Job ID = 2640477 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:09:46 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 ) 2019-08-24T08:10:04 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 ) 2019-08-24T08:10:24 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 ) 2019-08-24T08:10:24 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 ) 2019-08-24T08:12:10 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 ) 2019-08-24T08:12:10 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 ) 2019-08-24T08:12:10 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 ) 2019-08-24T08:12:26 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 ) 2019-08-24T08:13:38 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 ) 2019-08-24T08:14:21 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 ) 2019-08-24T08:14:40 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 ) 2019-08-24T08:16:16 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 ) 2019-08-24T08:16:16 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 ) 2019-08-24T08:17:20 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 ) 2019-08-24T08:21:06 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 ) 2019-08-24T08:21:52 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 : 28,562,106 reads read : 57,124,212 reads written : 28,562,106 reads 0-length : 28,562,106 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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:17:03 28562106 reads; of these: 28562106 (100.00%) were unpaired; of these: 658195 (2.30%) aligned 0 times 23669915 (82.87%) aligned exactly 1 time 4233996 (14.82%) aligned >1 times 97.70% overall alignment rate Time searching: 00:17:06 Overall time: 00:17:06 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 12 files... [bam_rmdupse_core] 12799024 / 27903911 = 0.4587 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:45:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.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 17:45:29: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:45:29: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:45:38: 1000000 INFO @ Sat, 24 Aug 2019 17:45:46: 2000000 INFO @ Sat, 24 Aug 2019 17:45:53: 3000000 INFO @ Sat, 24 Aug 2019 17:45:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.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 17:45:59: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:45:59: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:46:01: 4000000 INFO @ Sat, 24 Aug 2019 17:46:06: 1000000 INFO @ Sat, 24 Aug 2019 17:46:09: 5000000 INFO @ Sat, 24 Aug 2019 17:46:13: 2000000 INFO @ Sat, 24 Aug 2019 17:46:17: 6000000 INFO @ Sat, 24 Aug 2019 17:46:20: 3000000 INFO @ Sat, 24 Aug 2019 17:46:25: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:46:27: 4000000 INFO @ Sat, 24 Aug 2019 17:46:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.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 17:46:29: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:46:29: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:46:33: 8000000 INFO @ Sat, 24 Aug 2019 17:46:34: 5000000 INFO @ Sat, 24 Aug 2019 17:46:38: 1000000 INFO @ Sat, 24 Aug 2019 17:46:41: 6000000 INFO @ Sat, 24 Aug 2019 17:46:42: 9000000 INFO @ Sat, 24 Aug 2019 17:46:48: 2000000 INFO @ Sat, 24 Aug 2019 17:46:48: 7000000 INFO @ Sat, 24 Aug 2019 17:46:51: 10000000 INFO @ Sat, 24 Aug 2019 17:46:55: 8000000 INFO @ Sat, 24 Aug 2019 17:46:57: 3000000 INFO @ Sat, 24 Aug 2019 17:47:01: 11000000 INFO @ Sat, 24 Aug 2019 17:47:03: 9000000 INFO @ Sat, 24 Aug 2019 17:47:07: 4000000 INFO @ Sat, 24 Aug 2019 17:47:10: 10000000 INFO @ Sat, 24 Aug 2019 17:47:10: 12000000 INFO @ Sat, 24 Aug 2019 17:47:16: 5000000 INFO @ Sat, 24 Aug 2019 17:47:17: 11000000 INFO @ Sat, 24 Aug 2019 17:47:20: 13000000 INFO @ Sat, 24 Aug 2019 17:47:24: 12000000 INFO @ Sat, 24 Aug 2019 17:47:26: 6000000 INFO @ Sat, 24 Aug 2019 17:47:29: 14000000 INFO @ Sat, 24 Aug 2019 17:47:31: 13000000 INFO @ Sat, 24 Aug 2019 17:47:35: 7000000 INFO @ Sat, 24 Aug 2019 17:47:38: 14000000 INFO @ Sat, 24 Aug 2019 17:47:38: 15000000 INFO @ Sat, 24 Aug 2019 17:47:39: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:47:39: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:47:39: #1 total tags in treatment: 15104887 INFO @ Sat, 24 Aug 2019 17:47:39: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:47:39: #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 17:47:40: #1 tags after filtering in treatment: 15104679 INFO @ Sat, 24 Aug 2019 17:47:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:47:40: #1 finished! INFO @ Sat, 24 Aug 2019 17:47:40: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:47:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:47:43: 8000000 INFO @ Sat, 24 Aug 2019 17:47:44: #2 number