Job ID = 2003191 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T03:01:47 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 ) 2019-07-05T03:01:48 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 : 48,288,269 reads read : 48,288,269 reads written : 48,288,269 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR498450.sra.cache’: 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: 00:19:31 48288269 reads; of these: 48288269 (100.00%) were unpaired; of these: 8817122 (18.26%) aligned 0 times 30592552 (63.35%) aligned exactly 1 time 8878595 (18.39%) aligned >1 times 81.74% overall alignment rate Time searching: 00:19:32 Overall time: 00:19:32 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] 9445182 / 39471147 = 0.2393 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 12:46:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.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 12:46:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:46:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:46:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.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 12:46:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:46:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:46:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.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 12:46:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:46:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:46:29: 1000000 INFO @ Fri, 05 Jul 2019 12:46:30: 1000000 INFO @ Fri, 05 Jul 2019 12:46:33: 1000000 INFO @ Fri, 05 Jul 2019 12:46:39: 2000000 INFO @ Fri, 05 Jul 2019 12:46:39: 2000000 INFO @ Fri, 05 Jul 2019 12:46:45: 2000000 INFO @ Fri, 05 Jul 2019 12:46:49: 3000000 INFO @ Fri, 05 Jul 2019 12:46:50: 3000000 INFO @ Fri, 05 Jul 2019 12:46:57: 3000000 INFO @ Fri, 05 Jul 2019 12:47:00: 4000000 INFO @ Fri, 05 Jul 2019 12:47:02: 4000000 INFO @ Fri, 05 Jul 2019 12:47:10: 4000000 INFO @ Fri, 05 Jul 2019 12:47:11: 5000000 INFO @ Fri, 05 Jul 2019 12:47:13: 5000000 INFO @ Fri, 05 Jul 2019 12:47:20: 6000000 INFO @ Fri, 05 Jul 2019 12:47:22: 5000000 INFO @ Fri, 05 Jul 2019 12:47:23: 6000000 INFO @ Fri, 05 Jul 2019 12:47:29: 7000000 INFO @ Fri, 05 Jul 2019 12:47:33: 7000000 INFO @ Fri, 05 Jul 2019 12:47:34: 6000000 INFO @ Fri, 05 Jul 2019 12:47:39: 8000000 INFO @ Fri, 05 Jul 2019 12:47:43: 8000000 INFO @ Fri, 05 Jul 2019 12:47:43: 7000000 INFO @ Fri, 05 Jul 2019 12:47:48: 9000000 INFO @ Fri, 05 Jul 2019 12:47:53: 8000000 INFO @ Fri, 05 Jul 2019 12:47:53: 9000000 INFO @ Fri, 05 Jul 2019 12:47:58: 10000000 INFO @ Fri, 05 Jul 2019 12:48:03: 10000000 INFO @ Fri, 05 Jul 2019 12:48:03: 9000000 INFO @ Fri, 05 Jul 2019 12:48:08: 11000000 INFO @ Fri, 05 Jul 2019 12:48:14: 11000000 INFO @ Fri, 05 Jul 2019 12:48:14: 10000000 INFO @ Fri, 05 Jul 2019 12:48:19: 12000000 INFO @ Fri, 05 Jul 2019 12:48:24: 12000000 INFO @ Fri, 05 Jul 2019 12:48:24: 11000000 INFO @ Fri, 05 Jul 2019 12:48:29: 13000000 INFO @ Fri, 05 Jul 2019 12:48:34: 12000000 INFO @ Fri, 05 Jul 2019 12:48:34: 13000000 INFO @ Fri, 05 Jul 2019 12:48:38: 14000000 INFO @ Fri, 05 Jul 2019 12:48:44: 13000000 INFO @ Fri, 05 Jul 2019 12:48:45: 14000000 INFO @ Fri, 05 Jul 2019 12:48:48: 15000000 INFO @ Fri, 05 Jul 2019 12:48:53: 14000000 INFO @ Fri, 05 Jul 2019 12:48:55: 15000000 INFO @ Fri, 05 Jul 2019 12:48:58: 16000000 INFO @ Fri, 05 Jul 2019 12:49:03: 15000000 INFO @ Fri, 05 Jul 2019 12:49:06: 16000000 INFO @ Fri, 05 Jul 2019 12:49:08: 