2019 11:31:38: #2 alternative fragment length(s) may be 210 bps INFO @ Mon, 03 Jun 2019 11:31:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.10_model.r WARNING @ Mon, 03 Jun 2019 11:31:38: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:31:38: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Mon, 03 Jun 2019 11:31:38: #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 11:31:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:31:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:31:41: 3000000 INFO @ Mon, 03 Jun 2019 11:31:41: 3000000 INFO @ Mon, 03 Jun 2019 11:31:43: #1 tag size is determined as 151 bps INFO @ Mon, 03 Jun 2019 11:31:43: #1 tag size = 151 INFO @ Mon, 03 Jun 2019 11:31:43: #1 total tags in treatment: 3163120 INFO @ Mon, 03 Jun 2019 11:31:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:31:43: #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 11:31:43: #1 tags after filtering in treatment: 3163120 INFO @ Mon, 03 Jun 2019 11:31:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:31:43: #1 finished! INFO @ Mon, 03 Jun 2019 11:31:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:31:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:31:43: #1 tag size is determined as 151 bps INFO @ Mon, 03 Jun 2019 11:31:43: #1 tag size = 151 INFO @ Mon, 03 Jun 2019 11:31:43: #1 total tags in treatment: 3163120 INFO @ Mon, 03 Jun 2019 11:31:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:31:43: #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 11:31:43: #1 tags after filtering in treatment: 3163120 INFO @ Mon, 03 Jun 2019 11:31:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:31:43: #1 finished! INFO @ Mon, 03 Jun 2019 11:31:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:31:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:31:44: #2 number of paired peaks: 4872 INFO @ Mon, 03 Jun 2019 11:31:44: start model_add_line... INFO @ Mon, 03 Jun 2019 11:31:44: start X-correlation... INFO @ Mon, 03 Jun 2019 11:31:44: end of X-cor INFO @ Mon, 03 Jun 2019 11:31:44: #2 finished! INFO @ Mon, 03 Jun 2019 11:31:44: #2 predicted fragment length is 210 bps INFO @ Mon, 03 Jun 2019 11:31:44: #2 alternative fragment length(s) may be 210 bps INFO @ Mon, 03 Jun 2019 11:31:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.05_model.r WARNING @ Mon, 03 Jun 2019 11:31:44: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:31:44: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Mon, 03 Jun 2019 11:31:44: #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 11:31:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:31:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:31:44: #2 number of paired peaks: 4872 INFO @ Mon, 03 Jun 2019 11:31:44: start model_add_line... INFO @ Mon, 03 Jun 2019 11:31:44: start X-correlation... INFO @ Mon, 03 Jun 2019 11:31:44: end of X-cor INFO @ Mon, 03 Jun 2019 11:31:44: #2 finished! INFO @ Mon, 03 Jun 2019 11:31:44: #2 predicted fragment length is 210 bps INFO @ Mon, 03 Jun 2019 11:31:44: #2 alternative fragment length(s) may be 210 bps INFO @ Mon, 03 Jun 2019 11:31:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.20_model.r WARNING @ Mon, 03 Jun 2019 11:31:44: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:31:44: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Mon, 03 Jun 2019 11:31:44: #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 11:31:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:31:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:31:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:31:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:31:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:31:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.10_summits.bed INFO @ Mon, 03 Jun 2019 11:31:56: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4184 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:31:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:31:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:32:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:32:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:32:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.05_summits.bed INFO @ Mon, 03 Jun 2019 11:32:02: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5374 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:32:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:32:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:32:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX315132/SRX315132.20_summits.bed INFO @ Mon, 03 Jun 2019 11:32:02: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2964 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。