Job ID = 2001529 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T19:21:08 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 ) 2019-07-04T19:26:21 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 ) 2019-07-04T19:34:14 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 ) 2019-07-04T19:36:11 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 : 57,463,250 reads read : 57,463,250 reads written : 57,463,250 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:42:05 57463250 reads; of these: 57463250 (100.00%) were unpaired; of these: 1438014 (2.50%) aligned 0 times 49999616 (87.01%) aligned exactly 1 time 6025620 (10.49%) aligned >1 times 97.50% overall alignment rate Time searching: 00:42:06 Overall time: 00:42:06 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 24 files... [bam_rmdupse_core] 32444411 / 56025236 = 0.5791 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 05:40:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.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 05:40:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:40:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:40:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.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 05:40:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:40:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:40:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.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 05:40:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:40:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:40:25: 1000000 INFO @ Fri, 05 Jul 2019 05:40:26: 1000000 INFO @ Fri, 05 Jul 2019 05:40:27: 1000000 INFO @ Fri, 05 Jul 2019 05:40:36: 2000000 INFO @ Fri, 05 Jul 2019 05:40:40: 2000000 INFO @ Fri, 05 Jul 2019 05:40:41: 2000000 INFO @ Fri, 05 Jul 2019 05:40:46: 3000000 INFO @ Fri, 05 Jul 2019 05:40:55: 3000000 INFO @ Fri, 05 Jul 2019 05:40:57: 4000000 INFO @ Fri, 05 Jul 2019 05:40:57: 3000000 INFO @ Fri, 05 Jul 2019 05:41:06: 5000000 INFO @ Fri, 05 Jul 2019 05:41:10: 4000000 INFO @ Fri, 05 Jul 2019 05:41:12: 4000000 INFO @ Fri, 05 Jul 2019 05:41:16: 6000000 INFO @ Fri, 05 Jul 2019 05:41:24: 5000000 INFO @ Fri, 05 Jul 2019 05:41:26: 7000000 INFO @ Fri, 05 Jul 2019 05:41:26: 5000000 INFO @ Fri, 05 Jul 2019 05:41:35: 8000000 INFO @ Fri, 05 Jul 2019 05:41:38: 6000000 INFO @ Fri, 05 Jul 2019 05:41:41: 6000000 INFO @ Fri, 05 Jul 2019 05:41:46: 9000000 INFO @ Fri, 05 Jul 2019 05:41:52: 7000000 INFO @ Fri, 05 Jul 2019 05:41:55: 7000000 INFO @ Fri, 05 Jul 2019 05:41:55: 10000000 INFO @ Fri, 05 Jul 2019 05:42:06: 11000000 INFO @ Fri, 05 Jul 2019 05:42:07: 8000000 INFO @ Fri, 05 Jul 2019 05:42:09: 8000000 INFO @ Fri, 05 Jul 2019 05:42:16: 12000000 INFO @ Fri, 05 Jul 2019 05:42:20: 9000000 INFO @ Fri, 05 Jul 2019 05:42:24: 9000000 INFO @ Fri, 05 Jul 2019 05:42:28: 13000000 INFO @ Fri, 05 Jul 2019 05:42:34: 10000000 INFO @ Fri, 05 Jul 2019 05:42:37: 14000000 INFO @ Fri, 05 Jul 2019 05:42:38: 10000000 INFO @ Fri, 05 Jul 2019 05:42:46: 15000000 INFO @ Fri, 05 Jul 2019 05:42:49: 11000000 INFO @ Fri, 05 Jul 2019 05:42:52: 11000000 INFO @ Fri, 05 Jul 2019 05:42:58: 16000000 INFO @ Fri, 05 Jul 2019 05:43:03: 12000000 INFO @ Fri, 05 Jul 2019 05:43:06: 12000000 INFO @ Fri, 05 Jul 2019 05:43:09: 17000000 INFO @ Fri, 05 Jul 2019 05:43:17: 13000000 INFO @ Fri, 05 Jul 2019 05:43:19: 18000000 INFO @ Fri, 05 Jul 2019 05:43:20: 13000000 INFO @ Fri, 05 Jul 2019 05:43:30: 19000000 INFO @ Fri, 05 Jul 2019 05:43:33: 14000000 INFO @ Fri, 05 Jul 2019 05:43:34: 14000000 INFO @ Fri, 05 Jul 2019 05:43:42: 20000000 INFO @ Fri, 05 Jul 2019 05:43:48: 15000000 INFO @ Fri, 05 Jul 2019 05:43:50: 15000000 INFO @ Fri, 05 Jul 2019 05:43:54: 21000000 INFO @ Fri, 05 Jul 2019 05:44:02: 16000000 INFO @ Fri, 05 Jul 2019 05:44:05: 16000000 INFO @ Fri, 05 Jul 2019 05:44:05: 22000000 INFO @ Fri, 05 Jul 2019 05:44:15: 23000000 INFO @ Fri, 05 Jul 2019 05:44:17: 17000000 INFO @ Fri, 05 Jul 2019 05:44:18: 17000000 INFO @ Fri, 05 Jul 2019 05:44:22: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 05:44:22: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 05:44:22: #1 total tags in treatment: 23580825 INFO @ Fri, 05 Jul 2019 05:44:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:44:22: #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 05:44:22: #1 tags after filtering in treatment: 23580578 INFO @ Fri, 05 Jul 2019 05:44:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:44:22: #1 finished! INFO @ Fri, 05 Jul 2019 05:44:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:44:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:44:28: 18000000 INFO @ Fri, 05 Jul 2019 05:44:28: 18000000 INFO @ Fri, 05 Jul 2019 05:44:28: #2 number of paired peaks: 61131 INFO @ Fri, 05 Jul 2019 05:44:28: start model_add_line... INFO @ Fri, 05 Jul 2019 05:44:29: start X-correlation... INFO @ Fri, 05 Jul 2019 05:44:29: end