Job ID = 2640594 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:58:20 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 : 23,966,546 reads read : 47,933,092 reads written : 23,966,546 reads 0-length : 23,966,546 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:16:15 23966546 reads; of these: 23966546 (100.00%) were unpaired; of these: 515340 (2.15%) aligned 0 times 18328929 (76.48%) aligned exactly 1 time 5122277 (21.37%) aligned >1 times 97.85% overall alignment rate Time searching: 00:16:18 Overall time: 00:16:18 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 12 files... [bam_rmdupse_core] 4606049 / 23451206 = 0.1964 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:25:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.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 @ Sat, 24 Aug 2019 18:25:44: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:25:44: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:25:51: 1000000 INFO @ Sat, 24 Aug 2019 18:25:58: 2000000 INFO @ Sat, 24 Aug 2019 18:26:05: 3000000 INFO @ Sat, 24 Aug 2019 18:26:12: 4000000 INFO @ Sat, 24 Aug 2019 18:26:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.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 @ Sat, 24 Aug 2019 18:26:13: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:26:13: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:26:20: 5000000 INFO @ Sat, 24 Aug 2019 18:26:20: 1000000 INFO @ Sat, 24 Aug 2019 18:26:27: 6000000 INFO @ Sat, 24 Aug 2019 18:26:27: 2000000 INFO @ Sat, 24 Aug 2019 18:26:34: 7000000 INFO @ Sat, 24 Aug 2019 18:26:34: 3000000 INFO @ Sat, 24 Aug 2019 18:26:41: 4000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:26:41: 8000000 INFO @ Sat, 24 Aug 2019 18:26:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.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 @ Sat, 24 Aug 2019 18:26:43: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:26:43: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:26:47: 5000000 INFO @ Sat, 24 Aug 2019 18:26:48: 9000000 INFO @ Sat, 24 Aug 2019 18:26:51: 1000000 INFO @ Sat, 24 Aug 2019 18:26:54: 6000000 INFO @ Sat, 24 Aug 2019 18:26:55: 10000000 INFO @ Sat, 24 Aug 2019 18:26:58: 2000000 INFO @ Sat, 24 Aug 2019 18:27:01: 7000000 INFO @ Sat, 24 Aug 2019 18:27:03: 11000000 INFO @ Sat, 24 Aug 2019 18:27:05: 3000000 INFO @ Sat, 24 Aug 2019 18:27:07: 8000000 INFO @ Sat, 24 Aug 2019 18:27:10: 12000000 INFO @ Sat, 24 Aug 2019 18:27:12: 4000000 INFO @ Sat, 24 Aug 2019 18:27:14: 9000000 INFO @ Sat, 24 Aug 2019 18:27:17: 13000000 INFO @ Sat, 24 Aug 2019 18:27:20: 5000000 INFO @ Sat, 24 Aug 2019 18:27:21: 10000000 INFO @ Sat, 24 Aug 2019 18:27:25: 14000000 INFO @ Sat, 24 Aug 2019 18:27:27: 6000000 INFO @ Sat, 24 Aug 2019 18:27:27: 11000000 INFO @ Sat, 24 Aug 2019 18:27:32: 15000000 INFO @ Sat, 24 Aug 2019 18:27:34: 12000000 INFO @ Sat, 24 Aug 2019 18:27:34: 7000000 INFO @ Sat, 24 Aug 2019 18:27:39: 16000000 INFO @ Sat, 24 Aug 2019 18:27:40: 13000000 INFO @ Sat, 24 Aug 2019 18:27:41: 8000000 INFO @ Sat, 24 Aug 2019 18:27:47: 17000000 INFO @ Sat, 24 Aug 2019 18:27:47: 14000000 INFO @ Sat, 24 Aug 2019 18:27:48: 9000000 INFO @ Sat, 24 Aug 2019 18:27:54: 15000000 INFO @ Sat, 24 Aug 2019 18:27:54: 18000000 INFO @ Sat, 24 Aug 2019 18:27:55: 10000000 INFO @ Sat, 24 Aug 2019 18:28:00: 16000000 INFO @ Sat, 24 Aug 2019 18:28:00: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:28:00: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:28:00: #1 total tags in treatment: 18845157 INFO @ Sat, 24 Aug 2019 18:28:00: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:28:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:28:01: #1 tags after filtering in treatment: 18844985 INFO @ Sat, 24 Aug 2019 18:28:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:28:01: #1 finished! INFO @ Sat, 24 Aug 2019 18:28:01: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:28:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:28:03: 11000000 INFO @ Sat, 24 Aug 2019 18:28:05: #2 number of paired peaks: 43744 INFO @ Sat, 24 Aug 2019 18:28:05: start model_add_line... INFO @ Sat, 24 Aug 2019 18:28:05: start X-correlation... INFO @ Sat, 24 Aug 2019 18:28:05: end of X-cor INFO @ Sat, 24 Aug 2019 18:28:05: #2 finished! INFO @ Sat, 24 Aug 2019 18:28:05: #2 predicted fragment length is 162 bps INFO @ Sat, 24 Aug 2019 18:28:05: #2 alternative fragment length(s) may be 162 bps INFO @ Sat, 24 Aug 2019 