Job ID = 4288926 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T03:39:06 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 ) 2019-12-10T03:39:06 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 : 25,044,312 reads read : 50,088,624 reads written : 25,044,312 reads 0-length : 25,044,312 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: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:28:57 25044312 reads; of these: 25044312 (100.00%) were unpaired; of these: 1675002 (6.69%) aligned 0 times 19889236 (79.42%) aligned exactly 1 time 3480074 (13.90%) aligned >1 times 93.31% overall alignment rate Time searching: 00:29:02 Overall time: 00:29:02 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] 5163766 / 23369310 = 0.2210 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:28:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.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 @ Tue, 10 Dec 2019 13:28:46: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:28:46: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:28:54: 1000000 INFO @ Tue, 10 Dec 2019 13:29:02: 2000000 INFO @ Tue, 10 Dec 2019 13:29:09: 3000000 INFO @ Tue, 10 Dec 2019 13:29:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.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 @ Tue, 10 Dec 2019 13:29:16: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:29:16: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:29:17: 4000000 INFO @ Tue, 10 Dec 2019 13:29:25: 5000000 INFO @ Tue, 10 Dec 2019 13:29:28: 1000000 INFO @ Tue, 10 Dec 2019 13:29:33: 6000000 INFO @ Tue, 10 Dec 2019 13:29:39: 2000000 INFO @ Tue, 10 Dec 2019 13:29:41: 7000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:29:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.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 @ Tue, 10 Dec 2019 13:29:46: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:29:46: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:29:49: 8000000 INFO @ Tue, 10 Dec 2019 13:29:50: 3000000 INFO @ Tue, 10 Dec 2019 13:29:57: 1000000 INFO @ Tue, 10 Dec 2019 13:29:57: 9000000 INFO @ Tue, 10 Dec 2019 13:30:01: 4000000 INFO @ Tue, 10 Dec 2019 13:30:05: 10000000 INFO @ Tue, 10 Dec 2019 13:30:07: 2000000 INFO @ Tue, 10 Dec 2019 13:30:12: 5000000 INFO @ Tue, 10 Dec 2019 13:30:13: 11000000 INFO @ Tue, 10 Dec 2019 13:30:18: 3000000 INFO @ Tue, 10 Dec 2019 13:30:21: 12000000 INFO @ Tue, 10 Dec 2019 13:30:24: 6000000 INFO @ Tue, 10 Dec 2019 13:30:29: 4000000 INFO @ Tue, 10 Dec 2019 13:30:30: 13000000 INFO @ Tue, 10 Dec 2019 13:30:35: 7000000 INFO @ Tue, 10 Dec 2019 13:30:38: 14000000 INFO @ Tue, 10 Dec 2019 13:30:39: 5000000 INFO @ Tue, 10 Dec 2019 13:30:46: 15000000 INFO @ Tue, 10 Dec 2019 13:30:46: 8000000 INFO @ Tue, 10 Dec 2019 13:30:50: 6000000 INFO @ Tue, 10 Dec 2019 13:30:54: 16000000 INFO @ Tue, 10 Dec 2019 13:30:57: 9000000 INFO @ Tue, 10 Dec 2019 13:31:00: 7000000 INFO @ Tue, 10 Dec 2019 13:31:03: 17000000 INFO @ Tue, 10 Dec 2019 13:31:09: 10000000 INFO @ Tue, 10 Dec 2019 13:31:11: 8000000 INFO @ Tue, 10 Dec 2019 13:31:12: 18000000 INFO @ Tue, 10 Dec 2019 13:31:15: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:31:15: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:31:15: #1 total tags in treatment: 18205544 INFO @ Tue, 10 Dec 2019 13:31:15: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:31:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:31:15: #1 tags after filtering in treatment: 18205349 INFO @ Tue, 10 Dec 2019 13:31:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:31:15: #1 finished! INFO @ Tue, 10 Dec 2019 13:31:15: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:31:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:31:20: #2 number of paired peaks: 69595 INFO @ Tue, 10 Dec 2019 13:31:20: start model_add_line... INFO @ Tue, 10 Dec 2019 13:31:20: 11000000 INFO @ Tue, 10 Dec 2019 13:31:20: start X-correlation... INFO @ Tue, 10 Dec 2019 13:31:20: end of X-cor INFO @ Tue, 10 Dec 2019 13:31:20: #2 finished! INFO @ Tue, 10 Dec 2019 13:31:20: #2 predicted fragment length is 203 bps INFO @ Tue, 10 Dec 2019 13:31:20: #2 alternative fragment length(s) may be 203 bps INFO @ Tue, 10 Dec 2019 13:31:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.05_model.r INFO @ Tue, 10 Dec 2019 13:31:20: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:31:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:31:22: 9000000 INFO @ Tue, 10 Dec 2019 13:31:31: 12000000 INFO @ Tue, 10 Dec 