Job ID = 1297792 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T08:01:49 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 ) 2019-06-03T08:01:49 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 ) 2019-06-03T08:01:49 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 ) 2019-06-03T08:01:49 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 ) 2019-06-03T08:07:55 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 ) 2019-06-03T08:11:19 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 ) 2019-06-03T08:11:19 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 ) 2019-06-03T08:11:20 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 ) 2019-06-03T08:14:03 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 ) 2019-06-03T08:14:03 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 : 38,694,012 reads read : 77,388,024 reads written : 77,388,024 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:09:09 38694012 reads; of these: 38694012 (100.00%) were paired; of these: 37143600 (95.99%) aligned concordantly 0 times 1216470 (3.14%) aligned concordantly exactly 1 time 333942 (0.86%) aligned concordantly >1 times ---- 37143600 pairs aligned concordantly 0 times; of these: 4278 (0.01%) aligned discordantly 1 time ---- 37139322 pairs aligned 0 times concordantly or discordantly; of these: 74278644 mates make up the pairs; of these: 73696849 (99.22%) aligned 0 times 212777 (0.29%) aligned exactly 1 time 369018 (0.50%) aligned >1 times 4.77% overall alignment rate Time searching: 00:09:09 Overall time: 00:09:09 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 65337 / 1551859 = 0.0421 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 03 Jun 2019 17:27:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.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 @ Mon, 03 Jun 2019 17:27:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:27:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:27:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.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 @ Mon, 03 Jun 2019 17:27:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:27:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:27:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.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 @ Mon, 03 Jun 2019 17:27:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:27:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:27:52: 1000000 INFO @ Mon, 03 Jun 2019 17:27:54: 1000000 INFO @ Mon, 03 Jun 2019 17:27:55: 1000000 INFO @ Mon, 03 Jun 2019 17:28:00: 2000000 INFO @ Mon, 03 Jun 2019 17:28:03: 2000000 INFO @ Mon, 03 Jun 2019 17:28:04: 2000000 INFO @ Mon, 03 Jun 2019 17:28:07: 3000000 INFO @ Mon, 03 Jun 2019 17:28:11: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:28:11: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:28:11: #1 total tags in treatment: 1485203 INFO @ Mon, 03 Jun 2019 17:28:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:28:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 17:28:11: #1 tags after filtering in treatment: 1438076 INFO @ Mon, 03 Jun 2019 17:28:11: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 17:28:11: #1 finished! INFO @ Mon, 03 Jun 2019 17:28:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:28:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:28:11: 3000000 INFO @ Mon, 03 Jun 2019 17:28:11: #2 number of paired peaks: 2235 INFO @ Mon, 03 Jun 2019 17:28:11: start model_add_line... INFO @ Mon, 03 Jun 2019 17:28:11: start X-correlation... INFO @ Mon, 03 Jun 2019 17:28:11: end of X-cor INFO @ Mon, 03 Jun 2019 17:28:11: #2 finished! INFO @ Mon, 03 Jun 2019 17:28:11: #2 predicted fragment length is 147 bps INFO @ Mon, 03 Jun 2019 17:28:11: #2 alternative fragment length(s) may be 147 bps INFO @ Mon, 03 Jun 2019 17:28:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.05_model.r INFO @ Mon, 03 Jun 2019 17:28:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:28:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:28:14: 3000000 INFO @ Mon, 03 Jun 2019 17:28:15: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:28:15: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:28:15: #1 total tags in treatment: 1485203 INFO @ Mon, 03 Jun 2019 17:28:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:28:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 17:28:16: #1 tags after filtering in treatment: 1438076 INFO @ Mon, 03 Jun 2019 17:28:16: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 17:28:16: #1 finished! INFO @ Mon, 03 Jun 2019 17:28:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:28:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:28:16: #2 number of paired peaks: 2235 INFO @ Mon, 03 Jun 2019 17:28:16: start model_add_line... INFO @ Mon, 03 Jun 2019 17:28:16: start X-correlation... INFO @ Mon, 03 Jun 2019 17:28:16: end of X-cor INFO @ Mon, 03 Jun 2019 17:28:16: #2 finished! INFO @ Mon, 03 Jun 2019 17:28:16: #2 predicted fragment length is 147 bps INFO @ Mon, 03 Jun 2019 17:28:16: #2 alternative fragment length(s) may be 147 bps INFO @ Mon, 03 Jun 2019 17:28:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.10_model.r INFO @ Mon, 03 Jun 2019 17:28:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:28:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:28:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:28:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.05_peaks.xls INFO @ Mon, 03 Jun 2019 17:28:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:28:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.05_summits.bed INFO @ Mon, 03 Jun 2019 17:28:18: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (286 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:28:19: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:28:19: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:28:19: #1 total tags in treatment: 1485203 INFO @ Mon, 03 Jun 2019 17:28:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:28:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 17:28:19: #1 tags after filtering in treatment: 1438076 INFO @ Mon, 03 Jun 2019 17:28:19: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 17:28:19: #1 finished! INFO @ Mon, 03 Jun 2019 17:28:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:28:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:28:19: #2 number of paired peaks: 2235 INFO @ Mon, 03 Jun 2019 17:28:19: start model_add_line... INFO @ Mon, 03 Jun 2019 17:28:19: start X-correlation... INFO @ Mon, 03 Jun 2019 17:28:19: end of X-cor INFO @ Mon, 03 Jun 2019 17:28:19: #2 finished! INFO @ Mon, 03 Jun 2019 17:28:19: #2 predicted fragment length is 147 bps INFO @ Mon, 03 Jun 2019 17:28:19: #2 alternative fragment length(s) may be 147 bps INFO @ Mon, 03 Jun 2019 17:28:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.20_model.r INFO @ Mon, 03 Jun 2019 17:28:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:28:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:28:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:28:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.10_peaks.xls INFO @ Mon, 03 Jun 2019 17:28:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:28:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.10_summits.bed INFO @ Mon, 03 Jun 2019 17:28:23: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (150 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:28:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:28:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.20_peaks.xls INFO @ Mon, 03 Jun 2019 17:28:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:28:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650868/SRX4650868.20_summits.bed INFO @ Mon, 03 Jun 2019 17:28:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (59 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。