Job ID = 2640466 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T08:02:46 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 ) 2019-08-24T08:06:25 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 ) 2019-08-24T08:06:25 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 ) 2019-08-24T08:06:25 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 ) 2019-08-24T08:07:03 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 ) 2019-08-24T08:07:03 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.24' from '172.19.7.14' 2019-08-24T08:07:03 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' (130.14.250.24) from '172.19.7.14' 2019-08-24T08:07:44 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 ) 2019-08-24T08:07:44 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 ) 2019-08-24T08:07:51 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 ) 2019-08-24T08:08:07 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 ) 2019-08-24T08:08:51 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 ) 2019-08-24T08:08:51 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 ) 2019-08-24T08:09:39 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 ) 2019-08-24T08:10:04 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 ) 2019-08-24T08:10:32 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 ) 2019-08-24T08:12:18 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 ) 2019-08-24T08:13:38 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 ) 2019-08-24T08:14:40 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 ) spots read : 24,664,363 reads read : 49,328,726 reads written : 24,664,363 reads 0-length : 24,664,363 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: 00:00:00 Multiseed full-index search: 00:19:01 24664363 reads; of these: 24664363 (100.00%) were unpaired; of these: 1158561 (4.70%) aligned 0 times 17389544 (70.50%) aligned exactly 1 time 6116258 (24.80%) aligned >1 times 95.30% overall alignment rate Time searching: 00:19:03 Overall time: 00:19:03 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] 1655298 / 23505802 = 0.0704 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:43:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.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 17:43:12: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:43:12: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:43:19: 1000000 INFO @ Sat, 24 Aug 2019 17:43:26: 2000000 INFO @ Sat, 24 Aug 2019 17:43:33: 3000000 INFO @ Sat, 24 Aug 2019 17:43:40: 4000000 INFO @ Sat, 24 Aug 2019 17:43:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.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 17:43:42: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:43:42: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:43:47: 5000000 INFO @ Sat, 24 Aug 2019 17:43:51: 1000000 INFO @ Sat, 24 Aug 2019 17:43:55: 6000000 INFO @ Sat, 24 Aug 2019 17:44:01: 2000000 INFO @ Sat, 24 Aug 2019 17:44:02: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:44:09: 8000000 INFO @ Sat, 24 Aug 2019 17:44:10: 3000000 INFO @ Sat, 24 Aug 2019 17:44:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.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 17:44:12: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:44:12: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:44:17: 9000000 INFO @ Sat, 24 Aug 2019 17:44:19: 4000000 INFO @ Sat, 24 Aug 2019 17:44:20: 1000000 INFO @ Sat, 24 Aug 2019 17:44:24: 10000000 INFO @ Sat, 24 Aug 2019 17:44:28: 2000000 INFO @ Sat, 24 Aug 2019 17:44:29: 5000000 INFO @ Sat, 24 Aug 2019 17:44:31: 11000000 INFO @ Sat, 24 Aug 2019 17:44:37: 3000000 INFO @ Sat, 24 Aug 2019 17:44:38: 6000000 INFO @ Sat, 24 Aug 2019 17:44:39: 12000000 INFO @ Sat, 24 Aug 2019 17:44:45: 4000000 INFO @ Sat, 24 Aug 2019 17:44:46: 13000000 INFO @ Sat, 24 Aug 2019 17:44:48: 7000000 INFO @ Sat, 24 Aug 2019 17:44:53: 5000000 INFO @ Sat, 24 Aug 2019 17:44:53: 14000000 INFO @ Sat, 24 Aug 2019 17:44:57: 8000000 INFO @ Sat, 24 Aug 2019 17:45:01: 15000000 INFO @ Sat, 24 Aug 2019 17:45:01: 6000000 INFO @ Sat, 24 Aug 2019 17:45:07: 9000000 INFO @ Sat, 24 Aug 2019 17:45:08: 16000000 INFO @ Sat, 24 Aug 2019 17:45:09: 7000000 INFO @ Sat, 24 Aug 2019 17:45:15: 17000000 INFO @ Sat, 24 Aug 2019 17:45:16: 10000000 INFO @ Sat, 24 Aug 2019 17:45:18: 8000000 INFO @ Sat, 24 Aug 2019 17:45:23: 18000000 INFO @ Sat, 24 Aug 2019 17:45:25: 11000000 INFO @ Sat, 24 Aug 2019 17:45:26: 9000000 INFO @ Sat, 24 Aug 2019 17:45:30: 19000000 INFO @ Sat, 24 Aug 2019 17:45:34: 10000000 INFO @ Sat, 24 Aug 2019 17:45:34: 12000000 INFO @ Sat, 24 Aug 2019 17:45:37: 20000000 INFO @ Sat, 24 Aug 2019 17:45:42: 11000000 INFO @ Sat, 24 Aug 2019 17:45:44: 13000000 INFO @ Sat, 24 Aug 2019 17:45:45: 21000000 INFO @ Sat, 24 Aug 2019 17:45:50: 12000000 INFO @ Sat, 24 Aug 2019 17:45:51: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:45:51: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:45:51: #1 total tags in treatment: 21850504 INFO @ Sat, 24 Aug 2019 17:45:51: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:45:51: #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 17:45:52: #1 tags after filtering in treatment: 21850374 INFO @ Sat, 24 Aug 2019 17:45:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:45:52: #1 finished! INFO @ Sat, 