Job ID = 2001621 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T21:29:49 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 ) 2019-07-04T21:29:49 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 ) 2019-07-04T21:34:09 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 ) 2019-07-04T21:34:09 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 ) 2019-07-04T21:48:23 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 ) 2019-07-04T22:04:58 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 ) 2019-07-04T22:12:15 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 ) 2019-07-04T22:12:53 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -76 ( NET - Reading information from the socket failed ) 2019-07-04T22:12:53 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.27' from '172.19.7.67' 2019-07-04T22:12:53 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (130.14.250.27) from '172.19.7.67' spots read : 115,584,858 reads read : 115,584,858 reads written : 115,584,858 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: 00:57:34 115584858 reads; of these: 115584858 (100.00%) were unpaired; of these: 2083122 (1.80%) aligned 0 times 101503170 (87.82%) aligned exactly 1 time 11998566 (10.38%) aligned >1 times 98.20% overall alignment rate Time searching: 00:57:38 Overall time: 00:57:38 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 48 files... [bam_rmdupse_core] 74999400 / 113501736 = 0.6608 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 08:45:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.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 08:45:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:45:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:45:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.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 08:45:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:45:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:45:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.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 08:45:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:45:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:45:13: 1000000 INFO @ Fri, 05 Jul 2019 08:45:14: 1000000 INFO @ Fri, 05 Jul 2019 08:45:14: 1000000 INFO @ Fri, 05 Jul 2019 08:45:22: 2000000 INFO @ Fri, 05 Jul 2019 08:45:23: 2000000 INFO @ Fri, 05 Jul 2019 08:45:23: 2000000 INFO @ Fri, 05 Jul 2019 08:45:31: 3000000 INFO @ Fri, 05 Jul 2019 08:45:32: 3000000 INFO @ Fri, 05 Jul 2019 08:45:32: 3000000 INFO @ Fri, 05 Jul 2019 08:45:40: 4000000 INFO @ Fri, 05 Jul 2019 08:45:41: 4000000 INFO @ Fri, 05 Jul 2019 08:45:42: 4000000 INFO @ Fri, 05 Jul 2019 08:45:49: 5000000 INFO @ Fri, 05 Jul 2019 08:45:51: 5000000 INFO @ Fri, 05 Jul 2019 08:45:51: 5000000 INFO @ Fri, 05 Jul 2019 08:45:57: 6000000 INFO @ Fri, 05 Jul 2019 08:46:00: 6000000 INFO @ Fri, 05 Jul 2019 08:46:00: 6000000 INFO @ Fri, 05 Jul 2019 08:46:06: 7000000 INFO @ Fri, 05 Jul 2019 08:46:08: 7000000 INFO @ Fri, 05 Jul 2019 08:46:09: 7000000 INFO @ Fri, 05 Jul 2019 08:46:15: 8000000 INFO @ Fri, 05 Jul 2019 08:46:17: 8000000 INFO @ Fri, 05 Jul 2019 08:46:18: 8000000 INFO @ Fri, 05 Jul 2019 08:46:24: 9000000 INFO @ Fri, 05 Jul 2019 08:46:26: 9000000 INFO @ Fri, 05 Jul 2019 08:46:27: 9000000 INFO @ Fri, 05 Jul 2019 08:46:33: 10000000 INFO @ Fri, 05 Jul 2019 08:46:34: 10000000 INFO @ Fri, 05 Jul 2019 08:46:36: 10000000 INFO @ Fri, 05 Jul 2019 08:46:42: 11000000 INFO @ Fri, 05 Jul 2019 08:46:43: 11000000 INFO @ Fri, 05 Jul 2019 08:46:45: 11000000 INFO @ Fri, 05 Jul 2019 08:46:51: 12000000 INFO @ Fri, 05 Jul 2019 08:46:52: 12000000 INFO @ Fri, 05 Jul 2019 08:46:54: 12000000 INFO @ Fri, 05 Jul 2019 08:47:00: 13000000 INFO @ Fri, 05 Jul 2019 08:47:01: 13000000 INFO @ Fri, 05 Jul 2019 08:47:03: 13000000 INFO @ Fri, 05 Jul 2019 08:47:08: 14000000 INFO @ Fri, 05 Jul 2019 08:47:09: 14000000 INFO @ Fri, 05 Jul 2019 08:47:12: 14000000 INFO @ Fri, 05 Jul 2019 08:47:16: 15000000 INFO @ Fri, 05 Jul 2019 08:47:18: 15000000 INFO @ Fri, 05 Jul 2019 08:47:21: 15000000 INFO @ Fri, 05 Jul 2019 08:47:24: 16000000 INFO @ Fri, 05 Jul 2019 08:47:27: 16000000 INFO @ Fri, 05 Jul 2019 08:47:29: 16000000 INFO @ Fri, 05 Jul 2019 08:47:32: 17000000 INFO @ Fri, 05 Jul 2019 08:47:35: 17000000 INFO @ Fri, 05 Jul 2019 08:47:38: 17000000 INFO @ Fri, 05 Jul 2019 08:47:41: 18000000 INFO @ Fri, 05 Jul 2019 08:47:44: 18000000 INFO @ Fri, 05 Jul 2019 08:47:46: 18000000 INFO @ Fri, 05 Jul 2019 08:47:49: 19000000 INFO @ Fri, 05 Jul 2019 08:47:52: 19000000 INFO @ Fri, 05 Jul 2019 08:47:54: 19000000 INFO @ Fri, 05 Jul 2019 08:47:57: 20000000 INFO @ Fri, 05 Jul 2019 08:48:01: 20000000 INFO @ Fri, 05 Jul 2019 08:48:03: 20000000 INFO @ Fri, 05 Jul 2019 08:48:05: 21000000 INFO @ Fri, 05 Jul 2019 08:48:10: 21000000 INFO @ Fri, 05 Jul 2019 08:48:12: 21000000 INFO @ Fri, 05 Jul 2019 08:48:13: 22000000 INFO @ Fri, 05 Jul 2019 08:48:18: 22000000 INFO @ Fri, 05 Jul 2019 08:48:20: 22000000 INFO @ Fri, 05 Jul 2019 08:48:21: 23000000 INFO @ Fri, 05 Jul 2019 08:48:27: 23000000 INFO @ Fri, 05 Jul 2019 08:48:29: 23000000 INFO @ Fri, 05 Jul 2019 08:48:29: 24000000 INFO @ Fri, 05 Jul 2019 08:48:35: 24000000 INFO @ Fri, 05 Jul 2019 08:48:37: 25000000 INFO @ Fri, 05 Jul 2019 08:48:37: 24000000 INFO @ Fri, 05 Jul 2019 08:48:44: 25000000 INFO @ Fri, 05 Jul 2019 08:48:45: 26000000 INFO @ Fri, 05 Jul 2019 08:48:46: 25000000 INFO @ Fri, 05 Jul 2019 08:48:52: 26000000 INFO @ Fri, 05 Jul 2019 08:48:53: 27000000 INFO @ Fri, 05 Jul 2019 08:48:54: 26000000 INFO @ Fri, 05 Jul 2019 08:49:00: 27000000 INFO @ Fri, 05 Jul 2019 08:49:01: 28000000 INFO @ Fri, 05 Jul 2019 08:49:02: 27000000 INFO @ Fri, 05 Jul 2019 08:49:09: 28000000 INFO @ Fri, 05 Jul 2019 08:49:09: 29000000 INFO @ Fri, 05 Jul 2019 08:49:11: 28000000 INFO @ Fri, 05 Jul 2019 08:49:17: 30000000 INFO @ Fri, 05 Jul 2019 08:49:17: 29000000 INFO @ Fri, 05 Jul 2019 08:49:19: 29000000 INFO @ Fri, 05 Jul 2019 08:49:25: 31000000 INFO @ Fri, 05 Jul 2019 08:49:26: 30000000 INFO @ Fri, 05 Jul 2019 08:49:27: 30000000 INFO @ Fri, 05 Jul 2019 08:49:33: 32000000 INFO @ Fri, 05 Jul 2019 08:49:34: 31000000 INFO @ Fri, 05 Jul 2019 08:49:35: 31000000 INFO @ Fri, 05 Jul 2019 08:49:41: 33000000 INFO @ Fri, 05 Jul 2019 08:49:42: 32000000 INFO @ Fri, 05 Jul 2019 08:49:43: 32000000 INFO @ Fri, 05 Jul 2019 08:49:49: 34000000 INFO @ Fri, 05 Jul 2019 08:49:50: 33000000 INFO @ Fri, 05 Jul 2019 08:49:50: 33000000 INFO @ Fri, 05 Jul 2019 08:49:58: 35000000 INFO @ Fri, 05 Jul 2019 08:49:58: 34000000 INFO @ Fri, 05 Jul 2019 08:49:59: 34000000 INFO @ Fri, 05 Jul 2019 08:50:06: 36000000 INFO @ Fri, 05 Jul 2019 08:50:07: 35000000 INFO @ Fri, 05 Jul 2019 08:50:07: 35000000 INFO @ Fri, 05 Jul 2019 08:50:14: 37000000 INFO @ Fri, 05 Jul 2019 08:50:15: 36000000 INFO @ Fri, 05 Jul 2019 08:50:16: 36000000 INFO @ Fri, 05 Jul 2019 08:50:22: 38000000 INFO @ Fri, 05 Jul 2019 08:50:22: 37000000 INFO @ Fri, 05 Jul 2019 08:50:24: 37000000 INFO @ Fri, 05 Jul 2019 08:50:27: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 08:50:27: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 08:50:27: #1 total tags in treatment: 38502336 INFO @ Fri, 05 Jul 2019 08:50:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:50:27: #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 08:50:28: #1 tags after filtering in treatment: 38502149 INFO @ Fri, 05 Jul 2019 08:50:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:50:28: #1 finished! INFO @ Fri, 05 Jul 2019 08:50:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:50:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:50:30: 38000000 INFO @ Fri, 05 Jul 2019 08:50:32: 38000000 INFO @ Fri, 05 Jul 2019 08:50:34: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 08:50:34: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 08:50:34: #1 total tags in treatment: 38502336 INFO @ Fri, 05 Jul 2019 08:50:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:50:34: #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 08:50:35: #1 tags after filtering in treatment: 38502149 INFO @ Fri, 05 Jul 2019 08:50:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:50:35: #1 finished! INFO @ Fri, 05 Jul 2019 