Job ID = 1307340 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T13:27:31 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 ) 2019-06-03T13:27:31 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 ) 2019-06-03T13:27:31 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 : 27,467,102 reads read : 54,934,204 reads written : 54,934,204 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: 00:09:25 27467102 reads; of these: 27467102 (100.00%) were paired; of these: 24081599 (87.67%) aligned concordantly 0 times 2634259 (9.59%) aligned concordantly exactly 1 time 751244 (2.74%) aligned concordantly >1 times ---- 24081599 pairs aligned concordantly 0 times; of these: 3402 (0.01%) aligned discordantly 1 time ---- 24078197 pairs aligned 0 times concordantly or discordantly; of these: 48156394 mates make up the pairs; of these: 47894652 (99.46%) aligned 0 times 134563 (0.28%) aligned exactly 1 time 127179 (0.26%) aligned >1 times 12.81% overall alignment rate Time searching: 00:09:25 Overall time: 00:09:25 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] 184146 / 3386872 = 0.0544 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 22:42:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.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 22:42:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:42:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:42:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.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 22:42:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:42:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:42:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.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 22:42:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:42:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:42:50: 1000000 INFO @ Mon, 03 Jun 2019 22:42:51: 1000000 INFO @ Mon, 03 Jun 2019 22:42:52: 1000000 INFO @ Mon, 03 Jun 2019 22:42:58: 2000000 INFO @ Mon, 03 Jun 2019 22:43:00: 2000000 INFO @ Mon, 03 Jun 2019 22:43:03: 2000000 INFO @ Mon, 03 Jun 2019 22:43:05: 3000000 INFO @ Mon, 03 Jun 2019 22:43:10: 3000000 INFO @ Mon, 03 Jun 2019 22:43:13: 4000000 INFO @ Mon, 03 Jun 2019 22:43:14: 3000000 INFO @ Mon, 03 Jun 2019 22:43:20: 4000000 INFO @ Mon, 03 Jun 2019 22:43:22: 5000000 INFO @ Mon, 03 Jun 2019 22:43:26: 4000000 INFO @ Mon, 03 Jun 2019 22:43:30: 5000000 INFO @ Mon, 03 Jun 2019 22:43:32: 6000000 INFO @ Mon, 03 Jun 2019 22:43:37: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 22:43:37: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 22:43:37: #1 total tags in treatment: 3201461 INFO @ Mon, 03 Jun 2019 22:43:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:43:37: #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 22:43:37: #1 tags after filtering in treatment: 3026528 INFO @ Mon, 03 Jun 2019 22:43:37: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 22:43:37: #1 finished! INFO @ Mon, 03 Jun 2019 22:43:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:43:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:43:37: #2 number of paired peaks: 894 WARNING @ Mon, 03 Jun 2019 22:43:37: Fewer paired peaks (894) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 894 pairs to build model! INFO @ Mon, 03 Jun 2019 22:43:37: start model_add_line... INFO @ Mon, 03 Jun 2019 22:43:38: start X-correlation... INFO @ Mon, 03 Jun 2019 22:43:38: end of X-cor INFO @ Mon, 03 Jun 2019 22:43:38: #2 finished! INFO @ Mon, 03 Jun 2019 22:43:38: #2 predicted fragment length is 144 bps INFO @ Mon, 03 Jun 2019 22:43:38: #2 alternative fragment length(s) may be 3,144 bps INFO @ Mon, 03 Jun 2019 22:43:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.05_model.r INFO @ Mon, 03 Jun 2019 22:43:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:43:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:43:38: 5000000 INFO @ Mon, 03 Jun 2019 22:43:40: 6000000 INFO @ Mon, 03 Jun 2019 22:43:46: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 22:43:46: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 22:43:46: #1 total tags in treatment: 3201461 INFO @ Mon, 03 Jun 2019 22:43:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:43:46: #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 22:43:46: #1 tags after filtering in treatment: 3026528 INFO @ Mon, 03 Jun 2019 22:43:46: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 22:43:46: #1 finished! INFO @ Mon, 03 Jun 2019 22:43:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:43:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:43:46: #2 number of paired peaks: 894 WARNING @ Mon, 03 Jun 2019 22:43:46: Fewer paired peaks (894) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 894 pairs to build model! INFO @ Mon, 03 Jun 2019 22:43:46: start model_add_line... INFO @ Mon, 03 Jun 2019 22:43:46: start X-correlation... INFO @ Mon, 03 Jun 2019 22:43:46: end of X-cor INFO @ Mon, 03 Jun 2019 22:43:46: #2 finished! INFO @ Mon, 03 Jun 2019 22:43:46: #2 predicted fragment length is 144 bps INFO @ Mon, 03 Jun 2019 22:43:46: #2 alternative fragment length(s) may be 3,144 bps INFO @ Mon, 03 Jun 2019 22:43:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.20_model.r INFO @ Mon, 03 Jun 2019 22:43:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:43:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:43:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:43:48: 6000000 INFO @ Mon, 03 Jun 2019 22:43:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:43:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:43:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.05_summits.bed INFO @ Mon, 03 Jun 2019 22:43:52: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (428 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:43:55: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 22:43:55: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 22:43:55: #1 total tags in treatment: 3201461 INFO @ Mon, 03 Jun 2019 22:43:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:43:55: #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 22:43:55: #1 tags after filtering in treatment: 3026528 INFO @ Mon, 03 Jun 2019 22:43:55: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 22:43:55: #1 finished! INFO @ Mon, 03 Jun 2019 22:43:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:43:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:43:56: #2 number of paired peaks: 894 WARNING @ Mon, 03 Jun 2019 22:43:56: Fewer paired peaks (894) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 894 pairs to build model! INFO @ Mon, 03 Jun 2019 22:43:56: start model_add_line... INFO @ Mon, 03 Jun 2019 22:43:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:43:56: start X-correlation... INFO @ Mon, 03 Jun 2019 22:43:56: end of X-cor INFO @ Mon, 03 Jun 2019 22:43:56: #2 finished! INFO @ Mon, 03 Jun 2019 22:43:56: #2 predicted fragment length is 144 bps INFO @ Mon, 03 Jun 2019 22:43:56: #2 alternative fragment length(s) may be 3,144 bps INFO @ Mon, 03 Jun 2019 22:43:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.10_model.r INFO @ Mon, 03 Jun 2019 22:43:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:43:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:44:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:44:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:44:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.20_summits.bed INFO @ Mon, 03 Jun 2019 22:44:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (97 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:44:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:44:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:44:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:44:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5299377/SRX5299377.10_summits.bed INFO @ Mon, 03 Jun 2019 22:44:10: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (224 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。