Job ID = 1291767 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T07:26:11 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 ) 2019-06-02T07:28:45 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 : 25,703,370 reads read : 25,703,370 reads written : 25,703,370 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: 00:02:50 25703370 reads; of these: 25703370 (100.00%) were unpaired; of these: 18478750 (71.89%) aligned 0 times 6091955 (23.70%) aligned exactly 1 time 1132665 (4.41%) aligned >1 times 28.11% overall alignment rate Time searching: 00:02:50 Overall time: 00:02:50 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] 3668249 / 7224620 = 0.5077 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 16:38:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.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 16:38:08: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:38:08: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:38:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.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 16:38:08: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:38:08: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:38:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.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 16:38:08: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:38:08: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:38:15: 1000000 INFO @ Sun, 02 Jun 2019 16:38:16: 1000000 INFO @ Sun, 02 Jun 2019 16:38:18: 1000000 INFO @ Sun, 02 Jun 2019 16:38:23: 2000000 INFO @ Sun, 02 Jun 2019 16:38:23: 2000000 INFO @ Sun, 02 Jun 2019 16:38:27: 2000000 INFO @ Sun, 02 Jun 2019 16:38:30: 3000000 INFO @ Sun, 02 Jun 2019 16:38:30: 3000000 INFO @ Sun, 02 Jun 2019 16:38:34: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:38:34: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:38:34: #1 total tags in treatment: 3556371 INFO @ Sun, 02 Jun 2019 16:38:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:38:34: #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 16:38:34: #1 tags after filtering in treatment: 3556371 INFO @ Sun, 02 Jun 2019 16:38:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:38:34: #1 finished! INFO @ Sun, 02 Jun 2019 16:38:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:38:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:38:34: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:38:34: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:38:34: #1 total tags in treatment: 3556371 INFO @ Sun, 02 Jun 2019 16:38:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:38:34: #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 16:38:34: #1 tags after filtering in treatment: 3556371 INFO @ Sun, 02 Jun 2019 16:38:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:38:34: #1 finished! INFO @ Sun, 02 Jun 2019 16:38:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:38:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:38:34: #2 number of paired peaks: 1050 INFO @ Sun, 02 Jun 2019 16:38:34: start model_add_line... INFO @ Sun, 02 Jun 2019 16:38:34: start X-correlation... INFO @ Sun, 02 Jun 2019 16:38:34: end of X-cor INFO @ Sun, 02 Jun 2019 16:38:34: #2 finished! INFO @ Sun, 02 Jun 2019 16:38:34: #2 predicted fragment length is 106 bps INFO @ Sun, 02 Jun 2019 16:38:34: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 02 Jun 2019 16:38:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.20_model.r INFO @ Sun, 02 Jun 2019 16:38:34: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:38:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:38:35: #2 number of paired peaks: 1050 INFO @ Sun, 02 Jun 2019 16:38:35: start model_add_line... INFO @ Sun, 02 Jun 2019 16:38:35: start X-correlation... INFO @ Sun, 02 Jun 2019 16:38:35: end of X-cor INFO @ Sun, 02 Jun 2019 16:38:35: #2 finished! INFO @ Sun, 02 Jun 2019 16:38:35: #2 predicted fragment length is 106 bps INFO @ Sun, 02 Jun 2019 16:38:35: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 02 Jun 2019 16:38:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.05_model.r INFO @ Sun, 02 Jun 2019 16:38:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:38:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:38:37: 3000000 INFO @ Sun, 02 Jun 2019 16:38:42: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:38:42: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:38:42: #1 total tags in treatment: 3556371 INFO @ Sun, 02 Jun 2019 16:38:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:38:42: #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 16:38:42: #1 tags after filtering in treatment: 3556371 INFO @ Sun, 02 Jun 2019 16:38:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:38:42: #1 finished! INFO @ Sun, 02 Jun 2019 16:38:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:38:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:38:42: #2 number of paired peaks: 1050 INFO @ Sun, 02 Jun 2019 16:38:42: start model_add_line... INFO @ Sun, 02 Jun 2019 16:38:42: start X-correlation... INFO @ Sun, 02 Jun 2019 16:38:42: end of X-cor INFO @ Sun, 02 Jun 2019 16:38:42: #2 finished! INFO @ Sun, 02 Jun 2019 16:38:42: #2 predicted fragment length is 106 bps INFO @ Sun, 02 Jun 2019 16:38:42: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 02 Jun 2019 16:38:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.10_model.r INFO @ Sun, 02 Jun 2019 16:38:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:38:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:38:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:38:46: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:38:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:38:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:38:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.20_summits.bed INFO @ Sun, 02 Jun 2019 16:38:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1090 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:38:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:38:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:38:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.05_summits.bed INFO @ Sun, 02 Jun 2019 16:38:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3277 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:38:53: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:38:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:38:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:38:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX245916/SRX245916.10_summits.bed INFO @ Sun, 02 Jun 2019 16:38:59: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2074 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。