Job ID = 2640473 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:07:44 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 ) 2019-08-24T08:07:44 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 ) 2019-08-24T08:07:44 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 ) 2019-08-24T08:08:51 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 ) 2019-08-24T08:08:51 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 ) 2019-08-24T08:10:04 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 ) 2019-08-24T08:10:24 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 ) 2019-08-24T08:10:32 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 ) 2019-08-24T08:12:18 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 ) 2019-08-24T08:12:34 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 ) 2019-08-24T08:13:28 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 ) 2019-08-24T08:13:40 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 : 14,743,295 reads read : 29,486,590 reads written : 14,743,295 reads 0-length : 14,743,295 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: 00:09:52 14743295 reads; of these: 14743295 (100.00%) were unpaired; of these: 1066550 (7.23%) aligned 0 times 11832133 (80.25%) aligned exactly 1 time 1844612 (12.51%) aligned >1 times 92.77% overall alignment rate Time searching: 00:09:55 Overall time: 00:09:55 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] 1968057 / 13676745 = 0.1439 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:30:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.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 17:30:07: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:30:07: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:30:14: 1000000 INFO @ Sat, 24 Aug 2019 17:30:23: 2000000 INFO @ Sat, 24 Aug 2019 17:30:30: 3000000 INFO @ Sat, 24 Aug 2019 17:30:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.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 17:30:37: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:30:37: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:30:37: 4000000 INFO @ Sat, 24 Aug 2019 17:30:47: 1000000 INFO @ Sat, 24 Aug 2019 17:30:48: 5000000 INFO @ Sat, 24 Aug 2019 17:30:56: 2000000 INFO @ Sat, 24 Aug 2019 17:30:57: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:31:06: 3000000 INFO @ Sat, 24 Aug 2019 17:31:06: 7000000 INFO @ Sat, 24 Aug 2019 17:31:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.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 17:31:07: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:31:07: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:31:13: 4000000 INFO @ Sat, 24 Aug 2019 17:31:14: 8000000 INFO @ Sat, 24 Aug 2019 17:31:15: 1000000 INFO @ Sat, 24 Aug 2019 17:31:21: 5000000 INFO @ Sat, 24 Aug 2019 17:31:21: 9000000 INFO @ Sat, 24 Aug 2019 17:31:23: 2000000 INFO @ Sat, 24 Aug 2019 17:31:30: 6000000 INFO @ Sat, 24 Aug 2019 17:31:31: 10000000 INFO @ Sat, 24 Aug 2019 17:31:32: 3000000 INFO @ Sat, 24 Aug 2019 17:31:38: 11000000 INFO @ Sat, 24 Aug 2019 17:31:38: 7000000 INFO @ Sat, 24 Aug 2019 17:31:38: 4000000 INFO @ Sat, 24 Aug 2019 17:31:43: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:31:43: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:31:43: #1 total tags in treatment: 11708688 INFO @ Sat, 24 Aug 2019 17:31:43: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:31:43: #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 17:31:43: #1 tags after filtering in treatment: 11708398 INFO @ Sat, 24 Aug 2019 17:31:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:31:43: #1 finished! INFO @ Sat, 24 Aug 2019 17:31:43: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:31:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:31:45: 5000000 INFO @ Sat, 24 Aug 2019 17:31:46: 8000000 INFO @ Sat, 24 Aug 2019 17:31:47: #2 number of paired peaks: 85166 INFO @ Sat, 24 Aug 2019 17:31:47: start model_add_line... INFO @ Sat, 24 Aug 2019 17:31:48: start X-correlation... INFO @ Sat, 24 Aug 2019 17:31:48: end of X-cor INFO @ Sat, 24 Aug 2019 17:31:48: #2 finished! INFO @ Sat, 24 Aug 2019 17:31:48: #2 predicted fragment length is 158 bps INFO @ Sat, 24 Aug 2019 17:31:48: #2 alternative fragment length(s) may be 158 bps INFO @ Sat, 24 Aug 2019 17:31:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.05_model.r INFO @ Sat, 24 Aug 2019 