Job ID = 1293344 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T14:17:52 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 ) 2019-06-02T14:17:52 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 ) 2019-06-02T14:17:52 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 : 30,277,713 reads read : 60,555,426 reads written : 60,555,426 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: 00:45:32 30277713 reads; of these: 30277713 (100.00%) were paired; of these: 16889638 (55.78%) aligned concordantly 0 times 9634691 (31.82%) aligned concordantly exactly 1 time 3753384 (12.40%) aligned concordantly >1 times ---- 16889638 pairs aligned concordantly 0 times; of these: 61605 (0.36%) aligned discordantly 1 time ---- 16828033 pairs aligned 0 times concordantly or discordantly; of these: 33656066 mates make up the pairs; of these: 32731075 (97.25%) aligned 0 times 433777 (1.29%) aligned exactly 1 time 491214 (1.46%) aligned >1 times 45.95% overall alignment rate Time searching: 00:45:32 Overall time: 00:45:32 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 12 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] 9632248 / 13438796 = 0.7167 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 00:21:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.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 00:21:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:21:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:21:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.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 00:21:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:21:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:21:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.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 00:21:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:21:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:22:02: 1000000 INFO @ Mon, 03 Jun 2019 00:22:02: 1000000 INFO @ Mon, 03 Jun 2019 00:22:02: 1000000 INFO @ Mon, 03 Jun 2019 00:22:10: 2000000 INFO @ Mon, 03 Jun 2019 00:22:11: 2000000 INFO @ Mon, 03 Jun 2019 00:22:11: 2000000 INFO @ Mon, 03 Jun 2019 00:22:18: 3000000 INFO @ Mon, 03 Jun 2019 00:22:20: 3000000 INFO @ Mon, 03 Jun 2019 00:22:20: 3000000 INFO @ Mon, 03 Jun 2019 00:22:25: 4000000 INFO @ Mon, 03 Jun 2019 00:22:28: 4000000 INFO @ Mon, 03 Jun 2019 00:22:28: 4000000 INFO @ Mon, 03 Jun 2019 00:22:33: 5000000 INFO @ Mon, 03 Jun 2019 00:22:36: 5000000 INFO @ Mon, 03 Jun 2019 00:22:37: 5000000 INFO @ Mon, 03 Jun 2019 00:22:40: 6000000 INFO @ Mon, 03 Jun 2019 00:22:45: 6000000 INFO @ Mon, 03 Jun 2019 00:22:45: 6000000 INFO @ Mon, 03 Jun 2019 00:22:48: 7000000 INFO @ Mon, 03 Jun 2019 00:22:53: 7000000 INFO @ Mon, 03 Jun 2019 00:22:53: 7000000 INFO @ Mon, 03 Jun 2019 00:22:55: 8000000 INFO @ Mon, 03 Jun 2019 00:22:59: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 00:22:59: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 00:22:59: #1 total tags in treatment: 3782481 INFO @ Mon, 03 Jun 2019 00:22:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:22:59: #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 00:22:59: #1 tags after filtering in treatment: 3514437 INFO @ Mon, 03 Jun 2019 00:22:59: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 00:22:59: #1 finished! INFO @ Mon, 03 Jun 2019 00:22:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:22:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:22:59: #2 number of paired peaks: 974 WARNING @ Mon, 03 Jun 2019 00:22:59: Fewer paired peaks (974) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 974 pairs to build model! INFO @ Mon, 03 Jun 2019 00:22:59: start model_add_line... INFO @ Mon, 03 Jun 2019 00:22:59: start X-correlation... INFO @ Mon, 03 Jun 2019 00:22:59: end of X-cor INFO @ Mon, 03 Jun 2019 00:22:59: #2 finished! INFO @ Mon, 03 Jun 2019 00:22:59: #2 predicted fragment length is 171 bps INFO @ Mon, 03 Jun 2019 00:22:59: #2 alternative fragment length(s) may be 171 bps INFO @ Mon, 03 Jun 2019 00:22:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.20_model.r INFO @ Mon, 03 Jun 2019 00:22:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:22:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:23:01: 8000000 INFO @ Mon, 03 Jun 2019 00:23:01: 8000000 INFO @ Mon, 03 Jun 2019 00:23:05: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 00:23:05: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 00:23:05: #1 total tags in treatment: 3782481 INFO @ Mon, 03 Jun 2019 00:23:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:23:05: #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 00:23:05: #1 tags after filtering in treatment: 3514437 INFO @ Mon, 03 Jun 2019 00:23:05: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 00:23:05: #1 finished! INFO @ Mon, 03 Jun 2019 00:23:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:23:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:23:06: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 00:23:06: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 00:23:06: #1 total tags in treatment: 3782481 INFO @ Mon, 03 Jun 2019 00:23:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:23:06: #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 00:23:06: #1 tags after filtering in treatment: 3514437 INFO @ Mon, 03 Jun 2019 00:23:06: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 00:23:06: #1 finished! INFO @ Mon, 03 Jun 2019 00:23:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:23:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:23:06: #2 number of paired peaks: 974 WARNING @ Mon, 03 Jun 2019 00:23:06: Fewer paired peaks (974) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 974 pairs to build model! INFO @ Mon, 03 Jun 2019 00:23:06: start model_add_line... INFO @ Mon, 03 Jun 2019 00:23:06: start X-correlation... INFO @ Mon, 03 Jun 2019 00:23:06: end of X-cor INFO @ Mon, 03 Jun 2019 00:23:06: #2 finished! INFO @ Mon, 03 Jun 2019 00:23:06: #2 predicted fragment length is 171 bps INFO @ Mon, 03 Jun 2019 00:23:06: #2 alternative fragment length(s) may be 171 bps INFO @ Mon, 03 Jun 2019 00:23:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.05_model.r INFO @ Mon, 03 Jun 2019 00:23:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:23:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:23:06: #2 number of paired peaks: 974 WARNING @ Mon, 03 Jun 2019 00:23:06: Fewer paired peaks (974) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 974 pairs to build model! INFO @ Mon, 03 Jun 2019 00:23:06: start model_add_line... INFO @ Mon, 03 Jun 2019 00:23:06: start X-correlation... INFO @ Mon, 03 Jun 2019 00:23:06: end of X-cor INFO @ Mon, 03 Jun 2019 00:23:06: #2 finished! INFO @ Mon, 03 Jun 2019 00:23:06: #2 predicted fragment length is 171 bps INFO @ Mon, 03 Jun 2019 00:23:06: #2 alternative fragment length(s) may be 171 bps INFO @ Mon, 03 Jun 2019 00:23:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.10_model.r INFO @ Mon, 03 Jun 2019 00:23:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:23:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:23:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:23:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.20_peaks.xls INFO @ Mon, 03 Jun 2019 00:23:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:23:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.20_summits.bed INFO @ Mon, 03 Jun 2019 00:23:16: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (234 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 00:23:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:23:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:23:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.05_peaks.xls INFO @ Mon, 03 Jun 2019 00:23:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:23:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.05_summits.bed INFO @ Mon, 03 Jun 2019 00:23:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2898 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 00:23:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.10_peaks.xls INFO @ Mon, 03 Jun 2019 00:23:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:23:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818270/ERX1818270.10_summits.bed INFO @ Mon, 03 Jun 2019 00:23:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (980 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。