of X-cor INFO @ Fri, 05 Jul 2019 05:44:29: #2 finished! INFO @ Fri, 05 Jul 2019 05:44:29: #2 predicted fragment length is 120 bps INFO @ Fri, 05 Jul 2019 05:44:29: #2 alternative fragment length(s) may be 120 bps INFO @ Fri, 05 Jul 2019 05:44:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.10_model.r INFO @ Fri, 05 Jul 2019 05:44:29: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:44:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:44:38: 19000000 INFO @ Fri, 05 Jul 2019 05:44:40: 19000000 INFO @ Fri, 05 Jul 2019 05:44:49: 20000000 INFO @ Fri, 05 Jul 2019 05:44:53: 20000000 INFO @ Fri, 05 Jul 2019 05:45:00: 21000000 INFO @ Fri, 05 Jul 2019 05:45:06: 21000000 INFO @ Fri, 05 Jul 2019 05:45:12: 22000000 INFO @ Fri, 05 Jul 2019 05:45:18: 22000000 INFO @ Fri, 05 Jul 2019 05:45:24: 23000000 INFO @ Fri, 05 Jul 2019 05:45:31: 23000000 INFO @ Fri, 05 Jul 2019 05:45:31: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 05:45:31: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 05:45:31: #1 total tags in treatment: 23580825 INFO @ Fri, 05 Jul 2019 05:45:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:45:31: #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 05:45:32: #1 tags after filtering in treatment: 23580578 INFO @ Fri, 05 Jul 2019 05:45:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:45:32: #1 finished! INFO @ Fri, 05 Jul 2019 05:45:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:45:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:45:38: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 05:45:38: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 05:45:38: #1 total tags in treatment: 23580825 INFO @ Fri, 05 Jul 2019 05:45:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:45:38: #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 05:45:39: #2 number of paired peaks: 61131 INFO @ Fri, 05 Jul 2019 05:45:39: start model_add_line... INFO @ Fri, 05 Jul 2019 05:45:39: #1 tags after filtering in treatment: 23580578 INFO @ Fri, 05 Jul 2019 05:45:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:45:39: #1 finished! INFO @ Fri, 05 Jul 2019 05:45:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:45:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:45:40: start X-correlation... INFO @ Fri, 05 Jul 2019 05:45:40: end of X-cor INFO @ Fri, 05 Jul 2019 05:45:40: #2 finished! INFO @ Fri, 05 Jul 2019 05:45:40: #2 predicted fragment length is 120 bps INFO @ Fri, 05 Jul 2019 05:45:40: #2 alternative fragment length(s) may be 120 bps INFO @ Fri, 05 Jul 2019 05:45:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.20_model.r INFO @ Fri, 05 Jul 2019 05:45:40: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:45:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:45:46: #2 number of paired peaks: 61131 INFO @ Fri, 05 Jul 2019 05:45:46: start model_add_line... INFO @ Fri, 05 Jul 2019 05:45:46: start X-correlation... INFO @ Fri, 05 Jul 2019 05:45:46: end of X-cor INFO @ Fri, 05 Jul 2019 05:45:46: #2 finished! INFO @ Fri, 05 Jul 2019 05:45:46: #2 predicted fragment length is 120 bps INFO @ Fri, 05 Jul 2019 05:45:46: #2 alternative fragment length(s) may be 120 bps INFO @ Fri, 05 Jul 2019 05:45:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.05_model.r INFO @ Fri, 05 Jul 2019 05:45:46: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:45:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:45:56: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:46:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.10_peaks.xls INFO @ Fri, 05 Jul 2019 05:46:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:46:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.10_summits.bed INFO @ Fri, 05 Jul 2019 05:46:48: Done! pass1 - making usageList (136 chroms): 15 millis pass2 - checking and writing primary data (44344 records, 4 fields): 72 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 05:47:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:47:10: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:47:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.05_peaks.xls INFO @ Fri, 05 Jul 2019 05:47:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:47:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.05_summits.bed INFO @ Fri, 05 Jul 2019 05:47:57: Done! pass1 - making usageList (165 chroms): 16 millis pass2 - checking and writing primary data (56010 records, 4 fields): 85 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:48:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.20_peaks.xls INFO @ Fri, 05 Jul 2019 05:48:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:48:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101873/ERX101873.20_summits.bed INFO @ Fri, 05 Jul 2019 05:48:01: Done! pass1 - making usageList (111 chroms): 8 millis pass2 - checking and writing primary data (32181 records, 4 fields): 60 millis CompletedMACS2peakCalling BigWig に変換しました。