24 Aug 2019 17:45:52: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:45:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:45:53: 14000000 INFO @ Sat, 24 Aug 2019 17:45:55: #2 number of paired peaks: 13228 INFO @ Sat, 24 Aug 2019 17:45:55: start model_add_line... INFO @ Sat, 24 Aug 2019 17:45:55: start X-correlation... INFO @ Sat, 24 Aug 2019 17:45:55: end of X-cor INFO @ Sat, 24 Aug 2019 17:45:55: #2 finished! INFO @ Sat, 24 Aug 2019 17:45:55: #2 predicted fragment length is 135 bps INFO @ Sat, 24 Aug 2019 17:45:55: #2 alternative fragment length(s) may be 135 bps INFO @ Sat, 24 Aug 2019 17:45:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.05_model.r INFO @ Sat, 24 Aug 2019 17:45:55: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:45:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:45:58: 13000000 INFO @ Sat, 24 Aug 2019 17:46:02: 15000000 INFO @ Sat, 24 Aug 2019 17:46:07: 14000000 INFO @ Sat, 24 Aug 2019 17:46:11: 16000000 INFO @ Sat, 24 Aug 2019 17:46:15: 15000000 INFO @ Sat, 24 Aug 2019 17:46:21: 17000000 INFO @ Sat, 24 Aug 2019 17:46:23: 16000000 INFO @ Sat, 24 Aug 2019 17:46:30: 18000000 INFO @ Sat, 24 Aug 2019 17:46:31: 17000000 INFO @ Sat, 24 Aug 2019 17:46:39: 18000000 INFO @ Sat, 24 Aug 2019 17:46:39: 19000000 INFO @ Sat, 24 Aug 2019 17:46:47: 19000000 INFO @ Sat, 24 Aug 2019 17:46:49: 20000000 INFO @ Sat, 24 Aug 2019 17:46:55: 20000000 INFO @ Sat, 24 Aug 2019 17:46:58: 21000000 INFO @ Sat, 24 Aug 2019 17:47:04: 21000000 INFO @ Sat, 24 Aug 2019 17:47:04: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:47:06: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:47:06: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:47:06: #1 total tags in treatment: 21850504 INFO @ Sat, 24 Aug 2019 17:47:06: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:47:06: #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 17:47:07: #1 tags after filtering in treatment: 21850374 INFO @ Sat, 24 Aug 2019 17:47:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:47:07: #1 finished! INFO @ Sat, 24 Aug 2019 17:47:07: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:47:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:47:10: #2 number of paired peaks: 13228 INFO @ Sat, 24 Aug 2019 17:47:10: start model_add_line... INFO @ Sat, 24 Aug 2019 17:47:10: start X-correlation... INFO @ Sat, 24 Aug 2019 17:47:10: end of X-cor INFO @ Sat, 24 Aug 2019 17:47:10: #2 finished! INFO @ Sat, 24 Aug 2019 17:47:10: #2 predicted fragment length is 135 bps INFO @ Sat, 24 Aug 2019 17:47:10: #2 alternative fragment length(s) may be 135 bps INFO @ Sat, 24 Aug 2019 17:47:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.10_model.r INFO @ Sat, 24 Aug 2019 17:47:10: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:47:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:47:11: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:47:11: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:47:11: #1 total tags in treatment: 21850504 INFO @ Sat, 24 Aug 2019 17:47:11: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:47:11: #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 17:47:11: #1 tags after filtering in treatment: 21850374 INFO @ Sat, 24 Aug 2019 17:47:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:47:11: #1 finished! INFO @ Sat, 24 Aug 2019 17:47:11: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:47:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:47:14: #2 number of paired peaks: 13228 INFO @ Sat, 24 Aug 2019 17:47:14: start model_add_line... INFO @ Sat, 24 Aug 2019 17:47:14: start X-correlation... INFO @ Sat, 24 Aug 2019 17:47:14: end of X-cor INFO @ Sat, 24 Aug 2019 17:47:14: #2 finished! INFO @ Sat, 24 Aug 2019 17:47:14: #2 predicted fragment length is 135 bps INFO @ Sat, 24 Aug 2019 17:47:14: #2 alternative fragment length(s) may be 135 bps INFO @ Sat, 24 Aug 2019 17:47:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.20_model.r INFO @ Sat, 24 Aug 2019 17:47:14: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:47:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:47:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:47:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:47:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.05_summits.bed INFO @ Sat, 24 Aug 2019 17:47:40: Done! pass1 - making usageList (65 chroms): 4 millis pass2 - checking and writing primary data (6881 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:48:19: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:48:23: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:48:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:48:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:48:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.10_summits.bed INFO @ Sat, 24 Aug 2019 17:48:55: Done! pass1 - making usageList (57 chroms): 2 millis pass2 - checking and writing primary data (4059 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:48:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:48:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:48:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374984/SRX5374984.20_summits.bed INFO @ Sat, 24 Aug 2019 17:48:59: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (2132 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。