08:50:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:50:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:50:37: #2 number of paired peaks: 70655 INFO @ Fri, 05 Jul 2019 08:50:37: start model_add_line... INFO @ Fri, 05 Jul 2019 08:50:37: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 08:50:37: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 08:50:37: #1 total tags in treatment: 38502336 INFO @ Fri, 05 Jul 2019 08:50:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:50:37: #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 08:50:38: start X-correlation... INFO @ Fri, 05 Jul 2019 08:50:38: #1 tags after filtering in treatment: 38502149 INFO @ Fri, 05 Jul 2019 08:50:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:50:38: #1 finished! INFO @ Fri, 05 Jul 2019 08:50:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:50:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:50:38: end of X-cor INFO @ Fri, 05 Jul 2019 08:50:38: #2 finished! INFO @ Fri, 05 Jul 2019 08:50:38: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 08:50:38: #2 alternative fragment length(s) may be 4,136 bps INFO @ Fri, 05 Jul 2019 08:50:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.05_model.r INFO @ Fri, 05 Jul 2019 08:50:38: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:50:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:50:44: #2 number of paired peaks: 70655 INFO @ Fri, 05 Jul 2019 08:50:44: start model_add_line... INFO @ Fri, 05 Jul 2019 08:50:45: start X-correlation... INFO @ Fri, 05 Jul 2019 08:50:45: end of X-cor INFO @ Fri, 05 Jul 2019 08:50:45: #2 finished! INFO @ Fri, 05 Jul 2019 08:50:45: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 08:50:45: #2 alternative fragment length(s) may be 4,136 bps INFO @ Fri, 05 Jul 2019 08:50:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.20_model.r INFO @ Fri, 05 Jul 2019 08:50:45: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:50:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:50:46: #2 number of paired peaks: 70655 INFO @ Fri, 05 Jul 2019 08:50:46: start model_add_line... INFO @ Fri, 05 Jul 2019 08:50:47: start X-correlation... INFO @ Fri, 05 Jul 2019 08:50:47: end of X-cor INFO @ Fri, 05 Jul 2019 08:50:47: #2 finished! INFO @ Fri, 05 Jul 2019 08:50:47: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 08:50:47: #2 alternative fragment length(s) may be 4,136 bps INFO @ Fri, 05 Jul 2019 08:50:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.10_model.r INFO @ Fri, 05 Jul 2019 08:50:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:50:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:52:32: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:52:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:52:46: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:53:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.05_peaks.xls INFO @ Fri, 05 Jul 2019 08:53:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:53:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.05_summits.bed INFO @ Fri, 05 Jul 2019 08:53:36: Done! pass1 - making usageList (164 chroms): 17 millis pass2 - checking and writing primary data (59830 records, 4 fields): 83 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:53:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.20_peaks.xls INFO @ Fri, 05 Jul 2019 08:53:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:53:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.20_summits.bed INFO @ Fri, 05 Jul 2019 08:53:41: Done! pass1 - making usageList (122 chroms): 12 millis pass2 - checking and writing primary data (36307 records, 4 fields): 51 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:53:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.10_peaks.xls INFO @ Fri, 05 Jul 2019 08:53:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:53:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101943/ERX101943.10_summits.bed INFO @ Fri, 05 Jul 2019 08:53:49: Done! pass1 - making usageList (146 chroms): 11 millis pass2 - checking and writing primary data (48268 records, 4 fields): 71 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。