Job ID = 2002167 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T01:42:45 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 ) 2019-07-05T01:42:45 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 ) 2019-07-05T01:53:22 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 ) 2019-07-05T01:53:22 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 : 25,650,380 reads read : 25,650,380 reads written : 25,650,380 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: 00:00:02 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:11:25 25650380 reads; of these: 25650380 (100.00%) were unpaired; of these: 824125 (3.21%) aligned 0 times 18037833 (70.32%) aligned exactly 1 time 6788422 (26.47%) aligned >1 times 96.79% overall alignment rate Time searching: 00:11:30 Overall time: 00:11:30 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] 2239534 / 24826255 = 0.0902 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 05 Jul 2019 11:17:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.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 BedGraph に変換中... INFO @ Fri, 05 Jul 2019 11:17:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.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 11:17:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:17:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:17:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:17:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:17:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.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 11:17:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:17:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:17:57: 1000000 INFO @ Fri, 05 Jul 2019 11:17:58: 1000000 INFO @ Fri, 05 Jul 2019 11:17:59: 1000000 INFO @ Fri, 05 Jul 2019 11:18:05: 2000000 INFO @ Fri, 05 Jul 2019 11:18:08: 2000000 INFO @ Fri, 05 Jul 2019 11:18:08: 2000000 INFO @ Fri, 05 Jul 2019 11:18:13: 3000000 INFO @ Fri, 05 Jul 2019 11:18:18: 3000000 INFO @ Fri, 05 Jul 2019 11:18:18: 3000000 INFO @ Fri, 05 Jul 2019 11:18:22: 4000000 INFO @ Fri, 05 Jul 2019 11:18:28: 4000000 INFO @ Fri, 05 Jul 2019 11:18:28: 4000000 INFO @ Fri, 05 Jul 2019 11:18:30: 5000000 INFO @ Fri, 05 Jul 2019 11:18:37: 5000000 INFO @ Fri, 05 Jul 2019 11:18:38: 6000000 INFO @ Fri, 05 Jul 2019 11:18:39: 5000000 INFO @ Fri, 05 Jul 2019 11:18:46: 7000000 INFO @ Fri, 05 Jul 2019 11:18:47: 6000000 INFO @ Fri, 05 Jul 2019 11:18:49: 6000000 INFO @ Fri, 05 Jul 2019 11:18:53: 8000000 INFO @ Fri, 05 Jul 2019 11:18:56: 7000000 INFO @ Fri, 05 Jul 2019 11:18:58: 7000000 INFO @ Fri, 05 Jul 2019 11:19:01: 9000000 INFO @ Fri, 05 Jul 2019 11:19:06: 8000000 INFO @ Fri, 05 Jul 2019 11:19:07: 8000000 INFO @ Fri, 05 Jul 2019 11:19:09: 10000000 INFO @ Fri, 05 Jul 2019 11:19:15: 9000000 INFO @ Fri, 05 Jul 2019 11:19:16: 9000000 INFO @ Fri, 05 Jul 2019 11:19:16: 11000000 INFO @ Fri, 05 Jul 2019 11:19:24: 10000000 INFO @ Fri, 05 Jul 2019 11:19:24: 12000000 INFO @ Fri, 05 Jul 2019 11:19:26: 10000000 INFO @ Fri, 05 Jul 2019 11:19:33: 13000000 INFO @ Fri, 05 Jul 2019 11:19:35: 11000000 INFO @ Fri, 05 Jul 2019 11:19:35: 11000000 INFO @ Fri, 05 Jul 2019 11:19:41: 14000000 INFO @ Fri, 05 Jul 2019 11:19:46: 12000000 INFO @ Fri, 05 Jul 2019 11:19:46: 12000000 INFO @ Fri, 05 Jul 2019 11:19:49: 15000000 INFO @ Fri, 05 Jul 2019 11:19:56: 13000000 INFO @ Fri, 05 Jul 2019 11:19:56: 13000000 INFO @ Fri, 05 Jul 2019 11:19:56: 16000000 INFO @ Fri, 05 Jul 2019 11:20:03: 17000000 INFO @ Fri, 05 Jul 2019 11:20:05: 14000000 INFO @ Fri, 05 Jul 2019 11:20:05: 14000000 INFO @ Fri, 05 Jul 2019 11:20:11: 18000000 INFO @ Fri, 05 Jul 2019 11:20:14: 15000000 INFO @ Fri, 05 Jul 2019 11:20:15: 15000000 INFO @ Fri, 05 Jul 2019 11:20:19: 19000000 INFO @ Fri, 05 Jul 2019 11:20:24: 16000000 INFO @ Fri, 05 Jul 2019 11:20:24: 16000000 INFO @ Fri, 05 Jul 2019 11:20:27: 20000000 INFO @ Fri, 05 Jul 2019 11:20:33: 17000000 INFO @ Fri, 05 Jul 2019 11:20:33: 17000000 INFO @ Fri, 05 Jul 2019 11:20:35: 21000000 INFO @ Fri, 05 Jul 2019 11:20:43: 22000000 INFO @ Fri, 05 Jul 2019 11:20:43: 18000000 INFO @ Fri, 05 Jul 2019 11:20:43: 18000000 INFO @ Fri, 05 Jul 2019 11:20:47: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:20:47: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:20:47: #1 total tags in treatment: 22586721 INFO @ Fri, 05 Jul 2019 11:20:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:20:47: #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 11:20:48: #1 tags after filtering in treatment: 22586600 INFO @ Fri, 05 Jul 2019 11:20:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:20:48: #1 finished! INFO @ Fri, 05 Jul 2019 11:20:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:20:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:20:52: #2 number of paired peaks: 31725 