Job ID = 1291662 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T07:12:33 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 : 14,525,466 reads read : 14,525,466 reads written : 14,525,466 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: 00:02:09 14525466 reads; of these: 14525466 (100.00%) were unpaired; of these: 10464708 (72.04%) aligned 0 times 2330666 (16.05%) aligned exactly 1 time 1730092 (11.91%) aligned >1 times 27.96% overall alignment rate Time searching: 00:02:09 Overall time: 00:02:09 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1949765 / 4060758 = 0.4801 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 @ Sun, 02 Jun 2019 16:16:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 16:16:23: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:16:23: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:16:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 16:16:23: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:16:23: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:16:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 16:16:24: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:16:24: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:16:32: 1000000 INFO @ Sun, 02 Jun 2019 16:16:33: 1000000 INFO @ Sun, 02 Jun 2019 16:16:33: 1000000 INFO @ Sun, 02 Jun 2019 16:16:40: 2000000 INFO @ Sun, 02 Jun 2019 16:16:40: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:16:40: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:16:40: #1 total tags in treatment: 2110993 INFO @ Sun, 02 Jun 2019 16:16:40: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:16:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:16:41: #1 tags after filtering in treatment: 2110993 INFO @ Sun, 02 Jun 2019 16:16:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:16:41: #1 finished! INFO @ Sun, 02 Jun 2019 16:16:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:16:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:16:41: #2 number of paired peaks: 1390 INFO @ Sun, 02 Jun 2019 16:16:41: start model_add_line... INFO @ Sun, 02 Jun 2019 16:16:41: start X-correlation... INFO @ Sun, 02 Jun 2019 16:16:41: end of X-cor INFO @ Sun, 02 Jun 2019 16:16:41: #2 finished! INFO @ Sun, 02 Jun 2019 16:16:41: #2 predicted fragment length is 222 bps INFO @ Sun, 02 Jun 2019 16:16:41: #2 alternative fragment length(s) may be 222 bps INFO @ Sun, 02 Jun 2019 16:16:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.10_model.r INFO @ Sun, 02 Jun 2019 16:16:41: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:16:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:16:42: 2000000 INFO @ Sun, 02 Jun 2019 16:16:43: 2000000 INFO @ Sun, 02 Jun 2019 16:16:43: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:16:43: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:16:43: #1 total tags in treatment: 2110993 INFO @ Sun, 02 Jun 2019 16:16:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:16:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:16:43: #1 tags after filtering in treatment: 2110993 INFO @ Sun, 02 Jun 2019 16:16:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:16:43: #1 finished! INFO @ Sun, 02 Jun 2019 16:16:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:16:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:16:44: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:16:44: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:16:44: #1 total tags in treatment: 2110993 INFO @ Sun, 02 Jun 2019 16:16:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:16:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:16:44: #1 tags after filtering in treatment: 2110993 INFO @ Sun, 02 Jun 2019 16:16:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:16:44: #1 finished! INFO @ Sun, 02 Jun 2019 16:16:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:16:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:16:44: #2 number of paired peaks: 1390 INFO @ Sun, 02 Jun 2019 16:16:44: start model_add_line... INFO @ Sun, 02 Jun 2019 16:16:44: start X-correlation... INFO @ Sun, 02 Jun 2019 16:16:44: end of X-cor INFO @ Sun, 02 Jun 2019 16:16:44: #2 finished! INFO @ Sun, 02 Jun 2019 16:16:44: #2 predicted fragment length is 222 bps INFO @ Sun, 02 Jun 2019 16:16:44: #2 alternative fragment length(s) may be 222 bps INFO @ Sun, 02 Jun 2019 16:16:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.05_model.r INFO @ Sun, 02 Jun 2019 16:16:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:16:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:16:44: #2 number of paired peaks: 1390 INFO @ Sun, 02 Jun 2019 16:16:44: start model_add_line... INFO @ Sun, 02 Jun 2019 16:16:44: start X-correlation... INFO @ Sun, 02 Jun 2019 16:16:44: end of X-cor INFO @ Sun, 02 Jun 2019 16:16:44: #2 finished! INFO @ Sun, 02 Jun 2019 16:16:44: #2 predicted fragment length is 222 bps INFO @ Sun, 02 Jun 2019 16:16:44: #2 alternative fragment length(s) may be 222 bps INFO @ Sun, 02 Jun 2019 16:16:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.20_model.r INFO @ Sun, 02 Jun 2019 16:16:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:16:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:16:49: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:16:52: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:16:52: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:16:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:16:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:16:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.10_summits.bed INFO @ Sun, 02 Jun 2019 16:16:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1033 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:16:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:16:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:16:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.20_summits.bed INFO @ Sun, 02 Jun 2019 16:16:56: Done! INFO @ Sun, 02 Jun 2019 16:16:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:16:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:16:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769990/SRX1769990.05_summits.bed INFO @ Sun, 02 Jun 2019 16:16:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (648 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1668 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。