Job ID = 3785833 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-11-01T05:33:24 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 ) 2019-11-01T05:34:10 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 ) 2019-11-01T05:34:10 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 ) 2019-11-01T05:34:10 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 ) 2019-11-01T05:34:10 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 ) 2019-11-01T05:35:38 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 ) 2019-11-01T05:35:38 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 ) 2019-11-01T05:36:13 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 ) 2019-11-01T05:36:13 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.26' from '172.19.7.17' 2019-11-01T05:36:13 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 '172.19.7.17' 2019-11-01T05:37:00 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 ) 2019-11-01T05:37:00 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 ) 2019-11-01T05:38:29 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 ) 2019-11-01T05:39:20 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 ) 2019-11-01T05:39:46 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 ) 2019-11-01T05:39:49 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 ) 2019-11-01T05:40:18 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 ) 2019-11-01T05:43:32 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 ) 2019-11-01T05:43:32 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 ) 2019-11-01T05:44:21 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 ) 2019-11-01T05:44:42 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 ) 2019-11-01T05:45:15 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 ) 2019-11-01T05:45:15 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 ) 2019-11-01T05:45:55 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 ) 2019-11-01T05:45:55 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 ) 2019-11-01T05:46:11 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 ) 2019-11-01T05:46:33 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 ) 2019-11-01T05:46:54 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 ) 2019-11-01T05:46:54 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 ) 2019-11-01T05:47:27 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 ) 2019-11-01T05:48:27 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 ) 2019-11-01T05:49:32 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 ) 2019-11-01T05:50:01 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 ) 2019-11-01T05:50:19 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 ) 2019-11-01T05:51:16 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 ) 2019-11-01T05:51:21 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 ) 2019-11-01T05:52:21 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 ) 2019-11-01T05:52:33 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 ) 2019-11-01T05:52:34 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 ) 2019-11-01T05:53:13 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 ) 2019-11-01T05:53:13 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 ) 2019-11-01T05:53:15 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 ) 2019-11-01T05:54:51 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 ) 2019-11-01T05:55:22 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 ) 2019-11-01T05:55:58 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 ) 2019-11-01T05:56:48 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 ) 2019-11-01T05:57:23 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 ) 2019-11-01T05:57:44 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 ) 2019-11-01T05:59:09 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 ) 2019-11-01T05:59:09 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 ) 2019-11-01T05:59:09 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 ) 2019-11-01T05:59:09 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 ) spots read : 66,332,057 reads read : 66,332,057 reads written : 66,332,057 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:27 66332057 reads; of these: 66332057 (100.00%) were unpaired; of these: 58213920 (87.76%) aligned 0 times 6692643 (10.09%) aligned exactly 1 time 1425494 (2.15%) aligned >1 times 12.24% overall alignment rate Time searching: 00:09:27 Overall time: 00:09:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 2460772 / 8118137 = 0.3031 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 01 Nov 2019 15:24:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 01 Nov 2019 15:24:06: #1 read tag files... INFO @ Fri, 01 Nov 2019 15:24:06: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 15:24:14: 1000000 INFO @ Fri, 01 Nov 2019 15:24:22: 2000000 INFO @ Fri, 01 Nov 2019 15:24:31: 3000000 INFO @ Fri, 01 Nov 2019 15:24:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 01 Nov 2019 15:24:33: #1 read tag files... INFO @ Fri, 01 Nov 2019 15:24:33: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 15:24:39: 4000000 INFO @ Fri, 01 Nov 2019 15:24:42: 1000000 INFO @ Fri, 01 Nov 2019 15:24:47: 5000000 INFO @ Fri, 01 Nov 2019 15:24:50: 2000000 INFO @ Fri, 01 Nov 2019 15:24:52: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 15:24:52: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 15:24:52: #1 total tags in treatment: 5657365 INFO @ Fri, 01 Nov 2019 15:24:52: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 15:24:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 01 Nov 