Job ID = 3785889 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-11-01T05:36:12 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 ) 2019-11-01T05:36:12 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 ) 2019-11-01T05:36:40 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 ) 2019-11-01T05:37:48 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 ) 2019-11-01T05:38:29 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 ) 2019-11-01T05:39:20 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 ) 2019-11-01T05:39:20 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 ) 2019-11-01T05:39:36 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: 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 ) 2019-11-01T05:40:18 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 ) 2019-11-01T05:43:32 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 ) 2019-11-01T05:44:05 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 ) 2019-11-01T05:44:44 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 ) 2019-11-01T05:44:44 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 ) 2019-11-01T05:44:44 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 ) 2019-11-01T05:45:15 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 ) 2019-11-01T05:46:33 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 ) 2019-11-01T05:46:37 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 ) 2019-11-01T05:46:37 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 ) 2019-11-01T05:46:54 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 ) 2019-11-01T05:47:08 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 ) 2019-11-01T05:47:15 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 ) 2019-11-01T05:47:30 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 ) 2019-11-01T05:48:30 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 ) 2019-11-01T05:48:41 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 ) 2019-11-01T05:50:19 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 ) 2019-11-01T05:50:35 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 ) 2019-11-01T05:50:46 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 ) 2019-11-01T05:51:10 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 ) 2019-11-01T05:51:10 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.27' from '172.19.7.64' 2019-11-01T05:51:10 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' (130.14.250.27) from '172.19.7.64' 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 ) 2019-11-01T05:53:11 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 ) 2019-11-01T05:54:18 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 ) 2019-11-01T05:56:00 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 ) 2019-11-01T06:01:27 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 ) spots read : 17,547,438 reads read : 35,094,876 reads written : 17,547,438 reads 0-length : 17,547,438 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:34 17547438 reads; of these: 17547438 (100.00%) were unpaired; of these: 17406293 (99.20%) aligned 0 times 11906 (0.07%) aligned exactly 1 time 129239 (0.74%) aligned >1 times 0.80% overall alignment rate Time searching: 00:02:35 Overall time: 00:02:35 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] 111264 / 141145 = 0.7883 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 01 Nov 2019 15:04:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.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 15:04:59: #1 read tag files... INFO @ Fri, 01 Nov 2019 15:04:59: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 15:04:59: #1 tag size is determined as 76 bps INFO @ Fri, 01 Nov 2019 15:04:59: #1 tag size = 76 INFO @ Fri, 01 Nov 2019 15:04:59: #1 total tags in treatment: 29881 INFO @ Fri, 01 Nov 2019 15:04:59: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 15:04:59: #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 15:04:59: #1 tags after filtering in treatment: 29878 INFO @ Fri, 01 Nov 2019 15:04:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 15:04:59: #1 finished! INFO @ Fri, 01 Nov 2019 15:04:59: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 15:04:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 15:04:59: #2 number of paired peaks: 622 WARNING @ Fri, 01 Nov 2019 15:04:59: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Fri, 01 Nov 2019 15:04:59: start model_add_line... INFO @ Fri, 01 Nov 2019 15:04:59: start X-correlation... INFO @ Fri, 01 Nov 2019 15:04:59: end of X-cor INFO @ Fri, 01 Nov 2019 15:04:59: #2 finished! INFO @ Fri, 01 Nov 2019 15:04:59: #2 predicted fragment length is 184 bps INFO @ Fri, 01 Nov 2019 15:04:59: #2 alternative fragment length(s) may be 69,96,125,184,257,268,296 bps INFO @ Fri, 01 Nov 2019 15:04:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.05_model.r INFO @ Fri, 01 Nov 2019 15:04:59: #3 Call peaks... INFO @ Fri, 01 Nov 2019 15:04:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 15:04:59: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 15:04:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.05_peaks.xls INFO @ Fri, 01 Nov 2019 15:04:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.05_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 15:04:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.05_summits.bed INFO @ Fri, 01 Nov 2019 15:04:59: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (162 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 01 Nov 2019 15:05:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.