Job ID = 1291791 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T07:32:52 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 : 17,571,797 reads read : 35,143,594 reads written : 17,571,797 reads 0-length : 17,571,797 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: 00:05:19 17571797 reads; of these: 17571797 (100.00%) were unpaired; of these: 6649223 (37.84%) aligned 0 times 8935550 (50.85%) aligned exactly 1 time 1987024 (11.31%) aligned >1 times 62.16% overall alignment rate Time searching: 00:05:19 Overall time: 00:05:19 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_sort_core] merging from 8 files... [bam_rmdupse_core] 4485426 / 10922574 = 0.4107 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 16:43:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.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 16:43:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:43:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:43:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.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 16:43:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:43:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:43:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.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 16:43:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:43:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:43:40: 1000000 INFO @ Sun, 02 Jun 2019 16:43:40: 1000000 INFO @ Sun, 02 Jun 2019 16:43:41: 1000000 INFO @ Sun, 02 Jun 2019 16:43:48: 2000000 INFO @ Sun, 02 Jun 2019 16:43:49: 2000000 INFO @ Sun, 02 Jun 2019 16:43:49: 2000000 INFO @ Sun, 02 Jun 2019 16:43:56: 3000000 INFO @ Sun, 02 Jun 2019 16:43:57: 3000000 INFO @ Sun, 02 Jun 2019 16:43:58: 3000000 INFO @ Sun, 02 Jun 2019 16:44:04: 4000000 INFO @ Sun, 02 Jun 2019 16:44:05: 4000000 INFO @ Sun, 02 Jun 2019 16:44:06: 4000000 INFO @ Sun, 02 Jun 2019 16:44:12: 5000000 INFO @ Sun, 02 Jun 2019 16:44:13: 5000000 INFO @ Sun, 02 Jun 2019 16:44:15: 5000000 INFO @ Sun, 02 Jun 2019 16:44:19: 6000000 INFO @ Sun, 02 Jun 2019 16:44:21: 6000000 INFO @ Sun, 02 Jun 2019 16:44:23: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 16:44:23: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 16:44:23: #1 total tags in treatment: 6437148 INFO @ Sun, 02 Jun 2019 16:44:23: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:44:23: #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 16:44:23: #1 tags after filtering in treatment: 6437148 INFO @ Sun, 02 Jun 2019 16:44:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:44:23: #1 finished! INFO @ Sun, 02 Jun 2019 16:44:23: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:44:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:44:23: 6000000 INFO @ Sun, 02 Jun 2019 16:44:23: #2 number of paired peaks: 1610 INFO @ Sun, 02 Jun 2019 16:44:23: start model_add_line... INFO @ Sun, 02 Jun 2019 16:44:24: start X-correlation... INFO @ Sun, 02 Jun 2019 16:44:24: end of X-cor INFO @ Sun, 02 Jun 2019 16:44:24: #2 finished! INFO @ Sun, 02 Jun 2019 16:44:24: #2 predicted fragment length is 206 bps INFO @ Sun, 02 Jun 2019 16:44:24: #2 alternative fragment length(s) may be 206 bps INFO @ Sun, 02 Jun 2019 16:44:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.20_model.r INFO @ Sun, 02 Jun 2019 16:44:24: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:44:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:44:24: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 16:44:24: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 16:44:24: #1 total tags in treatment: 6437148 INFO @ Sun, 02 Jun 2019 16:44:24: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:44:24: #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 16:44:24: #1 tags after filtering in treatment: 6437148 INFO @ Sun, 02 Jun 2019 16:44:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:44:24: #1 finished! INFO @ Sun, 02 Jun 2019 16:44:24: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:44:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:44:25: #2 number of paired peaks: 1610 INFO @ Sun, 02 Jun 2019 16:44:25: start model_add_line... INFO @ Sun, 02 Jun 2019 16:44:25: start X-correlation... INFO @ Sun, 02 Jun 2019 16:44:25: end of X-cor INFO @ Sun, 02 Jun 2019 16:44:25: #2 finished! INFO @ Sun, 02 Jun 2019 16:44:25: #2 predicted fragment length is 206 bps INFO @ Sun, 02 Jun 2019 16:44:25: #2 alternative fragment length(s) may be 206 bps INFO @ Sun, 02 Jun 2019 16:44:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.05_model.r INFO @ Sun, 02 Jun 2019 16:44:25: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:44:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:44:27: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 16:44:27: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 16:44:27: #1 total tags in treatment: 6437148 INFO @ Sun, 02 Jun 2019 16:44:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:44:27: #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 16:44:27: #1 tags after filtering in treatment: 6437148 INFO @ Sun, 02 Jun 2019 16:44:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:44:27: #1 finished! INFO @ Sun, 02 Jun 2019 16:44:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:44:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:44:28: #2 number of paired peaks: 1610 INFO @ Sun, 02 Jun 2019 16:44:28: start model_add_line... INFO @ Sun, 02 Jun 2019 16:44:28: start X-correlation... INFO @ Sun, 02 Jun 2019 16:44:28: end of X-cor INFO @ Sun, 02 Jun 2019 16:44:28: #2 finished! INFO @ Sun, 02 Jun 2019 16:44:28: #2 predicted fragment length is 206 bps INFO @ Sun, 02 Jun 2019 16:44:28: #2 alternative fragment length(s) may be 206 bps INFO @ Sun, 02 Jun 2019 16:44:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.10_model.r INFO @ Sun, 02 Jun 2019 16:44:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:44:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:44:46: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:44:47: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:44:50: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:44:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:44:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:44:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.20_summits.bed INFO @ Sun, 02 Jun 2019 16:44:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (731 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:44:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:44:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:44:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.05_summits.bed INFO @ Sun, 02 Jun 2019 16:44:57: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1729 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:45:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:45:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:45:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2543059/SRX2543059.10_summits.bed INFO @ Sun, 02 Jun 2019 16:45:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1153 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。