Job ID = 2640439 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:47:57 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 ) 2019-08-24T07:47:57 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 ) 2019-08-24T07:47:57 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 ) 2019-08-24T07:51:39 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 ) 2019-08-24T07:57:06 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 ) 2019-08-24T07:57:06 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 ) 2019-08-24T07:57:16 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 ) 2019-08-24T07:57:39 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 ) 2019-08-24T08:00:31 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 ) 2019-08-24T08:00:43 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 ) 2019-08-24T08:00:48 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 ) 2019-08-24T08:00:57 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 ) 2019-08-24T08:01:35 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 : 27,976,217 reads read : 55,952,434 reads written : 27,976,217 reads 0-length : 27,976,217 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: 00:00:01 Multiseed full-index search: 00:22:23 27976217 reads; of these: 27976217 (100.00%) were unpaired; of these: 3457739 (12.36%) aligned 0 times 19319722 (69.06%) aligned exactly 1 time 5198756 (18.58%) aligned >1 times 87.64% overall alignment rate Time searching: 00:22:28 Overall time: 00:22:28 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] 3374567 / 24518478 = 0.1376 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:42:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.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 17:42:14: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:42:14: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:42:22: 1000000 INFO @ Sat, 24 Aug 2019 17:42:30: 2000000 INFO @ Sat, 24 Aug 2019 17:42:38: 3000000 INFO @ Sat, 24 Aug 2019 17:42:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.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 17:42:44: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:42:44: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:42:46: 4000000 INFO @ Sat, 24 Aug 2019 17:42:52: 1000000 INFO @ Sat, 24 Aug 2019 17:42:54: 5000000 INFO @ Sat, 24 Aug 2019 17:43:00: 2000000 INFO @ Sat, 24 Aug 2019 17:43:02: 6000000 INFO @ Sat, 24 Aug 2019 17:43:08: 3000000 INFO @ Sat, 24 Aug 2019 17:43:09: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:43:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.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 17:43:14: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:43:14: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:43:16: 4000000 INFO @ Sat, 24 Aug 2019 17:43:18: 8000000 INFO @ Sat, 24 Aug 2019 17:43:22: 1000000 INFO @ Sat, 24 Aug 2019 17:43:24: 5000000 INFO @ Sat, 24 Aug 2019 17:43:26: 9000000 INFO @ Sat, 24 Aug 2019 17:43:31: 2000000 INFO @ Sat, 24 Aug 2019 17:43:33: 6000000 INFO @ Sat, 24 Aug 2019 17:43:36: 10000000 INFO @ Sat, 24 Aug 2019 17:43:39: 3000000 INFO @ Sat, 24 Aug 2019 17:43:41: 7000000 INFO @ Sat, 24 Aug 2019 17:43:45: 11000000 INFO @ Sat, 24 Aug 2019 17:43:47: 4000000 INFO @ Sat, 24 Aug 2019 17:43:49: 8000000 INFO @ Sat, 24 Aug 2019 17:43:54: 12000000 INFO @ Sat, 24 Aug 2019 17:43:56: 5000000 INFO @ Sat, 24 Aug 2019 17:43:57: 9000000 INFO @ Sat, 24 Aug 2019 17:44:02: 13000000 INFO @ Sat, 24 Aug 2019 17:44:04: 6000000 INFO @ Sat, 24 Aug 2019 17:44:06: 10000000 INFO @ Sat, 24 Aug 2019 17:44:11: 14000000 INFO @ Sat, 24 Aug 2019 17:44:12: 7000000 INFO @ Sat, 24 Aug 2019 17:44:15: 11000000 INFO @ Sat, 24 Aug 2019 17:44:20: 15000000 INFO @ Sat, 24 Aug 2019 17:44:20: 8000000 INFO @ Sat, 24 Aug 2019 17:44:24: 12000000 INFO @ Sat, 24 Aug 2019 17:44:28: 16000000 INFO @ Sat, 24 Aug 2019 17:44:29: 9000000 INFO @ Sat, 24 Aug 2019 17:44:33: 13000000 INFO @ Sat, 24 Aug 2019 17:44:37: 17000000 INFO @ Sat, 24 Aug 2019 17:44:38: 10000000 INFO @ Sat, 24 Aug 2019 17:44:41: 14000000 INFO @ Sat, 24 Aug 2019 17:44:45: 18000000 INFO @ Sat, 24 Aug 2019 17:44:47: 11000000 INFO @ Sat, 24 Aug 2019 17:44:50: 15000000 INFO @ Sat, 24 Aug 2019 17:44:54: 19000000 INFO @ Sat, 24 Aug 2019 17:44:56: 12000000 INFO @ Sat, 24 Aug 2019 17:44:58: 16000000 INFO @ Sat, 24 Aug 2019 17:45:03: 20000000 INFO @ Sat, 24 Aug 2019 17:45:05: 13000000 INFO @ Sat, 24 Aug 2019 17:45:07: 17000000 INFO @ Sat, 24 Aug 2019 17:45:11: 21000000 INFO @ Sat, 24 Aug 2019 17:45:13: #1 tag size is determined as 75 bps INFO @ Sat, 24 Aug 2019 17:45:13: #1 tag size = 75 INFO @ Sat, 24 Aug 2019 17:45:13: #1 total tags in treatment: 21143911 INFO @ Sat, 24 Aug 2019 17:45:13: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:45:13: #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 17:45:13: #1 tags after filtering in treatment: 21143772 INFO @ Sat, 24 Aug 2019 17:45:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:45:13: #1 finished! INFO @ Sat, 24 Aug 2019 17:45:13: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:45:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:45:14: 14000000 INFO @ Sat, 24 Aug 2019 17:45:15: 18000000 INFO @ Sat, 24 Aug 2019 17:45:16: #2 number of paired peaks: 16110 INFO @ Sat, 24 Aug 2019 17:45:16: start model_add_line... INFO @ Sat, 24 Aug 2019 17:45:17: