Job ID = 3785917 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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 ) 2019-11-01T05:38:29 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 ) 2019-11-01T05:38:29 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 ) 2019-11-01T05:39:49 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 ) 2019-11-01T05:39:49 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 ) 2019-11-01T05:39:49 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 ) 2019-11-01T05:40:06 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 ) 2019-11-01T05:40:06 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 ) 2019-11-01T05:41:16 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 ) 2019-11-01T05:41:16 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.25' from '172.19.7.70' 2019-11-01T05:41:16 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' (130.14.250.25) from '172.19.7.70' 2019-11-01T05:41:53 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 ) 2019-11-01T05:42:44 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 ) 2019-11-01T05:46:08 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 ) 2019-11-01T05:48:43 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 ) spots read : 8,971,171 reads read : 17,942,342 reads written : 8,971,171 reads 0-length : 8,971,171 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: 00:01:34 8971171 reads; of these: 8971171 (100.00%) were unpaired; of these: 8850624 (98.66%) aligned 0 times 59304 (0.66%) aligned exactly 1 time 61243 (0.68%) aligned >1 times 1.34% overall alignment rate Time searching: 00:01:35 Overall time: 00:01:35 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] 7306 / 120547 = 0.0606 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 01 Nov 2019 14:51:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.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 14:51:14: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:51:14: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:51:15: #1 tag size is determined as 76 bps INFO @ Fri, 01 Nov 2019 14:51:15: #1 tag size = 76 INFO @ Fri, 01 Nov 2019 14:51:15: #1 total tags in treatment: 113241 INFO @ Fri, 01 Nov 2019 14:51:15: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:51:15: #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 14:51:15: #1 tags after filtering in treatment: 113239 INFO @ Fri, 01 Nov 2019 14:51:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:51:15: #1 finished! INFO @ Fri, 01 Nov 2019 14:51:15: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:51:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:51:16: #2 number of paired peaks: 5475 INFO @ Fri, 01 Nov 2019 14:51:16: start model_add_line... INFO @ Fri, 01 Nov 2019 14:51:16: start X-correlation... INFO @ Fri, 01 Nov 2019 14:51:16: end of X-cor INFO @ Fri, 01 Nov 2019 14:51:16: #2 finished! INFO @ Fri, 01 Nov 2019 14:51:16: #2 predicted fragment length is 298 bps INFO @ Fri, 01 Nov 2019 14:51:16: #2 alternative fragment length(s) may be 77,278,298 bps INFO @ Fri, 01 Nov 2019 14:51:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.05_model.r INFO @ Fri, 01 Nov 2019 14:51:16: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:51:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:51:16: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:51:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.05_peaks.xls INFO @ Fri, 01 Nov 2019 14:51:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.05_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:51:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.05_summits.bed INFO @ Fri, 01 Nov 2019 14:51:16: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (103 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 01 Nov 2019 14:51:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.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 14:51:43: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:51:43: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:51:44: #1 tag size is determined as 76 bps INFO @ Fri, 01 Nov 2019 14:51:44: #1 tag size = 76 INFO @ Fri, 01 Nov 2019 14:51:44: #1 total tags in treatment: 113241 INFO @ Fri, 01 Nov 2019 14:51:44: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:51:44: #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 14:51:44: #1 tags after filtering in treatment: 113239 INFO @ Fri, 01 Nov 2019 14:51:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:51:44: #1 finished! INFO @ Fri, 01 Nov 2019 14:51:44: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:51:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:51:45: #2 number of paired peaks: 5475 INFO @ Fri, 01 Nov 2019 14:51:45: start model_add_line... INFO @ Fri, 01 Nov 2019 14:51:45: start X-correlation... INFO @ Fri, 01 Nov 2019 14:51:45: end of X-cor INFO @ Fri, 01 Nov 2019 14:51:45: #2 finished! INFO @ Fri, 01 Nov 2019 14:51:45: #2 predicted fragment length is 298 bps INFO @ Fri, 01 Nov 2019 14:51:45: #2 alternative fragment length(s) may be 77,278,298 bps INFO @ Fri, 01 Nov 2019 14:51:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.10_model.r INFO @ Fri, 01 Nov 2019 14:51:45: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:51:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:51:45: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:51:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.10_peaks.xls INFO @ Fri, 01 Nov 2019 14:51:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.10_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:51:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.10_summits.bed INFO @ Fri, 01 Nov 2019 14:51:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (63 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 01 Nov 2019 14:52:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.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 14:52:13: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:52:13: #1 read treatment tags... BigWig に変換しました。 INFO @ Fri, 01 Nov 2019 14:52:14: #1 tag size is determined as 76 bps INFO @ Fri, 01 Nov 2019 14:52:14: #1 tag size = 76 INFO @ Fri, 01 Nov 2019 14:52:14: #1 total tags in treatment: 113241 INFO @ Fri, 01 Nov 2019 14:52:14: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:52:14: #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 14:52:14: #1 tags after filtering in treatment: 113239 INFO @ Fri, 01 Nov 2019 14:52:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:52:14: #1 finished! INFO @ Fri, 01 Nov 2019 14:52:14: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:52:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:52:15: #2 number of paired peaks: 5475 INFO @ Fri, 01 Nov 2019 14:52:15: start model_add_line... INFO @ Fri, 01 Nov 2019 14:52:15: start X-correlation... INFO @ Fri, 01 Nov 2019 14:52:15: end of X-cor INFO @ Fri, 01 Nov 2019 14:52:15: #2 finished! INFO @ Fri, 01 Nov 2019 14:52:15: #2 predicted fragment length is 298 bps INFO @ Fri, 01 Nov 2019 14:52:15: #2 alternative fragment length(s) may be 77,278,298 bps INFO @ Fri, 01 Nov 2019 14:52:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.20_model.r INFO @ Fri, 01 Nov 2019 14:52:15: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:52:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:52:15: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:52:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.20_peaks.xls INFO @ Fri, 01 Nov 2019 14:52:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.20_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:52:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6370201/SRX6370201.20_summits.bed INFO @ Fri, 01 Nov 2019 14:52:15: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (25 records, 4 fields): 2 millis CompletedMACS2peakCalling