of paired peaks: 73016 INFO @ Sat, 24 Aug 2019 17:47:44: start model_add_line... INFO @ Sat, 24 Aug 2019 17:47:45: start X-correlation... INFO @ Sat, 24 Aug 2019 17:47:45: end of X-cor INFO @ Sat, 24 Aug 2019 17:47:45: #2 finished! INFO @ Sat, 24 Aug 2019 17:47:45: #2 predicted fragment length is 171 bps INFO @ Sat, 24 Aug 2019 17:47:45: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 24 Aug 2019 17:47:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.05_model.r INFO @ Sat, 24 Aug 2019 17:47:45: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:47:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:47:46: 15000000 INFO @ Sat, 24 Aug 2019 17:47:47: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:47:47: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:47:47: #1 total tags in treatment: 15104887 INFO @ Sat, 24 Aug 2019 17:47:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:47:47: #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 17:47:47: #1 tags after filtering in treatment: 15104679 INFO @ Sat, 24 Aug 2019 17:47:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:47:47: #1 finished! INFO @ Sat, 24 Aug 2019 17:47:47: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:47:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:47:51: 9000000 INFO @ Sat, 24 Aug 2019 17:47:51: #2 number of paired peaks: 73016 INFO @ Sat, 24 Aug 2019 17:47:52: start model_add_line... INFO @ Sat, 24 Aug 2019 17:47:52: start X-correlation... INFO @ Sat, 24 Aug 2019 17:47:52: end of X-cor INFO @ Sat, 24 Aug 2019 17:47:52: #2 finished! INFO @ Sat, 24 Aug 2019 17:47:52: #2 predicted fragment length is 171 bps INFO @ Sat, 24 Aug 2019 17:47:52: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 24 Aug 2019 17:47:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.10_model.r INFO @ Sat, 24 Aug 2019 17:47:52: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:47:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:47:59: 10000000 INFO @ Sat, 24 Aug 2019 17:48:08: 11000000 INFO @ Sat, 24 Aug 2019 17:48:16: 12000000 INFO @ Sat, 24 Aug 2019 17:48:25: 13000000 INFO @ Sat, 24 Aug 2019 17:48:34: 14000000 INFO @ Sat, 24 Aug 2019 17:48:35: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:48:42: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:48:43: 15000000 INFO @ Sat, 24 Aug 2019 17:48:44: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:48:44: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:48:44: #1 total tags in treatment: 15104887 INFO @ Sat, 24 Aug 2019 17:48:44: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:48:44: #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 17:48:44: #1 tags after filtering in treatment: 15104679 INFO @ Sat, 24 Aug 2019 17:48:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:48:44: #1 finished! INFO @ Sat, 24 Aug 2019 17:48:44: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:48:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:48:48: #2 number of paired peaks: 73016 INFO @ Sat, 24 Aug 2019 17:48:48: start model_add_line... INFO @ Sat, 24 Aug 2019 17:48:49: start X-correlation... INFO @ Sat, 24 Aug 2019 17:48:49: end of X-cor INFO @ Sat, 24 Aug 2019 17:48:49: #2 finished! INFO @ Sat, 24 Aug 2019 17:48:49: #2 predicted fragment length is 171 bps INFO @ Sat, 24 Aug 2019 17:48:49: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 24 Aug 2019 17:48:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.20_model.r INFO @ Sat, 24 Aug 2019 17:48:49: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:48:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:49:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:49:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:49:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.05_summits.bed INFO @ Sat, 24 Aug 2019 17:49:04: Done! pass1 - making usageList (119 chroms): 14 millis pass2 - checking and writing primary data (33051 records, 4 fields): 47 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:49:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:49:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:49:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.10_summits.bed INFO @ Sat, 24 Aug 2019 17:49:10: Done! pass1 - making usageList (94 chroms): 5 millis pass2 - checking and writing primary data (22750 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:49:37: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:50:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:50:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:50:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374990/SRX5374990.20_summits.bed INFO @ Sat, 24 Aug 2019 17:50:03: Done! pass1 - making usageList (68 chroms): 6 millis pass2 - checking and writing primary data (11744 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。