start X-correlation... INFO @ Sat, 24 Aug 2019 17:45:17: end of X-cor INFO @ Sat, 24 Aug 2019 17:45:17: #2 finished! INFO @ Sat, 24 Aug 2019 17:45:17: #2 predicted fragment length is 147 bps INFO @ Sat, 24 Aug 2019 17:45:17: #2 alternative fragment length(s) may be 147 bps INFO @ Sat, 24 Aug 2019 17:45:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.05_model.r WARNING @ Sat, 24 Aug 2019 17:45:17: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:45:17: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sat, 24 Aug 2019 17:45:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 17:45:17: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:45:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:45:22: 15000000 INFO @ Sat, 24 Aug 2019 17:45:23: 19000000 INFO @ Sat, 24 Aug 2019 17:45:30: 16000000 INFO @ Sat, 24 Aug 2019 17:45:32: 20000000 INFO @ Sat, 24 Aug 2019 17:45:38: 17000000 INFO @ Sat, 24 Aug 2019 17:45:40: 21000000 INFO @ Sat, 24 Aug 2019 17:45:42: #1 tag size is determined as 75 bps INFO @ Sat, 24 Aug 2019 17:45:42: #1 tag size = 75 INFO @ Sat, 24 Aug 2019 17:45:42: #1 total tags in treatment: 21143911 INFO @ Sat, 24 Aug 2019 17:45:42: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:45:42: #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 17:45:42: #1 tags after filtering in treatment: 21143772 INFO @ Sat, 24 Aug 2019 17:45:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:45:42: #1 finished! INFO @ Sat, 24 Aug 2019 17:45:42: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:45:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:45:45: #2 number of paired peaks: 16110 INFO @ Sat, 24 Aug 2019 17:45:45: start model_add_line... INFO @ Sat, 24 Aug 2019 17:45:46: start X-correlation... INFO @ Sat, 24 Aug 2019 17:45:46: end of X-cor INFO @ Sat, 24 Aug 2019 17:45:46: #2 finished! INFO @ Sat, 24 Aug 2019 17:45:46: #2 predicted fragment length is 147 bps INFO @ Sat, 24 Aug 2019 17:45:46: #2 alternative fragment length(s) may be 147 bps INFO @ Sat, 24 Aug 2019 17:45:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.10_model.r WARNING @ Sat, 24 Aug 2019 17:45:46: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:45:46: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sat, 24 Aug 2019 17:45:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 17:45:46: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:45:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:45:46: 18000000 INFO @ Sat, 24 Aug 2019 17:45:54: 19000000 INFO @ Sat, 24 Aug 2019 17:46:02: 20000000 INFO @ Sat, 24 Aug 2019 17:46:10: 21000000 INFO @ Sat, 24 Aug 2019 17:46:12: #1 tag size is determined as 75 bps INFO @ Sat, 24 Aug 2019 17:46:12: #1 tag size = 75 INFO @ Sat, 24 Aug 2019 17:46:12: #1 total tags in treatment: 21143911 INFO @ Sat, 24 Aug 2019 17:46:12: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:46:12: #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 17:46:12: #1 tags after filtering in treatment: 21143772 INFO @ Sat, 24 Aug 2019 17:46:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:46:12: #1 finished! INFO @ Sat, 24 Aug 2019 17:46:12: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:46:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:46:15: #2 number of paired peaks: 16110 INFO @ Sat, 24 Aug 2019 17:46:15: start model_add_line... INFO @ Sat, 24 Aug 2019 17:46:15: start X-correlation... INFO @ Sat, 24 Aug 2019 17:46:15: end of X-cor INFO @ Sat, 24 Aug 2019 17:46:15: #2 finished! INFO @ Sat, 24 Aug 2019 17:46:15: #2 predicted fragment length is 147 bps INFO @ Sat, 24 Aug 2019 17:46:15: #2 alternative fragment length(s) may be 147 bps INFO @ Sat, 24 Aug 2019 17:46:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.20_model.r WARNING @ Sat, 24 Aug 2019 17:46:15: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:46:15: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sat, 24 Aug 2019 17:46:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 17:46:15: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:46:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:46:24: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:46:53: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:47:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:47:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:47:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.05_summits.bed INFO @ Sat, 24 Aug 2019 17:47:01: Done! pass1 - making usageList (75 chroms): 4 millis pass2 - checking and writing primary data (7599 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:47:30: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:47:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:47:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:47:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.10_summits.bed INFO @ Sat, 24 Aug 2019 17:47:45: Done! pass1 - making usageList (52 chroms): 3 millis pass2 - checking and writing primary data (1866 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:48:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:48:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:48:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4320107/SRX4320107.20_summits.bed INFO @ Sat, 24 Aug 2019 17:48:12: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (420 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。