INFO @ Fri, 05 Jul 2019 11:20:52: start model_add_line... INFO @ Fri, 05 Jul 2019 11:20:52: 19000000 INFO @ Fri, 05 Jul 2019 11:20:52: 19000000 INFO @ Fri, 05 Jul 2019 11:20:52: start X-correlation... INFO @ Fri, 05 Jul 2019 11:20:53: end of X-cor INFO @ Fri, 05 Jul 2019 11:20:53: #2 finished! INFO @ Fri, 05 Jul 2019 11:20:53: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 11:20:53: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 05 Jul 2019 11:20:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.10_model.r INFO @ Fri, 05 Jul 2019 11:20:53: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:20:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:21:01: 20000000 INFO @ Fri, 05 Jul 2019 11:21:02: 20000000 INFO @ Fri, 05 Jul 2019 11:21:10: 21000000 INFO @ Fri, 05 Jul 2019 11:21:11: 21000000 INFO @ Fri, 05 Jul 2019 11:21:20: 22000000 INFO @ Fri, 05 Jul 2019 11:21:21: 22000000 INFO @ Fri, 05 Jul 2019 11:21:26: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:21:26: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:21:26: #1 total tags in treatment: 22586721 INFO @ Fri, 05 Jul 2019 11:21:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:21:26: #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 11:21:27: #1 tags after filtering in treatment: 22586600 INFO @ Fri, 05 Jul 2019 11:21:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:21:27: #1 finished! INFO @ Fri, 05 Jul 2019 11:21:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:21:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:21:27: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:21:27: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:21:27: #1 total tags in treatment: 22586721 INFO @ Fri, 05 Jul 2019 11:21:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:21:27: #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 11:21:27: #1 tags after filtering in treatment: 22586600 INFO @ Fri, 05 Jul 2019 11:21:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:21:27: #1 finished! INFO @ Fri, 05 Jul 2019 11:21:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:21:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:21:30: #2 number of paired peaks: 31725 INFO @ Fri, 05 Jul 2019 11:21:30: start model_add_line... INFO @ Fri, 05 Jul 2019 11:21:31: start X-correlation... INFO @ Fri, 05 Jul 2019 11:21:31: end of X-cor INFO @ Fri, 05 Jul 2019 11:21:31: #2 finished! INFO @ Fri, 05 Jul 2019 11:21:31: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 11:21:31: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 05 Jul 2019 11:21:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.20_model.r INFO @ Fri, 05 Jul 2019 11:21:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:21:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:21:31: #2 number of paired peaks: 31725 INFO @ Fri, 05 Jul 2019 11:21:31: start model_add_line... INFO @ Fri, 05 Jul 2019 11:21:31: start X-correlation... INFO @ Fri, 05 Jul 2019 11:21:31: end of X-cor INFO @ Fri, 05 Jul 2019 11:21:31: #2 finished! INFO @ Fri, 05 Jul 2019 11:21:31: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 11:21:31: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 05 Jul 2019 11:21:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.05_model.r INFO @ Fri, 05 Jul 2019 11:21:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:21:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:22:07: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:22:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.10_peaks.xls INFO @ Fri, 05 Jul 2019 11:22:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:22:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:22:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.10_summits.bed INFO @ Fri, 05 Jul 2019 11:22:44: Done! INFO @ Fri, 05 Jul 2019 11:22:44: #3 Call peaks for each chromosome... pass1 - making usageList (74 chroms): 10 millis pass2 - checking and writing primary data (16697 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:23:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:23:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:23:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.20_summits.bed INFO @ Fri, 05 Jul 2019 11:23:21: Done! pass1 - making usageList (47 chroms): 2 millis pass2 - checking and writing primary data (8993 records, 4 fields): 16 millis INFO @ Fri, 05 Jul 2019 11:23:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:23:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:23:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190369/ERX190369.05_summits.bed INFO @ Fri, 05 Jul 2019 11:23:23: Done! pass1 - making usageList (94 chroms): 5 millis pass2 - checking and writing primary data (26069 records, 4 fields): 42 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。