Job ID = 2001644 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T21:50:12 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 ) 2019-07-04T22:00:53 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 ) 2019-07-04T22:00:53 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 ) 2019-07-04T22:01:27 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 ) 2019-07-04T22:01:27 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.12' 2019-07-04T22:01:27 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' (130.14.250.26) from '172.19.7.12' 2019-07-04T22:01:27 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 ) 2019-07-04T22:01:27 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.12' 2019-07-04T22:01:27 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' (130.14.250.26) from '172.19.7.12' 2019-07-04T22:07:48 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 ) 2019-07-04T22:08:05 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 ) 2019-07-04T22:08:05 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 ) 2019-07-04T22:09:09 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 ) 2019-07-04T22:09:09 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 ) 2019-07-04T22:12:02 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 ) 2019-07-04T22:12:44 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 ) 2019-07-04T22:15:00 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 : 115,120,716 reads read : 115,120,716 reads written : 115,120,716 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: 00:56:27 115120716 reads; of these: 115120716 (100.00%) were unpaired; of these: 2051827 (1.78%) aligned 0 times 101028634 (87.76%) aligned exactly 1 time 12040255 (10.46%) aligned >1 times 98.22% overall alignment rate Time searching: 00:56:30 Overall time: 00:56:30 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] 75594621 / 113068889 = 0.6686 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 09:10:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.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 09:10:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:10:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:10:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.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 09:10:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:10:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:10:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.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 09:10:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:10:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:10:25: 1000000 INFO @ Fri, 05 Jul 2019 09:10:27: 1000000 INFO @ Fri, 05 Jul 2019 09:10:28: 1000000 INFO @ Fri, 05 Jul 2019 09:10:33: 2000000 INFO @ Fri, 05 Jul 2019 09:10:37: 2000000 INFO @ Fri, 05 Jul 2019 09:10:37: 2000000 INFO @ Fri, 05 Jul 2019 09:10:41: 3000000 INFO @ Fri, 05 Jul 2019 09:10:47: 3000000 INFO @ Fri, 05 Jul 2019 09:10:47: 3000000 INFO @ Fri, 05 Jul 2019 09:10:49: 4000000 INFO @ Fri, 05 Jul 2019 09:10:56: 4000000 INFO @ Fri, 05 Jul 2019 09:10:56: 4000000 INFO @ Fri, 05 Jul 2019 09:10:57: 5000000 INFO @ Fri, 05 Jul 2019 09:11:05: 5000000 INFO @ Fri, 05 Jul 2019 09:11:05: 6000000 INFO @ Fri, 05 Jul 2019 09:11:06: 5000000 INFO @ Fri, 05 Jul 2019 09:11:14: 7000000 INFO @ Fri, 05 Jul 2019 09:11:14: 6000000 INFO @ Fri, 05 Jul 2019 09:11:15: 6000000 INFO @ Fri, 05 Jul 2019 09:11:22: 8000000 INFO @ Fri, 05 Jul 2019 09:11:24: 7000000 INFO @ Fri, 05 Jul 2019 09:11:25: 7000000 INFO @ Fri, 05 Jul 2019 09:11:30: 9000000 INFO @ Fri, 05 Jul 2019 09:11:33: 8000000 INFO @ Fri, 05 Jul 2019 09:11:34: 8000000 INFO @ Fri, 05 Jul 2019 09:11:38: 10000000 INFO @ Fri, 05 Jul 2019 09:11:42: 9000000 INFO @ Fri, 05 Jul 2019 09:11:44: 9000000 INFO @ Fri, 05 Jul 2019 09:11:46: 11000000 INFO @ Fri, 05 Jul 2019 09:11:51: 10000000 INFO @ Fri, 05 Jul 2019 09:11:53: 10000000 INFO @ Fri, 05 Jul 2019 09:11:55: 12000000 INFO @ Fri, 05 Jul 2019 09:12:01: 11000000 INFO @ Fri, 05 Jul 2019 09:12:03: 13000000 INFO @ Fri, 05 Jul 2019 09:12:03: 11000000 INFO @ Fri, 05 Jul 2019 09:12:10: 12000000 INFO @ Fri, 05 Jul 2019 09:12:11: 14000000 INFO @ Fri, 05 Jul 2019 09:12:12: 12000000 INFO @ Fri, 05 Jul 2019 09:12:19: 15000000 INFO @ Fri, 05 Jul 2019 09:12:19: 13000000 INFO @ Fri, 05 Jul 2019 09:12:22: 13000000 INFO @ Fri, 05 Jul 2019 09:12:27: 16000000 INFO @ Fri, 05 Jul 2019 09:12:28: 14000000 INFO @ Fri, 05 Jul 2019 09:12:31: 14000000 INFO @ Fri, 05 Jul 2019 09:12:36: 17000000 INFO @ Fri, 05 Jul 2019 09:12:38: 15000000 INFO @ Fri, 05 Jul 2019 09:12:41: 15000000 INFO @ Fri, 05 Jul 2019 09:12:44: 18000000 INFO @ Fri, 05 Jul 2019 09:12:47: 16000000 INFO @ Fri, 05 Jul 2019 09:12:51: 16000000 INFO @ Fri, 05 Jul 2019 09:12:52: 19000000 INFO @ Fri, 05 Jul 2019 09:12:56: 17000000 INFO @ Fri, 05 Jul 2019 09:13:01: 17000000 INFO @ Fri, 05 Jul 2019 09:13:01: 20000000 INFO @ Fri, 05 Jul 2019 09:13:06: 18000000 INFO @ Fri, 05 Jul 2019 09:13:09: 21000000 INFO @ Fri, 05 Jul 2019 09:13:10: 18000000 INFO @ Fri, 05 Jul 2019 09:13:15: 19000000 INFO @ Fri, 05 Jul 2019 09:13:17: 22000000 INFO @ Fri, 05 Jul 2019 09:13:20: 19000000 INFO @ Fri, 05 Jul 2019 09:13:24: 20000000 INFO @ Fri, 05 Jul 2019 09:13:25: 23000000 INFO @ Fri, 05 Jul 2019 09:13:29: 20000000 INFO @ Fri, 05 Jul 2019 09:13:34: 21000000 INFO @ Fri, 05 Jul 2019 09:13:34: 24000000 INFO @ Fri, 05 Jul 2019 09:13:39: 21000000 INFO @ Fri, 05 Jul 2019 09:13:42: 25000000 INFO @ Fri, 05 Jul 2019 09:13:43: 22000000 INFO @ Fri, 05 Jul 2019 09:13:48: 22000000 INFO @ Fri, 05 Jul 2019 09:13:50: 26000000 INFO @ Fri, 05 Jul 2019 09:13:52: 23000000 INFO @ Fri, 05 Jul 2019 09:13:58: 23000000 INFO @ Fri, 05 Jul 2019 09:13:59: 27000000 INFO @ Fri, 05 Jul 2019 09:14:01: 24000000 INFO @ Fri, 05 Jul 2019 09:14:07: 28000000 INFO @ Fri, 05 Jul 2019 09:14:08: 24000000 INFO @ Fri, 05 Jul 2019 09:14:11: 25000000 INFO @ Fri, 05 Jul 2019 09:14:15: 29000000 INFO @ Fri, 05 Jul 2019 09:14:18: 25000000 INFO @ Fri, 05 Jul 2019 09:14:20: 26000000 INFO @ Fri, 05 Jul 2019 09:14:23: 30000000 INFO @ Fri, 05 Jul 2019 09:14:27: 26000000 INFO @ Fri, 05 Jul 2019 09:14:30: 27000000 INFO @ Fri, 05 Jul 2019 09:14:32: 31000000 INFO @ Fri, 05 Jul 2019 09:14:37: 27000000 INFO @ Fri, 05 Jul 2019 09:14:39: 28000000 INFO @ Fri, 05 Jul 2019 09:14:40: 32000000 INFO @ Fri, 05 Jul 2019 09:14:47: 28000000 INFO @ Fri, 05 Jul 2019 09:14:48: 33000000 INFO @ Fri, 05 Jul 2019 09:14:48: 29000000 INFO @ Fri, 05 Jul 2019 09:14:56: 29000000 INFO @ Fri, 05 Jul 2019 09:14:56: 34000000 INFO @ Fri, 05 Jul 2019 09:14:57: 30000000 INFO @ Fri, 05 Jul 2019 09:15:05: 35000000 INFO @ Fri, 05 Jul 2019 09:15:06: 30000000 INFO @ Fri, 05 Jul 2019 09:15:07: 31000000 INFO @ Fri, 05 Jul 2019 09:15:13: 36000000 INFO @ Fri, 05 Jul 2019 09:15:15: 31000000 INFO @ Fri, 05 Jul 2019 09:15:16: 32000000 INFO @ Fri, 05 Jul 2019 09:15:22: 37000000 INFO @ Fri, 05 Jul 2019 09:15:24: 32000000 INFO @ Fri, 05 Jul 2019 09:15:25: 33000000 INFO @ Fri, 05 Jul 2019 09:15:27: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 09:15:27: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 09:15:27: #1 total tags in treatment: 37474268 INFO @ Fri, 05 Jul 2019 09:15:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:15:27: #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 09:15:28: #1 tags after filtering in treatment: 37474095 INFO @ Fri, 05 Jul 2019 09:15:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:15:28: #1 finished! INFO @ Fri, 05 Jul 2019 09:15:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:15:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:15:34: 33000000 INFO @ Fri, 05 Jul 2019 09:15:34: 34000000 INFO @ Fri, 05 Jul 2019 09:15:36: #2 number of paired peaks: 69550 INFO @ Fri, 05 Jul 2019 09:15:36: start model_add_line... INFO @ Fri, 05 Jul 2019 09:15:37: start X-correlation... INFO @ Fri, 05 Jul 2019 09:15:37: end of X-cor INFO @ Fri, 05 Jul 2019 09:15:37: #2 finished! INFO @ Fri, 05 Jul 2019 09:15:37: #2 predicted fragment length is 138 bps INFO @ Fri, 05 Jul 2019 09:15:37: #2 alternative fragment length(s) may be 4,138 bps INFO @ Fri, 05 Jul 2019 09:15:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.05_model.r INFO @ Fri, 05 Jul 2019 09:15:37: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:15:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:15:43: 35000000 INFO @ Fri, 05 Jul 2019 09:15:43: 34000000 INFO @ Fri, 05 Jul 2019 09:15:52: 