2019 15:24:52: #1 tags after filtering in treatment: 5657365 INFO @ Fri, 01 Nov 2019 15:24:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 15:24:52: #1 finished! INFO @ Fri, 01 Nov 2019 15:24:52: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 15:24:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 15:24:53: #2 number of paired peaks: 4672 INFO @ Fri, 01 Nov 2019 15:24:53: start model_add_line... INFO @ Fri, 01 Nov 2019 15:24:53: start X-correlation... INFO @ Fri, 01 Nov 2019 15:24:53: end of X-cor INFO @ Fri, 01 Nov 2019 15:24:53: #2 finished! INFO @ Fri, 01 Nov 2019 15:24:53: #2 predicted fragment length is 129 bps INFO @ Fri, 01 Nov 2019 15:24:53: #2 alternative fragment length(s) may be 129,291,455 bps INFO @ Fri, 01 Nov 2019 15:24:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.05_model.r INFO @ Fri, 01 Nov 2019 15:24:53: #3 Call peaks... INFO @ Fri, 01 Nov 2019 15:24:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 15:24:58: 3000000 BedGraph に変換中... INFO @ Fri, 01 Nov 2019 15:25:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 01 Nov 2019 15:25:03: #1 read tag files... INFO @ Fri, 01 Nov 2019 15:25:03: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 15:25:06: 4000000 INFO @ Fri, 01 Nov 2019 15:25:11: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 15:25:12: 1000000 INFO @ Fri, 01 Nov 2019 15:25:14: 5000000 INFO @ Fri, 01 Nov 2019 15:25:19: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 15:25:19: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 15:25:19: #1 total tags in treatment: 5657365 INFO @ Fri, 01 Nov 2019 15:25:19: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 15:25:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 01 Nov 2019 15:25:19: #1 tags after filtering in treatment: 5657365 INFO @ Fri, 01 Nov 2019 15:25:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 15:25:19: #1 finished! INFO @ Fri, 01 Nov 2019 15:25:19: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 15:25:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 15:25:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.05_peaks.xls INFO @ Fri, 01 Nov 2019 15:25:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.05_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 15:25:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.05_summits.bed INFO @ Fri, 01 Nov 2019 15:25:20: Done! INFO @ Fri, 01 Nov 2019 15:25:20: 2000000 INFO @ Fri, 01 Nov 2019 15:25:20: #2 number of paired peaks: 4672 INFO @ Fri, 01 Nov 2019 15:25:20: start model_add_line... pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3339 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 01 Nov 2019 15:25:20: start X-correlation... INFO @ Fri, 01 Nov 2019 15:25:20: end of X-cor INFO @ Fri, 01 Nov 2019 15:25:20: #2 finished! INFO @ Fri, 01 Nov 2019 15:25:20: #2 predicted fragment length is 129 bps INFO @ Fri, 01 Nov 2019 15:25:20: #2 alternative fragment length(s) may be 129,291,455 bps INFO @ Fri, 01 Nov 2019 15:25:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.10_model.r INFO @ Fri, 01 Nov 2019 15:25:20: #3 Call peaks... INFO @ Fri, 01 Nov 2019 15:25:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 15:25:28: 3000000 INFO @ Fri, 01 Nov 2019 15:25:36: 4000000 INFO @ Fri, 01 Nov 2019 15:25:39: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 15:25:43: 5000000 INFO @ Fri, 01 Nov 2019 15:25:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.10_peaks.xls INFO @ Fri, 01 Nov 2019 15:25:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.10_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 15:25:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.10_summits.bed INFO @ Fri, 01 Nov 2019 15:25:48: Done! INFO @ Fri, 01 Nov 2019 15:25:48: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 15:25:48: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 15:25:48: #1 total tags in treatment: 5657365 INFO @ Fri, 01 Nov 2019 15:25:48: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 15:25:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (993 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 01 Nov 2019 15:25:48: #1 tags after filtering in treatment: 5657365 INFO @ Fri, 01 Nov 2019 15:25:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 15:25:48: #1 finished! INFO @ Fri, 01 Nov 2019 15:25:48: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 15:25:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 15:25:49: #2 number of paired peaks: 4672 INFO @ Fri, 01 Nov 2019 15:25:49: start model_add_line... INFO @ Fri, 01 Nov 2019 15:25:49: start X-correlation... INFO @ Fri, 01 Nov 2019 15:25:49: end of X-cor INFO @ Fri, 01 Nov 2019 15:25:49: #2 finished! INFO @ Fri, 01 Nov 2019 15:25:49: #2 predicted fragment length is 129 bps INFO @ Fri, 01 Nov 2019 15:25:49: #2 alternative fragment length(s) may be 129,291,455 bps INFO @ Fri, 01 Nov 2019 15:25:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.20_model.r INFO @ Fri, 01 Nov 2019 15:25:49: #3 Call peaks... INFO @ Fri, 01 Nov 2019 15:25:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 15:26:07: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 15:26:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.20_peaks.xls INFO @ Fri, 01 Nov 2019 15:26:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.20_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 15:26:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4579165/SRX4579165.20_summits.bed INFO @ Fri, 01 Nov 2019 15:26:16: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (303 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。