Job ID = 2640449 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:51:11 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 ) 2019-08-24T07:52:44 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 ) 2019-08-24T07:53:03 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 ) 2019-08-24T07:53:03 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 ) 2019-08-24T07:54:41 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-08-24T07:54:41 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-08-24T07:55:50 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 ) 2019-08-24T07:55:50 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 ) 2019-08-24T07:57:06 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 ) 2019-08-24T07:58:23 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 ) 2019-08-24T07:59:18 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 ) 2019-08-24T08:00:49 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 ) 2019-08-24T08:01:32 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 ) 2019-08-24T08:04:47 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 ) 2019-08-24T08:06:25 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 ) 2019-08-24T08:06:38 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 ) 2019-08-24T08:08:07 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 ) 2019-08-24T08:12:31 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 ) 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 ) 2019-08-24T08:15:16 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 ) 2019-08-24T08:27:17 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 ) 2019-08-24T08:40:27 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 ) 2019-08-24T08:41:25 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 ) 2019-08-24T08:43:17 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 ) 2019-08-24T08:43:20 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 ) 2019-08-24T08:45:27 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 ) 2019-08-24T08:45:31 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 ) 2019-08-24T08:51:02 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 ) 2019-08-24T08:51:25 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 ) 2019-08-24T09:04:06 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 ) 2019-08-24T09:12:56 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 ) 2019-08-24T09:21:21 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 ) spots read : 412,985,049 reads read : 825,970,098 reads written : 412,985,049 reads 0-length : 412,985,049 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:08:04 412985049 reads; of these: 412985049 (100.00%) were unpaired; of these: 353862764 (85.68%) aligned 0 times 33899203 (8.21%) aligned exactly 1 time 25223082 (6.11%) aligned >1 times 14.32% overall alignment rate Time searching: 01:08:06 Overall time: 01:08:06 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 16 files... [bam_rmdupse_core] 48324493 / 59122285 = 0.8174 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:42:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.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 19:42:31: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:42:31: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:42:38: 1000000 INFO @ Sat, 24 Aug 2019 19:42:45: 2000000 INFO @ Sat, 24 Aug 2019 19:42:51: 3000000 INFO @ Sat, 24 Aug 2019 19:42:58: 4000000 INFO @ Sat, 24 Aug 2019 19:43:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.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 19:43:01: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:43:01: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:43:05: 5000000 INFO @ Sat, 24 Aug 2019 19:43:08: 1000000 INFO @ Sat, 24 Aug 2019 19:43:12: 6000000 INFO @ Sat, 24 Aug 2019 19:43:15: 2000000 INFO @ Sat, 24 Aug 2019 19:43:18: 7000000 INFO @ Sat, 24 Aug 2019 19:43:22: 3000000 INFO @ Sat, 24 Aug 2019 19:43:26: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:43:29: 4000000 INFO @ Sat, 24 Aug 2019 19:43:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.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 19:43:31: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:43:31: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:43:32: 9000000 INFO @ Sat, 24 Aug 2019 19:43:36: 5000000 INFO @ Sat, 24 Aug 2019 19:43:38: 1000000 INFO @ Sat, 24 Aug 2019 19:43:39: 10000000 INFO @ Sat, 24 Aug 2019 19:43:42: 6000000 INFO @ Sat, 24 Aug 2019 19:43:45: #1 tag size is determined as 26 bps INFO @ Sat, 24 Aug 2019 19:43:45: #1 tag size = 26 INFO @ Sat, 24 Aug 2019 19:43:45: #1 total tags in treatment: 10797792 INFO @ Sat, 24 Aug 2019 19:43:45: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:43:45: #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 19:43:45: #1 tags after filtering in treatment: 10797628 INFO @ Sat, 24 Aug 2019 19:43:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:43:45: #1 finished! INFO @ Sat, 24 Aug 2019 19:43:45: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:43:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:43:45: 