Job ID = 1292509 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T10:10:00 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 ) 2019-06-02T10:10:00 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 : 10,244,663 reads read : 10,244,663 reads written : 10,244,663 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 10244663 reads; of these: 10244663 (100.00%) were unpaired; of these: 604485 (5.90%) aligned 0 times 8348579 (81.49%) aligned exactly 1 time 1291599 (12.61%) aligned >1 times 94.10% 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] 7029849 / 9640178 = 0.7292 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 19:14:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.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 19:14:56: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:14:56: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:14:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.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 19:14:56: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:14:56: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:14:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.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 19:14:56: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:14:56: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:15:03: 1000000 INFO @ Sun, 02 Jun 2019 19:15:04: 1000000 INFO @ Sun, 02 Jun 2019 19:15:06: 1000000 INFO @ Sun, 02 Jun 2019 19:15:10: 2000000 INFO @ Sun, 02 Jun 2019 19:15:12: 2000000 INFO @ Sun, 02 Jun 2019 19:15:15: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:15:15: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:15:15: #1 total tags in treatment: 2610329 INFO @ Sun, 02 Jun 2019 19:15:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:15:15: #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 19:15:15: #1 tags after filtering in treatment: 2610329 INFO @ Sun, 02 Jun 2019 19:15:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:15:15: #1 finished! INFO @ Sun, 02 Jun 2019 19:15:15: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:15:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:15:15: #2 number of paired peaks: 3277 INFO @ Sun, 02 Jun 2019 19:15:15: start model_add_line... INFO @ Sun, 02 Jun 2019 19:15:15: start X-correlation... INFO @ Sun, 02 Jun 2019 19:15:15: end of X-cor INFO @ Sun, 02 Jun 2019 19:15:15: #2 finished! INFO @ Sun, 02 Jun 2019 19:15:15: #2 predicted fragment length is 265 bps INFO @ Sun, 02 Jun 2019 19:15:15: #2 alternative fragment length(s) may be 265 bps INFO @ Sun, 02 Jun 2019 19:15:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.05_model.r INFO @ Sun, 02 Jun 2019 19:15:15: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:15:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:15:16: 2000000 INFO @ Sun, 02 Jun 2019 19:15:17: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:15:17: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:15:17: #1 total tags in treatment: 2610329 INFO @ Sun, 02 Jun 2019 19:15:17: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:15:17: #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 19:15:17: #1 tags after filtering in treatment: 2610329 INFO @ Sun, 02 Jun 2019 19:15:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:15:17: #1 finished! INFO @ Sun, 02 Jun 2019 19:15:17: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:15:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:15:17: #2 number of paired peaks: 3277 INFO @ Sun, 02 Jun 2019 19:15:17: start model_add_line... INFO @ Sun, 02 Jun 2019 19:15:17: start X-correlation... INFO @ Sun, 02 Jun 2019 19:15:17: end of X-cor INFO @ Sun, 02 Jun 2019 19:15:17: #2 finished! INFO @ Sun, 02 Jun 2019 19:15:17: #2 predicted fragment length is 265 bps INFO @ Sun, 02 Jun 2019 19:15:17: #2 alternative fragment length(s) may be 265 bps INFO @ Sun, 02 Jun 2019 19:15:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.20_model.r INFO @ Sun, 02 Jun 2019 19:15:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:15:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:15:22: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:15:22: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:15:22: #1 total tags in treatment: 2610329 INFO @ Sun, 02 Jun 2019 19:15:22: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:15:22: #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 19:15:22: #1 tags after filtering in treatment: 2610329 INFO @ Sun, 02 Jun 2019 19:15:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:15:22: #1 finished! INFO @ Sun, 02 Jun 2019 19:15:22: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:15:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:15:22: #2 number of paired peaks: 3277 INFO @ Sun, 02 Jun 2019 19:15:22: start model_add_line... INFO @ Sun, 02 Jun 2019 19:15:22: start X-correlation... INFO @ Sun, 02 Jun 2019 19:15:22: end of X-cor INFO @ Sun, 02 Jun 2019 19:15:22: #2 finished! INFO @ Sun, 02 Jun 2019 19:15:22: #2 predicted fragment length is 265 bps INFO @ Sun, 02 Jun 2019 19:15:22: #2 alternative fragment length(s) may be 265 bps INFO @ Sun, 02 Jun 2019 19:15:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.10_model.r INFO @ Sun, 02 Jun 2019 19:15:22: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:15:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:15:25: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:15:27: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:15:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:15:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:15:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.05_summits.bed INFO @ Sun, 02 Jun 2019 19:15:30: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (3836 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:15:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:15:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:15:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.20_summits.bed INFO @ Sun, 02 Jun 2019 19:15:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (785 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:15:33: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:15:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:15:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:15:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466522/SRX466522.10_summits.bed INFO @ Sun, 02 Jun 2019 19:15:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2227 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。