Job ID = 2001570 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T20:13:59 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 : 22,267,878 reads read : 22,267,878 reads written : 22,267,878 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:00 22267878 reads; of these: 22267878 (100.00%) were unpaired; of these: 493632 (2.22%) aligned 0 times 19217595 (86.30%) aligned exactly 1 time 2556651 (11.48%) aligned >1 times 97.78% overall alignment rate Time searching: 00:05:01 Overall time: 00:05:01 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 9110460 / 21774246 = 0.4184 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 @ Fri, 05 Jul 2019 05:27:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 05:27:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:27:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:27:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 05:27:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:27:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:27:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 05:27:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:27:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:28:02: 1000000 INFO @ Fri, 05 Jul 2019 05:28:04: 1000000 INFO @ Fri, 05 Jul 2019 05:28:05: 1000000 INFO @ Fri, 05 Jul 2019 05:28:10: 2000000 INFO @ Fri, 05 Jul 2019 05:28:11: 2000000 INFO @ Fri, 05 Jul 2019 05:28:14: 2000000 INFO @ Fri, 05 Jul 2019 05:28:18: 3000000 INFO @ Fri, 05 Jul 2019 05:28:18: 3000000 INFO @ Fri, 05 Jul 2019 05:28:23: 3000000 INFO @ Fri, 05 Jul 2019 05:28:26: 4000000 INFO @ Fri, 05 Jul 2019 05:28:26: 4000000 INFO @ Fri, 05 Jul 2019 05:28:32: 4000000 INFO @ Fri, 05 Jul 2019 05:28:33: 5000000 INFO @ Fri, 05 Jul 2019 05:28:33: 5000000 INFO @ Fri, 05 Jul 2019 05:28:40: 6000000 INFO @ Fri, 05 Jul 2019 05:28:41: 5000000 INFO @ Fri, 05 Jul 2019 05:28:41: 6000000 INFO @ Fri, 05 Jul 2019 05:28:48: 7000000 INFO @ Fri, 05 Jul 2019 05:28:49: 7000000 INFO @ Fri, 05 Jul 2019 05:28:50: 6000000 INFO @ Fri, 05 Jul 2019 05:28:55: 8000000 INFO @ Fri, 05 Jul 2019 05:28:57: 8000000 INFO @ Fri, 05 Jul 2019 05:28:59: 7000000 INFO @ Fri, 05 Jul 2019 05:29:02: 9000000 INFO @ Fri, 05 Jul 2019 05:29:04: 9000000 INFO @ Fri, 05 Jul 2019 05:29:08: 8000000 INFO @ Fri, 05 Jul 2019 05:29:10: 10000000 INFO @ Fri, 05 Jul 2019 05:29:12: 10000000 INFO @ Fri, 05 Jul 2019 05:29:17: 11000000 INFO @ Fri, 05 Jul 2019 05:29:17: 9000000 INFO @ Fri, 05 Jul 2019 05:29:20: 11000000 INFO @ Fri, 05 Jul 2019 05:29:24: 12000000 INFO @ Fri, 05 Jul 2019 05:29:26: 10000000 INFO @ Fri, 05 Jul 2019 05:29:27: 12000000 INFO @ Fri, 05 Jul 2019 05:29:29: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:29:29: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:29:29: #1 total tags in treatment: 12663786 INFO @ Fri, 05 Jul 2019 05:29:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:29:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 05:29:30: #1 tags after filtering in treatment: 12663529 INFO @ Fri, 05 Jul 2019 05:29:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:29:30: #1 finished! INFO @ Fri, 05 Jul 2019 05:29:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:29:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:29:33: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:29:33: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:29:33: #1 total tags in treatment: 12663786 INFO @ Fri, 05 Jul 2019 05:29:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:29:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 05:29:33: #1 tags after filtering in treatment: 12663529 INFO @ Fri, 05 Jul 2019 05:29:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:29:33: #1 finished! INFO @ Fri, 05 Jul 2019 05:29:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:29:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:29:33: #2 number of paired peaks: 46919 INFO @ Fri, 05 Jul 2019 05:29:33: start model_add_line... INFO @ Fri, 05 Jul 2019 05:29:33: start X-correlation... INFO @ Fri, 05 Jul 2019 05:29:33: end of X-cor INFO @ Fri, 05 Jul 2019 05:29:33: #2 finished! INFO @ Fri, 05 Jul 2019 05:29:33: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 05:29:33: #2 alternative fragment length(s) may be 4,130 bps INFO @ Fri, 05 Jul 2019 05:29:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.20_model.r INFO @ Fri, 05 Jul 2019 05:29:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:29:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:29:35: 11000000 INFO @ Fri, 05 Jul 2019 05:29:36: #2 number of paired peaks: 46919 INFO @ Fri, 05 Jul 2019 05:29:36: start model_add_line... INFO @ Fri, 05 Jul 2019 05:29:37: start X-correlation... INFO @ Fri, 05 Jul 2019 05:29:37: end of X-cor INFO @ Fri, 05 Jul 2019 05:29:37: #2 finished! INFO @ Fri, 05 Jul 2019 05:29:37: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 05:29:37: #2 alternative fragment length(s) may be 4,130 bps INFO @ Fri, 05 Jul 2019 05:29:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.05_model.r INFO @ Fri, 05 Jul 2019 05:29:37: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:29:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:29:43: 12000000 INFO @ Fri, 05 Jul 2019 05:29:49: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:29:49: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:29:49: #1 total tags in treatment: 12663786 INFO @ Fri, 05 Jul 2019 05:29:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:29:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 05:29:50: #1 tags after filtering in treatment: 12663529 INFO @ Fri, 05 Jul 2019 05:29:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:29:50: #1 finished! INFO @ Fri, 05 Jul 2019 05:29:50: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:29:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:29:53: #2 number of paired peaks: 46919 INFO @ Fri, 05 Jul 2019 05:29:53: start model_add_line... INFO @ Fri, 05 Jul 2019 05:29:53: start X-correlation... INFO @ Fri, 05 Jul 2019 05:29:53: end of X-cor INFO @ Fri, 05 Jul 2019 05:29:53: #2 finished! INFO @ Fri, 05 Jul 2019 05:29:53: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 05:29:53: #2 alternative fragment length(s) may be 4,130 bps INFO @ Fri, 05 Jul 2019 05:29:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.10_model.r INFO @ Fri, 05 Jul 2019 05:29:53: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:29:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:30:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:30:15: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:30:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:30:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.20_peaks.xls INFO @ Fri, 05 Jul 2019 05:30:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:30:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.20_summits.bed INFO @ Fri, 05 Jul 2019 05:30:35: Done! pass1 - making usageList (77 chroms): 8 millis pass2 - checking and writing primary data (20803 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:30:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.05_peaks.xls INFO @ Fri, 05 Jul 2019 05:30:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:30:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.05_summits.bed INFO @ Fri, 05 Jul 2019 05:30:38: Done! pass1 - making usageList (130 chroms): 14 millis pass2 - checking and writing primary data (41962 records, 4 fields): 57 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:30:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.10_peaks.xls INFO @ Fri, 05 Jul 2019 05:30:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:30:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101913/ERX101913.10_summits.bed INFO @ Fri, 05 Jul 2019 05:30:55: Done! pass1 - making usageList (104 chroms): 12 millis pass2 - checking and writing primary data (32800 records, 4 fields): 47 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。