Job ID = 1299373 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T09:08:15 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 ) 2019-06-03T09:09:22 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 ) 2019-06-03T09:11:31 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 ) 2019-06-03T09:14:17 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 : 16,520,915 reads read : 33,041,830 reads written : 33,041,830 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: 00:32:18 16520915 reads; of these: 16520915 (100.00%) were paired; of these: 3199661 (19.37%) aligned concordantly 0 times 10259315 (62.10%) aligned concordantly exactly 1 time 3061939 (18.53%) aligned concordantly >1 times ---- 3199661 pairs aligned concordantly 0 times; of these: 47683 (1.49%) aligned discordantly 1 time ---- 3151978 pairs aligned 0 times concordantly or discordantly; of these: 6303956 mates make up the pairs; of these: 5960244 (94.55%) aligned 0 times 270307 (4.29%) aligned exactly 1 time 73405 (1.16%) aligned >1 times 81.96% overall alignment rate Time searching: 00:32:18 Overall time: 00:32:18 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] 3508192 / 13353433 = 0.2627 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 19:03:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.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 19:03:19: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:03:19: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:03:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.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 19:03:19: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:03:19: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:03:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.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 19:03:19: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:03:19: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:03:26: 1000000 INFO @ Mon, 03 Jun 2019 19:03:26: 1000000 INFO @ Mon, 03 Jun 2019 19:03:28: 1000000 INFO @ Mon, 03 Jun 2019 19:03:33: 2000000 INFO @ Mon, 03 Jun 2019 19:03:33: 2000000 INFO @ Mon, 03 Jun 2019 19:03:36: 2000000 INFO @ Mon, 03 Jun 2019 19:03:39: 3000000 INFO @ Mon, 03 Jun 2019 19:03:40: 3000000 INFO @ Mon, 03 Jun 2019 19:03:45: 3000000 INFO @ Mon, 03 Jun 2019 19:03:46: 4000000 INFO @ Mon, 03 Jun 2019 19:03:47: 4000000 INFO @ Mon, 03 Jun 2019 19:03:53: 5000000 INFO @ Mon, 03 Jun 2019 19:03:53: 5000000 INFO @ Mon, 03 Jun 2019 19:03:54: 4000000 INFO @ Mon, 03 Jun 2019 19:04:00: 6000000 INFO @ Mon, 03 Jun 2019 19:04:00: 6000000 INFO @ Mon, 03 Jun 2019 19:04:02: 5000000 INFO @ Mon, 03 Jun 2019 19:04:07: 7000000 INFO @ Mon, 03 Jun 2019 19:04:07: 7000000 INFO @ Mon, 03 Jun 2019 19:04:11: 6000000 INFO @ Mon, 03 Jun 2019 19:04:14: 8000000 INFO @ Mon, 03 Jun 2019 19:04:14: 8000000 INFO @ Mon, 03 Jun 2019 19:04:20: 7000000 INFO @ Mon, 03 Jun 2019 19:04:20: 9000000 INFO @ Mon, 03 Jun 2019 19:04:21: 9000000 INFO @ Mon, 03 Jun 2019 19:04:27: 10000000 INFO @ Mon, 03 Jun 2019 19:04:27: 10000000 INFO @ Mon, 03 Jun 2019 19:04:28: 8000000 INFO @ Mon, 03 Jun 2019 19:04:34: 11000000 INFO @ Mon, 03 Jun 2019 19:04:34: 11000000 INFO @ Mon, 03 Jun 2019 19:04:37: 9000000 INFO @ Mon, 03 Jun 2019 19:04:41: 12000000 INFO @ Mon, 03 Jun 2019 19:04:41: 12000000 INFO @ Mon, 03 Jun 2019 19:04:46: 10000000 INFO @ Mon, 03 Jun 2019 19:04:48: 13000000 INFO @ Mon, 03 Jun 2019 19:04:48: 13000000 INFO @ Mon, 03 Jun 2019 19:04:54: 14000000 INFO @ Mon, 03 Jun 2019 19:04:54: 14000000 INFO @ Mon, 03 Jun 2019 19:04:55: 11000000 INFO @ Mon, 03 Jun 2019 19:05:01: 15000000 INFO @ Mon, 03 Jun 2019 19:05:01: 15000000 INFO @ Mon, 03 Jun 2019 19:05:04: 12000000 INFO @ Mon, 03 Jun 2019 19:05:08: 16000000 INFO @ Mon, 03 Jun 2019 19:05:08: 16000000 INFO @ Mon, 03 Jun 2019 19:05:12: 13000000 INFO @ Mon, 03 Jun 2019 19:05:15: 17000000 INFO @ Mon, 03 Jun 2019 19:05:15: 17000000 INFO @ Mon, 03 Jun 2019 19:05:21: 14000000 INFO @ Mon, 03 Jun 2019 19:05:22: 18000000 INFO @ Mon, 03 Jun 2019 19:05:22: 18000000 INFO @ Mon, 03 Jun 2019 19:05:29: 19000000 INFO @ Mon, 03 Jun 2019 19:05:29: 19000000 INFO @ Mon, 03 Jun 2019 19:05:30: 15000000 INFO @ Mon, 03 Jun 2019 19:05:35: 20000000 INFO @ Mon, 03 Jun 2019 19:05:36: 20000000 INFO @ Mon, 03 Jun 2019 19:05:36: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:05:36: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:05:36: #1 total tags in treatment: 9819383 INFO @ Mon, 03 Jun 2019 19:05:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:05:36: #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 19:05:36: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:05:36: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:05:36: #1 total tags in treatment: 9819383 INFO @ Mon, 03 Jun 2019 19:05:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:05:36: #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 19:05:36: #1 tags after filtering in treatment: 8519137 INFO @ Mon, 03 Jun 2019 19:05:36: #1 Redundant rate of treatment: 0.13 INFO @ Mon, 03 Jun 2019 19:05:36: #1 finished! INFO @ Mon, 03 Jun 2019 19:05:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:05:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:05:36: #1 tags after filtering in treatment: 8519137 INFO @ Mon, 03 Jun 2019 19:05:36: #1 Redundant rate of treatment: 0.13 INFO @ Mon, 03 Jun 2019 19:05:36: #1 finished! INFO @ Mon, 03 Jun 2019 19:05:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:05:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:05:37: #2 number of paired peaks: 371 WARNING @ Mon, 03 Jun 2019 19:05:37: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Mon, 03 Jun 2019 19:05:37: start model_add_line... INFO @ Mon, 03 Jun 2019 19:05:37: start X-correlation... INFO @ Mon, 03 Jun 2019 19:05:37: end of X-cor INFO @ Mon, 03 Jun 2019 19:05:37: #2 finished! INFO @ Mon, 03 Jun 2019 19:05:37: #2 predicted fragment length is 105 bps INFO @ Mon, 03 Jun 2019 19:05:37: #2 alternative fragment length(s) may be 105 bps INFO @ Mon, 03 Jun 2019 19:05:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.05_model.r INFO @ Mon, 03 Jun 2019 19:05:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:05:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:05:37: #2 number of paired peaks: 371 WARNING @ Mon, 03 Jun 2019 19:05:37: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Mon, 03 Jun 2019 19:05:37: start model_add_line... INFO @ Mon, 03 Jun 2019 19:05:37: start X-correlation... INFO @ Mon, 03 Jun 2019 19:05:37: end of X-cor INFO @ Mon, 03 Jun 2019 19:05:37: #2 finished! INFO @ Mon, 03 Jun 2019 19:05:37: #2 predicted fragment length is 105 bps INFO @ Mon, 03 Jun 2019 19:05:37: #2 alternative fragment length(s) may be 105 bps INFO @ Mon, 03 Jun 2019 19:05:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.20_model.r INFO @ Mon, 03 Jun 2019 19:05:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:05:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:05:38: 16000000 INFO @ Mon, 03 Jun 2019 19:05:47: 17000000 INFO @ Mon, 03 Jun 2019 19:05:55: 18000000 INFO @ Mon, 03 Jun 2019 19:06:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:06:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:06:04: 19000000 INFO @ Mon, 03 Jun 2019 19:06:12: 20000000 INFO @ Mon, 03 Jun 2019 19:06:13: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:06:13: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:06:13: #1 total tags in treatment: 9819383 INFO @ Mon, 03 Jun 2019 19:06:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:06:13: #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 19:06:13: #1 tags after filtering in treatment: 8519137 INFO @ Mon, 03 Jun 2019 19:06:13: #1 Redundant rate of treatment: 0.13 INFO @ Mon, 03 Jun 2019 19:06:13: #1 finished! INFO @ Mon, 03 Jun 2019 19:06:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:06:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:06:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:06:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:06:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.05_summits.bed INFO @ Mon, 03 Jun 2019 19:06:13: Done! INFO @ Mon, 03 Jun 2019 19:06:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:06:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:06:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.20_summits.bed INFO @ Mon, 03 Jun 2019 19:06:13: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1147 records, 4 fields): 6 millis CompletedMACS2peakCalling pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (520 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:06:14: #2 number of paired peaks: 371 WARNING @ Mon, 03 Jun 2019 19:06:14: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Mon, 03 Jun 2019 19:06:14: start model_add_line... INFO @ Mon, 03 Jun 2019 19:06:14: start X-correlation... INFO @ Mon, 03 Jun 2019 19:06:14: end of X-cor INFO @ Mon, 03 Jun 2019 19:06:14: #2 finished! INFO @ Mon, 03 Jun 2019 19:06:14: #2 predicted fragment length is 105 bps INFO @ Mon, 03 Jun 2019 19:06:14: #2 alternative fragment length(s) may be 105 bps INFO @ Mon, 03 Jun 2019 19:06:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.10_model.r INFO @ Mon, 03 Jun 2019 19:06:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:06:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:06:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:06:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:06:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:06:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474574/SRX474574.10_summits.bed INFO @ Mon, 03 Jun 2019 19:06:50: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (764 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。