Job ID = 1299515 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T09:20:48 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 ) spots read : 11,235,801 reads read : 22,471,602 reads written : 22,471,602 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: 00:00:01 Multiseed full-index search: 00:18:22 11235801 reads; of these: 11235801 (100.00%) were paired; of these: 5549220 (49.39%) aligned concordantly 0 times 4014551 (35.73%) aligned concordantly exactly 1 time 1672030 (14.88%) aligned concordantly >1 times ---- 5549220 pairs aligned concordantly 0 times; of these: 122012 (2.20%) aligned discordantly 1 time ---- 5427208 pairs aligned 0 times concordantly or discordantly; of these: 10854416 mates make up the pairs; of these: 10607908 (97.73%) aligned 0 times 140145 (1.29%) aligned exactly 1 time 106363 (0.98%) aligned >1 times 52.79% overall alignment rate Time searching: 00:18:23 Overall time: 00:18:23 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_sort_core] merging from 8 files... [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] 1617990 / 5801268 = 0.2789 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 18:48:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.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 18:48:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:48:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:48:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.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 18:48:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:48:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:48:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.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 18:48:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:48:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:48:36: 1000000 INFO @ Mon, 03 Jun 2019 18:48:36: 1000000 INFO @ Mon, 03 Jun 2019 18:48:37: 1000000 INFO @ Mon, 03 Jun 2019 18:48:43: 2000000 INFO @ Mon, 03 Jun 2019 18:48:43: 2000000 INFO @ Mon, 03 Jun 2019 18:48:45: 2000000 INFO @ Mon, 03 Jun 2019 18:48:50: 3000000 INFO @ Mon, 03 Jun 2019 18:48:50: 3000000 INFO @ Mon, 03 Jun 2019 18:48:52: 3000000 INFO @ Mon, 03 Jun 2019 18:48:58: 4000000 INFO @ Mon, 03 Jun 2019 18:48:58: 4000000 INFO @ Mon, 03 Jun 2019 18:49:00: 4000000 INFO @ Mon, 03 Jun 2019 18:49:05: 5000000 INFO @ Mon, 03 Jun 2019 18:49:05: 5000000 INFO @ Mon, 03 Jun 2019 18:49:09: 5000000 INFO @ Mon, 03 Jun 2019 18:49:12: 6000000 INFO @ Mon, 03 Jun 2019 18:49:12: 6000000 INFO @ Mon, 03 Jun 2019 18:49:17: 6000000 INFO @ Mon, 03 Jun 2019 18:49:19: 7000000 INFO @ Mon, 03 Jun 2019 18:49:19: 7000000 INFO @ Mon, 03 Jun 2019 18:49:25: 7000000 INFO @ Mon, 03 Jun 2019 18:49:26: 8000000 INFO @ Mon, 03 Jun 2019 18:49:26: 8000000 INFO @ Mon, 03 Jun 2019 18:49:30: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:49:30: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:49:30: #1 total tags in treatment: 4099625 INFO @ Mon, 03 Jun 2019 18:49:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:49:30: #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 18:49:30: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:49:30: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:49:30: #1 total tags in treatment: 4099625 INFO @ Mon, 03 Jun 2019 18:49:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:49:30: #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 18:49:30: #1 tags after filtering in treatment: 3747588 INFO @ Mon, 03 Jun 2019 18:49:30: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 03 Jun 2019 18:49:30: #1 finished! INFO @ Mon, 03 Jun 2019 18:49:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:49:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:49:31: #1 tags after filtering in treatment: 3747588 INFO @ Mon, 03 Jun 2019 18:49:31: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 03 Jun 2019 18:49:31: #1 finished! INFO @ Mon, 03 Jun 2019 18:49:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:49:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:49:31: #2 number of paired peaks: 635 WARNING @ Mon, 03 Jun 2019 18:49:31: Fewer paired peaks (635) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 635 pairs to build model! INFO @ Mon, 03 Jun 2019 18:49:31: start model_add_line... INFO @ Mon, 03 Jun 2019 18:49:31: #2 number of paired peaks: 635 WARNING @ Mon, 03 Jun 2019 18:49:31: Fewer paired peaks (635) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 635 pairs to build model! INFO @ Mon, 03 Jun 2019 18:49:31: start model_add_line... INFO @ Mon, 03 Jun 2019 18:49:31: start X-correlation... INFO @ Mon, 03 Jun 2019 18:49:31: start X-correlation... INFO @ Mon, 03 Jun 2019 18:49:31: end of X-cor INFO @ Mon, 03 Jun 2019 18:49:31: #2 finished! INFO @ Mon, 03 Jun 2019 18:49:31: #2 predicted fragment length is 116 bps INFO @ Mon, 03 Jun 2019 18:49:31: #2 alternative fragment length(s) may be 116 bps INFO @ Mon, 03 Jun 2019 18:49:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.10_model.r INFO @ Mon, 03 Jun 2019 18:49:31: end of X-cor INFO @ Mon, 03 Jun 2019 18:49:31: #2 finished! INFO @ Mon, 03 Jun 2019 18:49:31: #2 predicted fragment length is 116 bps INFO @ Mon, 03 Jun 2019 18:49:31: #2 alternative fragment length(s) may be 116 bps INFO @ Mon, 03 Jun 2019 18:49:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.20_model.r INFO @ Mon, 03 Jun 2019 18:49:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:49:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:49:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:49:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:49:32: 8000000 INFO @ Mon, 03 Jun 2019 18:49:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:49:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:49:37: #1 total tags in treatment: 4099625 INFO @ Mon, 03 Jun 2019 18:49:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:49:37: #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 18:49:37: #1 tags after filtering in treatment: 3747588 INFO @ Mon, 03 Jun 2019 18:49:37: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 03 Jun 2019 18:49:37: #1 finished! INFO @ Mon, 03 Jun 2019 18:49:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:49:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:49:38: #2 number of paired peaks: 635 WARNING @ Mon, 03 Jun 2019 18:49:38: Fewer paired peaks (635) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 635 pairs to build model! INFO @ Mon, 03 Jun 2019 18:49:38: start model_add_line... INFO @ Mon, 03 Jun 2019 18:49:38: start X-correlation... INFO @ Mon, 03 Jun 2019 18:49:38: end of X-cor INFO @ Mon, 03 Jun 2019 18:49:38: #2 finished! INFO @ Mon, 03 Jun 2019 18:49:38: #2 predicted fragment length is 116 bps INFO @ Mon, 03 Jun 2019 18:49:38: #2 alternative fragment length(s) may be 116 bps INFO @ Mon, 03 Jun 2019 18:49:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.05_model.r INFO @ Mon, 03 Jun 2019 18:49:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:49:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:49:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:49:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:49:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.20_peaks.xls INFO @ Mon, 03 Jun 2019 18:49:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:49:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.20_summits.bed INFO @ Mon, 03 Jun 2019 18:49:48: Done! INFO @ Mon, 03 Jun 2019 18:49:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.10_peaks.xls INFO @ Mon, 03 Jun 2019 18:49:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:49:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.10_summits.bed INFO @ Mon, 03 Jun 2019 18:49:48: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (506 records, 4 fields): 4 millis pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (773 records, 4 fields): 5 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:49:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:49:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.05_peaks.xls INFO @ Mon, 03 Jun 2019 18:49:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:49:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474586/SRX474586.05_summits.bed INFO @ Mon, 03 Jun 2019 18:49:55: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2207 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。