Job ID = 3785871 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-11-01T05:34:19 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 ) 2019-11-01T05:36:40 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 ) 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 ) 2019-11-01T05:37:47 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 ) 2019-11-01T05:39:18 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 ) 2019-11-01T05:39:18 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 ) 2019-11-01T05:39:36 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 ) 2019-11-01T05:39:51 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 ) 2019-11-01T05:39:56 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 ) 2019-11-01T05:40:10 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 ) 2019-11-01T05:42:44 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 ) 2019-11-01T05:43:10 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 ) 2019-11-01T05:44:12 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 ) 2019-11-01T05:44:58 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 ) 2019-11-01T05:46:13 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 ) spots read : 8,759,023 reads read : 17,518,046 reads written : 8,759,023 reads 0-length : 8,759,023 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: 00:01:31 8759023 reads; of these: 8759023 (100.00%) were unpaired; of these: 8616487 (98.37%) aligned 0 times 37039 (0.42%) aligned exactly 1 time 105497 (1.20%) aligned >1 times 1.63% overall alignment rate Time searching: 00:01:31 Overall time: 00:01:31 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] 87453 / 142536 = 0.6136 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 01 Nov 2019 14:50:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.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 14:50:05: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:50:05: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:50:06: #1 tag size is determined as 76 bps INFO @ Fri, 01 Nov 2019 14:50:06: #1 tag size = 76 INFO @ Fri, 01 Nov 2019 14:50:06: #1 total tags in treatment: 55083 INFO @ Fri, 01 Nov 2019 14:50:06: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:50:06: #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 14:50:06: #1 tags after filtering in treatment: 55083 INFO @ Fri, 01 Nov 2019 14:50:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:50:06: #1 finished! INFO @ Fri, 01 Nov 2019 14:50:06: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:50:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:50:06: #2 number of paired peaks: 2140 INFO @ Fri, 01 Nov 2019 14:50:06: start model_add_line... INFO @ Fri, 01 Nov 2019 14:50:06: start X-correlation... INFO @ Fri, 01 Nov 2019 14:50:06: end of X-cor INFO @ Fri, 01 Nov 2019 14:50:06: #2 finished! INFO @ Fri, 01 Nov 2019 14:50:06: #2 predicted fragment length is 295 bps INFO @ Fri, 01 Nov 2019 14:50:06: #2 alternative fragment length(s) may be 77,266,295 bps INFO @ Fri, 01 Nov 2019 14:50:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.05_model.r INFO @ Fri, 01 Nov 2019 14:50:06: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:50:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:50:06: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:50:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.05_peaks.xls INFO @ Fri, 01 Nov 2019 14:50:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.05_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:50:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.05_summits.bed INFO @ Fri, 01 Nov 2019 14:50:06: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (67 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 01 Nov 2019 14:50:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.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 14:50:35: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:50:35: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:50:36: #1 tag size is determined as 76 bps INFO @ Fri, 01 Nov 2019 14:50:36: #1 tag size = 76 INFO @ Fri, 01 Nov 2019 14:50:36: #1 total tags in treatment: 55083 INFO @ Fri, 01 Nov 2019 14:50:36: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:50:36: #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 14:50:36: #1 tags after filtering in treatment: 55083 INFO @ Fri, 01 Nov 2019 14:50:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:50:36: #1 finished! INFO @ Fri, 01 Nov 2019 14:50:36: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:50:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:50:36: #2 number of paired peaks: 2140 INFO @ Fri, 01 Nov 2019 14:50:36: start model_add_line... INFO @ Fri, 01 Nov 2019 14:50:36: start X-correlation... INFO @ Fri, 01 Nov 2019 14:50:36: end of X-cor INFO @ Fri, 01 Nov 2019 14:50:36: #2 finished! INFO @ Fri, 01 Nov 2019 14:50:36: #2 predicted fragment length is 295 bps INFO @ Fri, 01 Nov 2019 14:50:36: #2 alternative fragment length(s) may be 77,266,295 bps INFO @ Fri, 01 Nov 2019 14:50:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.10_model.r INFO @ Fri, 01 Nov 2019 14:50:36: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:50:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:50:36: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:50:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.10_peaks.xls INFO @ Fri, 01 Nov 2019 14:50:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.10_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:50:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.10_summits.bed INFO @ Fri, 01 Nov 2019 14:50:36: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (38 records, 4 fields): 4 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 14:51:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.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 14:51:05: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:51:05: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:51:06: #1 tag size is determined as 76 bps INFO @ Fri, 01 Nov 2019 14:51:06: #1 tag size = 76 INFO @ Fri, 01 Nov 2019 14:51:06: #1 total tags in treatment: 55083 INFO @ Fri, 01 Nov 2019 14:51:06: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:51:06: #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 14:51:06: #1 tags after filtering in treatment: 55083 INFO @ Fri, 01 Nov 2019 14:51:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:51:06: #1 finished! INFO @ Fri, 01 Nov 2019 14:51:06: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:51:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:51:06: #2 number of paired peaks: 2140 INFO @ Fri, 01 Nov 2019 14:51:06: start model_add_line... INFO @ Fri, 01 Nov 2019 14:51:06: start X-correlation... INFO @ Fri, 01 Nov 2019 14:51:06: end of X-cor INFO @ Fri, 01 Nov 2019 14:51:06: #2 finished! INFO @ Fri, 01 Nov 2019 14:51:06: #2 predicted fragment length is 295 bps INFO @ Fri, 01 Nov 2019 14:51:06: #2 alternative fragment length(s) may be 77,266,295 bps INFO @ Fri, 01 Nov 2019 14:51:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.20_model.r INFO @ Fri, 01 Nov 2019 14:51:06: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:51:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:51:06: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:51:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.20_peaks.xls INFO @ Fri, 01 Nov 2019 14:51:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.20_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:51:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5426112/SRX5426112.20_summits.bed INFO @ Fri, 01 Nov 2019 14:51:06: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (18 records, 4 fields): 2 millis CompletedMACS2peakCalling