36000000 INFO @ Fri, 05 Jul 2019 09:15:53: 35000000 INFO @ Fri, 05 Jul 2019 09:16:01: 37000000 INFO @ Fri, 05 Jul 2019 09:16:02: 36000000 INFO @ Fri, 05 Jul 2019 09:16:06: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 09:16:06: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 09:16:06: #1 total tags in treatment: 37474268 INFO @ Fri, 05 Jul 2019 09:16:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:16:06: #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 09:16:07: #1 tags after filtering in treatment: 37474095 INFO @ Fri, 05 Jul 2019 09:16:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:16:07: #1 finished! INFO @ Fri, 05 Jul 2019 09:16:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:16:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:16:12: 37000000 INFO @ Fri, 05 Jul 2019 09:16:15: #2 number of paired peaks: 69550 INFO @ Fri, 05 Jul 2019 09:16:15: start model_add_line... INFO @ Fri, 05 Jul 2019 09:16:16: start X-correlation... INFO @ Fri, 05 Jul 2019 09:16:16: end of X-cor INFO @ Fri, 05 Jul 2019 09:16:16: #2 finished! INFO @ Fri, 05 Jul 2019 09:16:16: #2 predicted fragment length is 138 bps INFO @ Fri, 05 Jul 2019 09:16:16: #2 alternative fragment length(s) may be 4,138 bps INFO @ Fri, 05 Jul 2019 09:16:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.20_model.r INFO @ Fri, 05 Jul 2019 09:16:16: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:16:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:16:16: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 09:16:16: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 09:16:16: #1 total tags in treatment: 37474268 INFO @ Fri, 05 Jul 2019 09:16:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:16:16: #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 09:16:17: #1 tags after filtering in treatment: 37474095 INFO @ Fri, 05 Jul 2019 09:16:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:16:17: #1 finished! INFO @ Fri, 05 Jul 2019 09:16:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:16:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:16:26: #2 number of paired peaks: 69550 INFO @ Fri, 05 Jul 2019 09:16:26: start model_add_line... INFO @ Fri, 05 Jul 2019 09:16:27: start X-correlation... INFO @ Fri, 05 Jul 2019 09:16:27: end of X-cor INFO @ Fri, 05 Jul 2019 09:16:27: #2 finished! INFO @ Fri, 05 Jul 2019 09:16:27: #2 predicted fragment length is 138 bps INFO @ Fri, 05 Jul 2019 09:16:27: #2 alternative fragment length(s) may be 4,138 bps INFO @ Fri, 05 Jul 2019 09:16:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.10_model.r INFO @ Fri, 05 Jul 2019 09:16:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:16:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:17:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:18:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:18:15: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:18:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.05_peaks.xls INFO @ Fri, 05 Jul 2019 09:18:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:18:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.05_summits.bed INFO @ Fri, 05 Jul 2019 09:18:24: Done! pass1 - making usageList (166 chroms): 13 millis pass2 - checking and writing primary data (58530 records, 4 fields): 81 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:19:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.20_peaks.xls INFO @ Fri, 05 Jul 2019 09:19:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:19:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.20_summits.bed INFO @ Fri, 05 Jul 2019 09:19:09: Done! pass1 - making usageList (123 chroms): 8 millis pass2 - checking and writing primary data (36024 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:19:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.10_peaks.xls INFO @ Fri, 05 Jul 2019 09:19:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:19:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101959/ERX101959.10_summits.bed INFO @ Fri, 05 Jul 2019 09:19:14: Done! pass1 - making usageList (151 chroms): 9 millis pass2 - checking and writing primary data (47549 records, 4 fields): 65 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。