18:28:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.05_model.r INFO @ Sat, 24 Aug 2019 18:28:05: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:28:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:28:07: 17000000 INFO @ Sat, 24 Aug 2019 18:28:10: 12000000 INFO @ Sat, 24 Aug 2019 18:28:14: 18000000 INFO @ Sat, 24 Aug 2019 18:28:17: 13000000 INFO @ Sat, 24 Aug 2019 18:28:20: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:28:20: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:28:20: #1 total tags in treatment: 18845157 INFO @ Sat, 24 Aug 2019 18:28:20: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:28:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:28:20: #1 tags after filtering in treatment: 18844985 INFO @ Sat, 24 Aug 2019 18:28:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:28:20: #1 finished! INFO @ Sat, 24 Aug 2019 18:28:20: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:28:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:28:24: #2 number of paired peaks: 43744 INFO @ Sat, 24 Aug 2019 18:28:24: start model_add_line... INFO @ Sat, 24 Aug 2019 18:28:24: 14000000 INFO @ Sat, 24 Aug 2019 18:28:24: start X-correlation... INFO @ Sat, 24 Aug 2019 18:28:24: end of X-cor INFO @ Sat, 24 Aug 2019 18:28:24: #2 finished! INFO @ Sat, 24 Aug 2019 18:28:24: #2 predicted fragment length is 162 bps INFO @ Sat, 24 Aug 2019 18:28:24: #2 alternative fragment length(s) may be 162 bps INFO @ Sat, 24 Aug 2019 18:28:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.10_model.r INFO @ Sat, 24 Aug 2019 18:28:24: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:28:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:28:31: 15000000 INFO @ Sat, 24 Aug 2019 18:28:38: 16000000 INFO @ Sat, 24 Aug 2019 18:28:45: 17000000 INFO @ Sat, 24 Aug 2019 18:28:52: 18000000 INFO @ Sat, 24 Aug 2019 18:28:59: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:28:59: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:28:59: #1 total tags in treatment: 18845157 INFO @ Sat, 24 Aug 2019 18:28:59: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:28:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:28:59: #1 tags after filtering in treatment: 18844985 INFO @ Sat, 24 Aug 2019 18:28:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:28:59: #1 finished! INFO @ Sat, 24 Aug 2019 18:28:59: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:28:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:29:03: #2 number of paired peaks: 43744 INFO @ Sat, 24 Aug 2019 18:29:03: start model_add_line... INFO @ Sat, 24 Aug 2019 18:29:03: start X-correlation... INFO @ Sat, 24 Aug 2019 18:29:03: end of X-cor INFO @ Sat, 24 Aug 2019 18:29:03: #2 finished! INFO @ Sat, 24 Aug 2019 18:29:03: #2 predicted fragment length is 162 bps INFO @ Sat, 24 Aug 2019 18:29:03: #2 alternative fragment length(s) may be 162 bps INFO @ Sat, 24 Aug 2019 18:29:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.20_model.r INFO @ Sat, 24 Aug 2019 18:29:03: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:29:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:29:07: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:29:26: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:29:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:29:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:29:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.05_summits.bed INFO @ Sat, 24 Aug 2019 18:29:39: Done! pass1 - making usageList (90 chroms): 6 millis pass2 - checking and writing primary data (14126 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:29:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:29:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:29:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.10_summits.bed INFO @ Sat, 24 Aug 2019 18:29:58: Done! pass1 - making usageList (65 chroms): 5 millis pass2 - checking and writing primary data (10327 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:30:05: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:30:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:30:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:30:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375029/SRX5375029.20_summits.bed INFO @ Sat, 24 Aug 2019 18:30:37: Done! pass1 - making usageList (48 chroms): 4 millis pass2 - checking and writing primary data (6182 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。