Job ID = 1297579 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T08:00:54 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 ) 2019-06-03T08:00:54 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 ) 2019-06-03T08:00:54 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 ) 2019-06-03T08:00:54 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 ) spots read : 38,169,171 reads read : 76,338,342 reads written : 76,338,342 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: 00:09:44 38169171 reads; of these: 38169171 (100.00%) were paired; of these: 36420102 (95.42%) aligned concordantly 0 times 1424818 (3.73%) aligned concordantly exactly 1 time 324251 (0.85%) aligned concordantly >1 times ---- 36420102 pairs aligned concordantly 0 times; of these: 9722 (0.03%) aligned discordantly 1 time ---- 36410380 pairs aligned 0 times concordantly or discordantly; of these: 72820760 mates make up the pairs; of these: 71881240 (98.71%) aligned 0 times 456040 (0.63%) aligned exactly 1 time 483480 (0.66%) aligned >1 times 5.84% overall alignment rate Time searching: 00:09:44 Overall time: 00:09:44 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] 58201 / 1751972 = 0.0332 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 17:24:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.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 17:24:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:24:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:24:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.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 17:24:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:24:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:24:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.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 17:24:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:24:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:24:47: 1000000 INFO @ Mon, 03 Jun 2019 17:24:47: 1000000 INFO @ Mon, 03 Jun 2019 17:24:48: 1000000 INFO @ Mon, 03 Jun 2019 17:24:55: 2000000 INFO @ Mon, 03 Jun 2019 17:24:56: 2000000 INFO @ Mon, 03 Jun 2019 17:24:57: 2000000 INFO @ Mon, 03 Jun 2019 17:25:04: 3000000 INFO @ Mon, 03 Jun 2019 17:25:05: 3000000 INFO @ Mon, 03 Jun 2019 17:25:06: 3000000 INFO @ Mon, 03 Jun 2019 17:25:12: 4000000 INFO @ Mon, 03 Jun 2019 17:25:13: 4000000 INFO @ Mon, 03 Jun 2019 17:25:14: 4000000 INFO @ Mon, 03 Jun 2019 17:25:14: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 17:25:14: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 17:25:14: #1 total tags in treatment: 1690958 INFO @ Mon, 03 Jun 2019 17:25:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:25:14: #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 17:25:15: #1 tags after filtering in treatment: 1631143 INFO @ Mon, 03 Jun 2019 17:25:15: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 03 Jun 2019 17:25:15: #1 finished! INFO @ Mon, 03 Jun 2019 17:25:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:25:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:25:15: #2 number of paired peaks: 1407 INFO @ Mon, 03 Jun 2019 17:25:15: start model_add_line... INFO @ Mon, 03 Jun 2019 17:25:15: start X-correlation... INFO @ Mon, 03 Jun 2019 17:25:15: end of X-cor INFO @ Mon, 03 Jun 2019 17:25:15: #2 finished! INFO @ Mon, 03 Jun 2019 17:25:15: #2 predicted fragment length is 142 bps INFO @ Mon, 03 Jun 2019 17:25:15: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 03 Jun 2019 17:25:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.05_model.r INFO @ Mon, 03 Jun 2019 17:25:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:25:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:25:16: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 17:25:16: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 17:25:16: #1 total tags in treatment: 1690958 INFO @ Mon, 03 Jun 2019 17:25:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:25:16: #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 17:25:16: #1 tags after filtering in treatment: 1631143 INFO @ Mon, 03 Jun 2019 17:25:16: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 03 Jun 2019 17:25:16: #1 finished! INFO @ Mon, 03 Jun 2019 17:25:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:25:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:25:16: #2 number of paired peaks: 1407 INFO @ Mon, 03 Jun 2019 17:25:16: start model_add_line... INFO @ Mon, 03 Jun 2019 17:25:16: start X-correlation... INFO @ Mon, 03 Jun 2019 17:25:16: end of X-cor INFO @ Mon, 03 Jun 2019 17:25:16: #2 finished! INFO @ Mon, 03 Jun 2019 17:25:16: #2 predicted fragment length is 142 bps INFO @ Mon, 03 Jun 2019 17:25:16: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 03 Jun 2019 17:25:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.20_model.r INFO @ Mon, 03 Jun 2019 17:25:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:25:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:25:17: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 17:25:17: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 17:25:17: #1 total tags in treatment: 1690958 INFO @ Mon, 03 Jun 2019 17:25:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:25:17: #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 17:25:17: #1 tags after filtering in treatment: 1631143 INFO @ Mon, 03 Jun 2019 17:25:17: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 03 Jun 2019 17:25:17: #1 finished! INFO @ Mon, 03 Jun 2019 17:25:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:25:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:25:17: #2 number of paired peaks: 1407 INFO @ Mon, 03 Jun 2019 17:25:17: start model_add_line... INFO @ Mon, 03 Jun 2019 17:25:17: start X-correlation... INFO @ Mon, 03 Jun 2019 17:25:17: end of X-cor INFO @ Mon, 03 Jun 2019 17:25:17: #2 finished! INFO @ Mon, 03 Jun 2019 17:25:17: #2 predicted fragment length is 142 bps INFO @ Mon, 03 Jun 2019 17:25:17: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 03 Jun 2019 17:25:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.10_model.r INFO @ Mon, 03 Jun 2019 17:25:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:25:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:25:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:25:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:25:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.05_peaks.xls INFO @ Mon, 03 Jun 2019 17:25:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:25:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:25:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.05_summits.bed INFO @ Mon, 03 Jun 2019 17:25:23: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (427 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:25:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.20_peaks.xls INFO @ Mon, 03 Jun 2019 17:25:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:25:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.20_summits.bed INFO @ Mon, 03 Jun 2019 17:25:24: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (84 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:25:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.10_peaks.xls INFO @ Mon, 03 Jun 2019 17:25:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:25:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650860/SRX4650860.10_summits.bed INFO @ Mon, 03 Jun 2019 17:25:26: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (238 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。