Job ID = 3785907 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-11-01T05:37:12 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 ) 2019-11-01T05:37:12 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 ) 2019-11-01T05:37:12 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 ) 2019-11-01T05:37:13 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 ) 2019-11-01T05:37:13 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 ) 2019-11-01T05:38:22 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 ) 2019-11-01T05:38:29 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 ) 2019-11-01T05:39:29 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 ) 2019-11-01T05:39:47 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 ) 2019-11-01T05:39:47 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 ) 2019-11-01T05:39:52 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 ) 2019-11-01T05:40:42 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 ) 2019-11-01T05:41:17 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 ) 2019-11-01T05:41:28 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 ) 2019-11-01T05:43:21 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 ) 2019-11-01T05:43:32 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 ) 2019-11-01T05:43:39 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 ) 2019-11-01T05:43:43 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 ) 2019-11-01T05:45:15 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 ) 2019-11-01T05:45:33 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 ) 2019-11-01T05:45:33 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 ) 2019-11-01T05:46:37 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 ) 2019-11-01T05:47:13 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 ) 2019-11-01T05:47:13 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 ) 2019-11-01T05:48:27 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 ) 2019-11-01T05:48:30 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 ) 2019-11-01T05:48:43 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 ) 2019-11-01T05:48:43 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 ) 2019-11-01T05:49:46 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 ) 2019-11-01T05:49:57 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 ) 2019-11-01T05:50:01 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 ) 2019-11-01T05:50:01 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 ) 2019-11-01T05:50:45 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 ) 2019-11-01T05:50:45 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 ) 2019-11-01T05:53:28 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 ) 2019-11-01T05:54:38 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 ) 2019-11-01T05:54:43 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 ) 2019-11-01T05:55:13 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 ) 2019-11-01T05:55:22 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 ) 2019-11-01T05:55:37 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 ) 2019-11-01T05:57:08 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 ) 2019-11-01T05:57:44 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 ) 2019-11-01T05:57:49 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 ) 2019-11-01T05:59:02 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 ) 2019-11-01T05:59:02 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 ) 2019-11-01T05:59:09 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 ) 2019-11-01T06:00:39 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 ) 2019-11-01T06:01:27 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 ) 2019-11-01T06:02:40 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 : 58,380,101 reads read : 116,760,202 reads written : 58,380,101 reads 0-length : 58,380,101 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: 00:07:34 58380101 reads; of these: 58380101 (100.00%) were unpaired; of these: 55117777 (94.41%) aligned 0 times 2190385 (3.75%) aligned exactly 1 time 1071939 (1.84%) aligned >1 times 5.59% overall alignment rate Time searching: 00:07:34 Overall time: 00:07:34 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] 267957 / 3262324 = 0.0821 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 01 Nov 2019 15:21:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.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 15:21:14: #1 read tag files... INFO @ Fri, 01 Nov 2019 15:21:14: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 15:21:21: 1000000 INFO @ Fri, 01 Nov 2019 15:21:28: 2000000 INFO @ Fri, 01 Nov 2019 15:21:35: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 15:21:35: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 15:21:35: #1 total tags in treatment: 2994367 INFO @ Fri, 01 Nov 2019 15:21:35: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 15:21:35: #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 15:21:35: #1 tags after filtering in treatment: 2994367 INFO @ Fri, 01 Nov 2019 15:21:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 15:21:35: #1 finished! INFO @ Fri, 01 Nov 2019 15:21:35: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 15:21:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 15:21:36: #2 number of paired peaks: 5654 INFO @ Fri, 01 Nov 2019 15:21:36: start model_add_line... INFO @ Fri, 01 Nov 2019 15:21:36: start X-correlation... INFO @ Fri, 01 Nov 2019 15:21:36: end of X-cor INFO @ Fri, 01 Nov 2019 15:21:36: #2 finished! INFO @ Fri, 01 Nov 2019 15:21:36: #2 predicted fragment length is 163 bps INFO @ Fri, 01 Nov 2019 15:21:36: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 01 Nov 2019 15:21:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.05_model.r INFO @ Fri, 01 Nov 2019 15:21:36: #3 Call peaks... INFO @ Fri, 01 Nov 2019 15:21:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 15:21:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.