2019 13:31:32: 10000000 INFO @ Tue, 10 Dec 2019 13:31:42: 13000000 INFO @ Tue, 10 Dec 2019 13:31:43: 11000000 INFO @ Tue, 10 Dec 2019 13:31:53: 14000000 INFO @ Tue, 10 Dec 2019 13:31:53: 12000000 INFO @ Tue, 10 Dec 2019 13:32:03: 15000000 INFO @ Tue, 10 Dec 2019 13:32:04: 13000000 INFO @ Tue, 10 Dec 2019 13:32:14: 16000000 INFO @ Tue, 10 Dec 2019 13:32:14: 14000000 INFO @ Tue, 10 Dec 2019 13:32:25: 17000000 INFO @ Tue, 10 Dec 2019 13:32:25: 15000000 INFO @ Tue, 10 Dec 2019 13:32:25: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:32:35: 18000000 INFO @ Tue, 10 Dec 2019 13:32:36: 16000000 INFO @ Tue, 10 Dec 2019 13:32:38: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:32:38: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:32:38: #1 total tags in treatment: 18205544 INFO @ Tue, 10 Dec 2019 13:32:38: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:32:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:32:38: #1 tags after filtering in treatment: 18205349 INFO @ Tue, 10 Dec 2019 13:32:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:32:38: #1 finished! INFO @ Tue, 10 Dec 2019 13:32:38: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:32:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:32:43: #2 number of paired peaks: 69595 INFO @ Tue, 10 Dec 2019 13:32:43: start model_add_line... INFO @ Tue, 10 Dec 2019 13:32:43: start X-correlation... INFO @ Tue, 10 Dec 2019 13:32:43: end of X-cor INFO @ Tue, 10 Dec 2019 13:32:43: #2 finished! INFO @ Tue, 10 Dec 2019 13:32:43: #2 predicted fragment length is 203 bps INFO @ Tue, 10 Dec 2019 13:32:43: #2 alternative fragment length(s) may be 203 bps INFO @ Tue, 10 Dec 2019 13:32:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.10_model.r INFO @ Tue, 10 Dec 2019 13:32:43: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:32:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:32:46: 17000000 INFO @ Tue, 10 Dec 2019 13:32:57: 18000000 INFO @ Tue, 10 Dec 2019 13:32:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:32:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:32:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.05_summits.bed INFO @ Tue, 10 Dec 2019 13:32:58: Done! pass1 - making usageList (93 chroms): 4 millis pass2 - checking and writing primary data (20084 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:32:59: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:32:59: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:32:59: #1 total tags in treatment: 18205544 INFO @ Tue, 10 Dec 2019 13:32:59: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:32:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:33:00: #1 tags after filtering in treatment: 18205349 INFO @ Tue, 10 Dec 2019 13:33:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:33:00: #1 finished! INFO @ Tue, 10 Dec 2019 13:33:00: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:33:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:33:04: #2 number of paired peaks: 69595 INFO @ Tue, 10 Dec 2019 13:33:04: start model_add_line... INFO @ Tue, 10 Dec 2019 13:33:05: start X-correlation... INFO @ Tue, 10 Dec 2019 13:33:05: end of X-cor INFO @ Tue, 10 Dec 2019 13:33:05: #2 finished! INFO @ Tue, 10 Dec 2019 13:33:05: #2 predicted fragment length is 203 bps INFO @ Tue, 10 Dec 2019 13:33:05: #2 alternative fragment length(s) may be 203 bps INFO @ Tue, 10 Dec 2019 13:33:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.20_model.r INFO @ Tue, 10 Dec 2019 13:33:05: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:33:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:33:44: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:34:06: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:34:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:34:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:34:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.10_summits.bed INFO @ Tue, 10 Dec 2019 13:34:16: Done! pass1 - making usageList (65 chroms): 5 millis pass2 - checking and writing primary data (9652 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:34:38: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:34:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:34:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460565/SRX5460565.20_summits.bed INFO @ Tue, 10 Dec 2019 13:34:38: Done! pass1 - making usageList (42 chroms): 3 millis pass2 - checking and writing primary data (3024 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。