17:31:48: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:31:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:31:52: 6000000 INFO @ Sat, 24 Aug 2019 17:31:53: 9000000 INFO @ Sat, 24 Aug 2019 17:32:01: 10000000 INFO @ Sat, 24 Aug 2019 17:32:02: 7000000 INFO @ Sat, 24 Aug 2019 17:32:12: 11000000 INFO @ Sat, 24 Aug 2019 17:32:12: 8000000 INFO @ Sat, 24 Aug 2019 17:32:17: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:32:17: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:32:17: #1 total tags in treatment: 11708688 INFO @ Sat, 24 Aug 2019 17:32:17: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:32:17: #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 17:32:18: #1 tags after filtering in treatment: 11708398 INFO @ Sat, 24 Aug 2019 17:32:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:32:18: #1 finished! INFO @ Sat, 24 Aug 2019 17:32:18: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:32:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:32:19: 9000000 INFO @ Sat, 24 Aug 2019 17:32:22: #2 number of paired peaks: 85166 INFO @ Sat, 24 Aug 2019 17:32:22: start model_add_line... INFO @ Sat, 24 Aug 2019 17:32:22: start X-correlation... INFO @ Sat, 24 Aug 2019 17:32:22: end of X-cor INFO @ Sat, 24 Aug 2019 17:32:22: #2 finished! INFO @ Sat, 24 Aug 2019 17:32:22: #2 predicted fragment length is 158 bps INFO @ Sat, 24 Aug 2019 17:32:22: #2 alternative fragment length(s) may be 158 bps INFO @ Sat, 24 Aug 2019 17:32:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.10_model.r INFO @ Sat, 24 Aug 2019 17:32:22: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:32:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:32:26: 10000000 INFO @ Sat, 24 Aug 2019 17:32:33: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:32:35: 11000000 INFO @ Sat, 24 Aug 2019 17:32:41: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:32:41: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:32:41: #1 total tags in treatment: 11708688 INFO @ Sat, 24 Aug 2019 17:32:41: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:32:41: #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 17:32:42: #1 tags after filtering in treatment: 11708398 INFO @ Sat, 24 Aug 2019 17:32:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:32:42: #1 finished! INFO @ Sat, 24 Aug 2019 17:32:42: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:32:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:32:47: #2 number of paired peaks: 85166 INFO @ Sat, 24 Aug 2019 17:32:47: start model_add_line... INFO @ Sat, 24 Aug 2019 17:32:47: start X-correlation... INFO @ Sat, 24 Aug 2019 17:32:47: end of X-cor INFO @ Sat, 24 Aug 2019 17:32:47: #2 finished! INFO @ Sat, 24 Aug 2019 17:32:47: #2 predicted fragment length is 158 bps INFO @ Sat, 24 Aug 2019 17:32:47: #2 alternative fragment length(s) may be 158 bps INFO @ Sat, 24 Aug 2019 17:32:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.20_model.r INFO @ Sat, 24 Aug 2019 17:32:47: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:32:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:32:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:32:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:32:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.05_summits.bed INFO @ Sat, 24 Aug 2019 17:32:56: Done! pass1 - making usageList (123 chroms): 13 millis pass2 - checking and writing primary data (38202 records, 4 fields): 60 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:33:05: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:33:25: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:33:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:33:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.10_summits.bed INFO @ Sat, 24 Aug 2019 17:33:25: Done! INFO @ Sat, 24 Aug 2019 17:33:25: #3 Call peaks for each chromosome... pass1 - making usageList (94 chroms): 6 millis pass2 - checking and writing primary data (23411 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:33:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:33:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:33:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374988/SRX5374988.20_summits.bed INFO @ Sat, 24 Aug 2019 17:33:45: Done! pass1 - making usageList (58 chroms): 6 millis pass2 - checking and writing primary data (10028 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。