17000000 INFO @ Fri, 05 Jul 2019 12:49:12: 16000000 INFO @ Fri, 05 Jul 2019 12:49:16: 17000000 INFO @ Fri, 05 Jul 2019 12:49:18: 18000000 INFO @ Fri, 05 Jul 2019 12:49:22: 17000000 INFO @ Fri, 05 Jul 2019 12:49:27: 18000000 INFO @ Fri, 05 Jul 2019 12:49:29: 19000000 INFO @ Fri, 05 Jul 2019 12:49:30: 18000000 INFO @ Fri, 05 Jul 2019 12:49:38: 19000000 INFO @ Fri, 05 Jul 2019 12:49:39: 20000000 INFO @ Fri, 05 Jul 2019 12:49:40: 19000000 INFO @ Fri, 05 Jul 2019 12:49:48: 20000000 INFO @ Fri, 05 Jul 2019 12:49:49: 21000000 INFO @ Fri, 05 Jul 2019 12:49:50: 20000000 INFO @ Fri, 05 Jul 2019 12:49:58: 21000000 INFO @ Fri, 05 Jul 2019 12:49:59: 21000000 INFO @ Fri, 05 Jul 2019 12:50:00: 22000000 INFO @ Fri, 05 Jul 2019 12:50:07: 22000000 INFO @ Fri, 05 Jul 2019 12:50:09: 22000000 INFO @ Fri, 05 Jul 2019 12:50:11: 23000000 INFO @ Fri, 05 Jul 2019 12:50:15: 23000000 INFO @ Fri, 05 Jul 2019 12:50:19: 23000000 INFO @ Fri, 05 Jul 2019 12:50:21: 24000000 INFO @ Fri, 05 Jul 2019 12:50:23: 24000000 INFO @ Fri, 05 Jul 2019 12:50:29: 24000000 INFO @ Fri, 05 Jul 2019 12:50:32: 25000000 INFO @ Fri, 05 Jul 2019 12:50:32: 25000000 INFO @ Fri, 05 Jul 2019 12:50:39: 25000000 INFO @ Fri, 05 Jul 2019 12:50:40: 26000000 INFO @ Fri, 05 Jul 2019 12:50:43: 26000000 INFO @ Fri, 05 Jul 2019 12:50:48: 26000000 INFO @ Fri, 05 Jul 2019 12:50:49: 27000000 INFO @ Fri, 05 Jul 2019 12:50:54: 27000000 INFO @ Fri, 05 Jul 2019 12:50:57: 28000000 INFO @ Fri, 05 Jul 2019 12:50:57: 27000000 INFO @ Fri, 05 Jul 2019 12:51:05: 28000000 INFO @ Fri, 05 Jul 2019 12:51:06: 29000000 INFO @ Fri, 05 Jul 2019 12:51:07: 28000000 INFO @ Fri, 05 Jul 2019 12:51:15: 30000000 INFO @ Fri, 05 Jul 2019 12:51:15: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 12:51:15: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 12:51:15: #1 total tags in treatment: 30025965 INFO @ Fri, 05 Jul 2019 12:51:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:51:15: #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 12:51:16: #1 tags after filtering in treatment: 30025860 INFO @ Fri, 05 Jul 2019 12:51:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:51:16: #1 finished! INFO @ Fri, 05 Jul 2019 12:51:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:51:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:51:16: 29000000 INFO @ Fri, 05 Jul 2019 12:51:16: 29000000 INFO @ Fri, 05 Jul 2019 12:51:21: #2 number of paired peaks: 16155 INFO @ Fri, 05 Jul 2019 12:51:21: start model_add_line... INFO @ Fri, 05 Jul 2019 12:51:21: start X-correlation... INFO @ Fri, 05 Jul 2019 12:51:21: end of X-cor INFO @ Fri, 05 Jul 2019 12:51:21: #2 finished! INFO @ Fri, 05 Jul 2019 12:51:21: #2 predicted fragment length is 199 bps INFO @ Fri, 05 Jul 2019 12:51:21: #2 alternative fragment length(s) may be 199 bps INFO @ Fri, 05 Jul 2019 12:51:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.20_model.r INFO @ Fri, 05 Jul 2019 12:51:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:51:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:51:26: 30000000 INFO @ Fri, 05 Jul 2019 12:51:27: 30000000 INFO @ Fri, 05 Jul 2019 12:51:27: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 12:51:27: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 12:51:27: #1 total tags in treatment: 30025965 INFO @ Fri, 05 Jul 2019 12:51:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:51:27: #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 12:51:28: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 