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 15:21:43: #1 read tag files... INFO @ Fri, 01 Nov 2019 15:21:43: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 15:21:46: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 15:21:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.05_peaks.xls INFO @ Fri, 01 Nov 2019 15:21:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.05_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 15:21:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.05_summits.bed INFO @ Fri, 01 Nov 2019 15:21:50: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3390 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 01 Nov 2019 15:21:51: 1000000 INFO @ Fri, 01 Nov 2019 15:21:59: 2000000 INFO @ Fri, 01 Nov 2019 15:22:07: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 15:22:07: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 15:22:07: #1 total tags in treatment: 2994367 INFO @ Fri, 01 Nov 2019 15:22:07: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 15:22:07: #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 15:22:07: #1 tags after filtering in treatment: 2994367 INFO @ Fri, 01 Nov 2019 15:22:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 15:22:07: #1 finished! INFO @ Fri, 01 Nov 2019 15:22:07: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 15:22:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 15:22:08: #2 number of paired peaks: 5654 INFO @ Fri, 01 Nov 2019 15:22:08: start model_add_line... INFO @ Fri, 01 Nov 2019 15:22:08: start X-correlation... INFO @ Fri, 01 Nov 2019 15:22:08: end of X-cor INFO @ Fri, 01 Nov 2019 15:22:08: #2 finished! INFO @ Fri, 01 Nov 2019 15:22:08: #2 predicted fragment length is 163 bps INFO @ Fri, 01 Nov 2019 15:22:08: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 01 Nov 2019 15:22:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.10_model.r INFO @ Fri, 01 Nov 2019 15:22:08: #3 Call peaks... INFO @ Fri, 01 Nov 2019 15:22:08: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... INFO @ Fri, 01 Nov 2019 15:22:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.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 15:22:13: #1 read tag files... INFO @ Fri, 01 Nov 2019 15:22:13: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 15:22:18: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 15:22:20: 1000000 INFO @ Fri, 01 Nov 2019 15:22:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.10_peaks.xls INFO @ Fri, 01 Nov 2019 15:22:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.10_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 15:22:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.10_summits.bed INFO @ Fri, 01 Nov 2019 15:22:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1256 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 01 Nov 2019 15:22:27: 2000000 INFO @ Fri, 01 Nov 2019 15:22:35: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 15:22:35: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 15:22:35: #1 total tags in treatment: 2994367 INFO @ Fri, 01 Nov 2019 15:22:35: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 15:22:35: #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 15:22:35: #1 tags after filtering in treatment: 2994367 INFO @ Fri, 01 Nov 2019 15:22:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 15:22:35: #1 finished! INFO @ Fri, 01 Nov 2019 15:22:35: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 15:22:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 15:22:35: #2 number of paired peaks: 5654 INFO @ Fri, 01 Nov 2019 15:22:35: start model_add_line... INFO @ Fri, 01 Nov 2019 15:22:35: start X-correlation... INFO @ Fri, 01 Nov 2019 15:22:35: end of X-cor INFO @ Fri, 01 Nov 2019 15:22:35: #2 finished! INFO @ Fri, 01 Nov 2019 15:22:35: #2 predicted fragment length is 163 bps INFO @ Fri, 01 Nov 2019 15:22:35: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 01 Nov 2019 15:22:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.20_model.r INFO @ Fri, 01 Nov 2019 15:22:35: #3 Call peaks... INFO @ Fri, 01 Nov 2019 15:22:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 15:22:45: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 15:22:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.20_peaks.xls INFO @ Fri, 01 Nov 2019 15:22:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.20_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 15:22:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5850001/SRX5850001.20_summits.bed INFO @ Fri, 01 Nov 2019 15:22:49: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (316 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。