Job ID = 1293845 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T17:43:52 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 : 16,951,478 reads read : 16,951,478 reads written : 16,951,478 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: 00:04:05 16951478 reads; of these: 16951478 (100.00%) were unpaired; of these: 13390663 (78.99%) aligned 0 times 1671665 (9.86%) aligned exactly 1 time 1889150 (11.14%) aligned >1 times 21.01% overall alignment rate Time searching: 00:04:05 Overall time: 00:04:05 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] 1093131 / 3560815 = 0.3070 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 02:50:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.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 02:50:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:50:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:50:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.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 02:50:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:50:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:50:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.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 02:50:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:50:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:50:50: 1000000 INFO @ Mon, 03 Jun 2019 02:50:51: 1000000 INFO @ Mon, 03 Jun 2019 02:50:51: 1000000 INFO @ Mon, 03 Jun 2019 02:51:00: 2000000 INFO @ Mon, 03 Jun 2019 02:51:02: 2000000 INFO @ Mon, 03 Jun 2019 02:51:02: 2000000 INFO @ Mon, 03 Jun 2019 02:51:04: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:51:04: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:51:04: #1 total tags in treatment: 2467684 INFO @ Mon, 03 Jun 2019 02:51:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:51:04: #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 02:51:04: #1 tags after filtering in treatment: 2467684 INFO @ Mon, 03 Jun 2019 02:51:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:51:04: #1 finished! INFO @ Mon, 03 Jun 2019 02:51:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:51:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:51:05: #2 number of paired peaks: 1230 INFO @ Mon, 03 Jun 2019 02:51:05: start model_add_line... INFO @ Mon, 03 Jun 2019 02:51:05: start X-correlation... INFO @ Mon, 03 Jun 2019 02:51:05: end of X-cor INFO @ Mon, 03 Jun 2019 02:51:05: #2 finished! INFO @ Mon, 03 Jun 2019 02:51:05: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 02:51:05: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 02:51:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.20_model.r WARNING @ Mon, 03 Jun 2019 02:51:05: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:51:05: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 02:51:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 02:51:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:51:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:51:07: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:51:07: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:51:07: #1 total tags in treatment: 2467684 INFO @ Mon, 03 Jun 2019 02:51:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:51:07: #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 02:51:07: #1 tags after filtering in treatment: 2467684 INFO @ Mon, 03 Jun 2019 02:51:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:51:07: #1 finished! INFO @ Mon, 03 Jun 2019 02:51:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:51:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:51:07: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:51:07: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:51:07: #1 total tags in treatment: 2467684 INFO @ Mon, 03 Jun 2019 02:51:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:51:07: #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 02:51:07: #1 tags after filtering in treatment: 2467684 INFO @ Mon, 03 Jun 2019 02:51:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:51:07: #1 finished! INFO @ Mon, 03 Jun 2019 02:51:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:51:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:51:08: #2 number of paired peaks: 1230 INFO @ Mon, 03 Jun 2019 02:51:08: start model_add_line... INFO @ Mon, 03 Jun 2019 02:51:08: start X-correlation... INFO @ Mon, 03 Jun 2019 02:51:08: end of X-cor INFO @ Mon, 03 Jun 2019 02:51:08: #2 finished! INFO @ Mon, 03 Jun 2019 02:51:08: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 02:51:08: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 02:51:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.05_model.r WARNING @ Mon, 03 Jun 2019 02:51:08: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:51:08: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 02:51:08: #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 02:51:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:51:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:51:08: #2 number of paired peaks: 1230 INFO @ Mon, 03 Jun 2019 02:51:08: start model_add_line... INFO @ Mon, 03 Jun 2019 02:51:08: start X-correlation... INFO @ Mon, 03 Jun 2019 02:51:08: end of X-cor INFO @ Mon, 03 Jun 2019 02:51:08: #2 finished! INFO @ Mon, 03 Jun 2019 02:51:08: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 02:51:08: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 02:51:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.10_model.r WARNING @ Mon, 03 Jun 2019 02:51:08: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:51:08: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 02:51:08: #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 02:51:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:51:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:51:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:51:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:51:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:51:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:51:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:51:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.20_summits.bed INFO @ Mon, 03 Jun 2019 02:51:16: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (746 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:51:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:51:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:51:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.10_summits.bed INFO @ Mon, 03 Jun 2019 02:51:20: Done! INFO @ Mon, 03 Jun 2019 02:51:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:51:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:51:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299926/SRX1299926.05_summits.bed INFO @ Mon, 03 Jun 2019 02:51:20: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1492 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2437 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。