12:51:28: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 12:51:28: #1 total tags in treatment: 30025965 INFO @ Fri, 05 Jul 2019 12:51:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:51:28: #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 12:51:28: #1 tags after filtering in treatment: 30025860 INFO @ Fri, 05 Jul 2019 12:51:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:51:28: #1 finished! INFO @ Fri, 05 Jul 2019 12:51:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:51:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:51:29: #1 tags after filtering in treatment: 30025860 INFO @ Fri, 05 Jul 2019 12:51:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:51:29: #1 finished! INFO @ Fri, 05 Jul 2019 12:51:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:51:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:51:33: #2 number of paired peaks: 16155 INFO @ Fri, 05 Jul 2019 12:51:33: start model_add_line... INFO @ Fri, 05 Jul 2019 12:51:33: start X-correlation... INFO @ Fri, 05 Jul 2019 12:51:33: end of X-cor INFO @ Fri, 05 Jul 2019 12:51:33: #2 finished! INFO @ Fri, 05 Jul 2019 12:51:33: #2 predicted fragment length is 199 bps INFO @ Fri, 05 Jul 2019 12:51:33: #2 alternative fragment length(s) may be 199 bps INFO @ Fri, 05 Jul 2019 12:51:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.10_model.r INFO @ Fri, 05 Jul 2019 12:51:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:51:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:51:33: #2 number of paired peaks: 16155 INFO @ Fri, 05 Jul 2019 12:51:33: start model_add_line... INFO @ Fri, 05 Jul 2019 12:51:34: start X-correlation... INFO @ Fri, 05 Jul 2019 12:51:34: end of X-cor INFO @ Fri, 05 Jul 2019 12:51:34: #2 finished! INFO @ Fri, 05 Jul 2019 12:51:34: #2 predicted fragment length is 199 bps INFO @ Fri, 05 Jul 2019 12:51:34: #2 alternative fragment length(s) may be 199 bps INFO @ Fri, 05 Jul 2019 12:51:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.05_model.r INFO @ Fri, 05 Jul 2019 12:51:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:51:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:53:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:53:20: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:53:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:54:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:54:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:54:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.20_summits.bed INFO @ Fri, 05 Jul 2019 12:54:07: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (1114 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:54:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:54:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:54:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.10_summits.bed INFO @ Fri, 05 Jul 2019 12:54:14: Done! pass1 - making usageList (47 chroms): 2 millis pass2 - checking and writing primary data (5877 records, 4 fields): 16 millis INFO @ Fri, 05 Jul 2019 12:54:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.05_peaks.xls CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:54:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:54:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX148696/SRX148696.05_summits.bed INFO @ Fri, 05 Jul 2019 12:54:18: Done! pass1 - making usageList (83 chroms): 4 millis pass2 - checking and writing primary data (12703 records, 4 fields): 25 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。