2000000 INFO @ Sat, 24 Aug 2019 19:43:47: #2 number of paired peaks: 7340 INFO @ Sat, 24 Aug 2019 19:43:47: start model_add_line... INFO @ Sat, 24 Aug 2019 19:43:47: start X-correlation... INFO @ Sat, 24 Aug 2019 19:43:47: end of X-cor INFO @ Sat, 24 Aug 2019 19:43:47: #2 finished! INFO @ Sat, 24 Aug 2019 19:43:47: #2 predicted fragment length is 94 bps INFO @ Sat, 24 Aug 2019 19:43:47: #2 alternative fragment length(s) may be 94 bps INFO @ Sat, 24 Aug 2019 19:43:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.05_model.r INFO @ Sat, 24 Aug 2019 19:43:47: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:43:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:43:48: 7000000 INFO @ Sat, 24 Aug 2019 19:43:52: 3000000 INFO @ Sat, 24 Aug 2019 19:43:54: 8000000 INFO @ Sat, 24 Aug 2019 19:43:59: 4000000 INFO @ Sat, 24 Aug 2019 19:44:00: 9000000 INFO @ Sat, 24 Aug 2019 19:44:06: 10000000 INFO @ Sat, 24 Aug 2019 19:44:06: 5000000 INFO @ Sat, 24 Aug 2019 19:44:11: #1 tag size is determined as 26 bps INFO @ Sat, 24 Aug 2019 19:44:11: #1 tag size = 26 INFO @ Sat, 24 Aug 2019 19:44:11: #1 total tags in treatment: 10797792 INFO @ Sat, 24 Aug 2019 19:44:11: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:44:11: #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 19:44:12: #1 tags after filtering in treatment: 10797628 INFO @ Sat, 24 Aug 2019 19:44:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:44:12: #1 finished! INFO @ Sat, 24 Aug 2019 19:44:12: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:44:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:44:13: 6000000 INFO @ Sat, 24 Aug 2019 19:44:14: #2 number of paired peaks: 7340 INFO @ Sat, 24 Aug 2019 19:44:14: start model_add_line... INFO @ Sat, 24 Aug 2019 19:44:14: start X-correlation... INFO @ Sat, 24 Aug 2019 19:44:14: end of X-cor INFO @ Sat, 24 Aug 2019 19:44:14: #2 finished! INFO @ Sat, 24 Aug 2019 19:44:14: #2 predicted fragment length is 94 bps INFO @ Sat, 24 Aug 2019 19:44:14: #2 alternative fragment length(s) may be 94 bps INFO @ Sat, 24 Aug 2019 19:44:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.10_model.r INFO @ Sat, 24 Aug 2019 19:44:14: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:44:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:44:20: 7000000 INFO @ Sat, 24 Aug 2019 19:44:21: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:44:28: 8000000 INFO @ Sat, 24 Aug 2019 19:44:35: 9000000 INFO @ Sat, 24 Aug 2019 19:44:38: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.05_peaks.xls INFO @ Sat, 24 Aug 2019 19:44:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:44:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.05_summits.bed INFO @ Sat, 24 Aug 2019 19:44:38: Done! pass1 - making usageList (25 chroms): 2 millis pass2 - checking and writing primary data (1189 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:44:42: 10000000 INFO @ Sat, 24 Aug 2019 19:44:47: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:44:47: #1 tag size is determined as 26 bps INFO @ Sat, 24 Aug 2019 19:44:47: #1 tag size = 26 INFO @ Sat, 24 Aug 2019 19:44:47: #1 total tags in treatment: 10797792 INFO @ Sat, 24 Aug 2019 19:44:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:44:47: #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 19:44:48: #1 tags after filtering in treatment: 10797628 INFO @ Sat, 24 Aug 2019 19:44:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:44:48: #1 finished! INFO @ Sat, 24 Aug 2019 19:44:48: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:44:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:44:50: #2 number of paired peaks: 7340 INFO @ Sat, 24 Aug 2019 19:44:50: start model_add_line... INFO @ Sat, 24 Aug 2019 19:44:50: start X-correlation... INFO @ Sat, 24 Aug 2019 19:44:50: end of X-cor INFO @ Sat, 24 Aug 2019 19:44:50: #2 finished! INFO @ Sat, 24 Aug 2019 19:44:50: #2 predicted fragment length is 94 bps INFO @ Sat, 24 Aug 2019 19:44:50: #2 alternative fragment length(s) may be 94 bps INFO @ Sat, 24 Aug 2019 19:44:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.20_model.r INFO @ Sat, 24 Aug 2019 19:44:50: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:44:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:45:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.10_peaks.xls INFO @ Sat, 24 Aug 2019 19:45:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:45:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.10_summits.bed INFO @ Sat, 24 Aug 2019 19:45:04: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (42 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:45:23: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:45:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.20_peaks.xls INFO @ Sat, 24 Aug 2019 19:45:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:45:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5094893/SRX5094893.20_summits.bed INFO @ Sat, 24 Aug 2019 19:45:40: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。