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 15:05:28: #1 read tag files... INFO @ Fri, 01 Nov 2019 15:05:28: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 15:05:28: #1 tag size is determined as 76 bps INFO @ Fri, 01 Nov 2019 15:05:28: #1 tag size = 76 INFO @ Fri, 01 Nov 2019 15:05:28: #1 total tags in treatment: 29881 INFO @ Fri, 01 Nov 2019 15:05:28: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 15:05:28: #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 15:05:28: #1 tags after filtering in treatment: 29878 INFO @ Fri, 01 Nov 2019 15:05:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 15:05:28: #1 finished! INFO @ Fri, 01 Nov 2019 15:05:28: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 15:05:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 15:05:28: #2 number of paired peaks: 622 WARNING @ Fri, 01 Nov 2019 15:05:28: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Fri, 01 Nov 2019 15:05:28: start model_add_line... INFO @ Fri, 01 Nov 2019 15:05:28: start X-correlation... INFO @ Fri, 01 Nov 2019 15:05:28: end of X-cor INFO @ Fri, 01 Nov 2019 15:05:28: #2 finished! INFO @ Fri, 01 Nov 2019 15:05:28: #2 predicted fragment length is 184 bps INFO @ Fri, 01 Nov 2019 15:05:28: #2 alternative fragment length(s) may be 69,96,125,184,257,268,296 bps INFO @ Fri, 01 Nov 2019 15:05:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.10_model.r INFO @ Fri, 01 Nov 2019 15:05:28: #3 Call peaks... INFO @ Fri, 01 Nov 2019 15:05:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 15:05:28: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 15:05:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.10_peaks.xls INFO @ Fri, 01 Nov 2019 15:05:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.10_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 15:05:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.10_summits.bed INFO @ Fri, 01 Nov 2019 15:05:28: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (77 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換中... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 01 Nov 2019 15:05:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.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 15:05:58: #1 read tag files... INFO @ Fri, 01 Nov 2019 15:05:58: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 15:05:58: #1 tag size is determined as 76 bps INFO @ Fri, 01 Nov 2019 15:05:58: #1 tag size = 76 INFO @ Fri, 01 Nov 2019 15:05:58: #1 total tags in treatment: 29881 INFO @ Fri, 01 Nov 2019 15:05:58: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 15:05:58: #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 15:05:58: #1 tags after filtering in treatment: 29878 INFO @ Fri, 01 Nov 2019 15:05:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 15:05:58: #1 finished! INFO @ Fri, 01 Nov 2019 15:05:58: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 15:05:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 15:05:58: #2 number of paired peaks: 622 WARNING @ Fri, 01 Nov 2019 15:05:58: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Fri, 01 Nov 2019 15:05:58: start model_add_line... INFO @ Fri, 01 Nov 2019 15:05:58: start X-correlation... INFO @ Fri, 01 Nov 2019 15:05:58: end of X-cor INFO @ Fri, 01 Nov 2019 15:05:58: #2 finished! INFO @ Fri, 01 Nov 2019 15:05:58: #2 predicted fragment length is 184 bps INFO @ Fri, 01 Nov 2019 15:05:58: #2 alternative fragment length(s) may be 69,96,125,184,257,268,296 bps INFO @ Fri, 01 Nov 2019 15:05:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.20_model.r INFO @ Fri, 01 Nov 2019 15:05:58: #3 Call peaks... INFO @ Fri, 01 Nov 2019 15:05:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 15:05:58: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 15:05:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.20_peaks.xls INFO @ Fri, 01 Nov 2019 15:05:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.20_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 15:05:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5426117/SRX5426117.20_summits.bed INFO @ Fri, 01 Nov 2019 15:05:58: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (32 records, 4 fields): 3 millis CompletedMACS2peakCalling