Job ID = 2590963 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-12T15:12:56 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 : 22,202,702 reads read : 44,405,404 reads written : 44,405,404 rm: cannot remove ‘[DSE]RR*’: 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: 00:33:49 22202702 reads; of these: 22202702 (100.00%) were paired; of these: 3129209 (14.09%) aligned concordantly 0 times 16125801 (72.63%) aligned concordantly exactly 1 time 2947692 (13.28%) aligned concordantly >1 times ---- 3129209 pairs aligned concordantly 0 times; of these: 308868 (9.87%) aligned discordantly 1 time ---- 2820341 pairs aligned 0 times concordantly or discordantly; of these: 5640682 mates make up the pairs; of these: 4791767 (84.95%) aligned 0 times 553032 (9.80%) aligned exactly 1 time 295883 (5.25%) aligned >1 times 89.21% overall alignment rate Time searching: 00:33:49 Overall time: 00:33:49 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 20 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] 1584371 / 19332852 = 0.0820 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 @ Tue, 13 Aug 2019 01:16:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.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 @ Tue, 13 Aug 2019 01:16:58: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:16:58: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:16:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.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 @ Tue, 13 Aug 2019 01:16:59: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:16:59: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:17:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.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 @ Tue, 13 Aug 2019 01:17:00: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:17:00: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:17:08: 1000000 INFO @ Tue, 13 Aug 2019 01:17:08: 1000000 INFO @ Tue, 13 Aug 2019 01:17:10: 1000000 INFO @ Tue, 13 Aug 2019 01:17:18: 2000000 INFO @ Tue, 13 Aug 2019 01:17:18: 2000000 INFO @ Tue, 13 Aug 2019 01:17:20: 2000000 INFO @ Tue, 13 Aug 2019 01:17:27: 3000000 INFO @ Tue, 13 Aug 2019 01:17:28: 3000000 INFO @ Tue, 13 Aug 2019 01:17:30: 3000000 INFO @ Tue, 13 Aug 2019 01:17:36: 4000000 INFO @ Tue, 13 Aug 2019 01:17:37: 4000000 INFO @ Tue, 13 Aug 2019 01:17:40: 4000000 INFO @ Tue, 13 Aug 2019 01:17:44: 5000000 INFO @ Tue, 13 Aug 2019 01:17:47: 5000000 INFO @ Tue, 13 Aug 2019 01:17:49: 5000000 INFO @ Tue, 13 Aug 2019 01:17:53: 6000000 INFO @ Tue, 13 Aug 2019 01:17:57: 6000000 INFO @ Tue, 13 Aug 2019 01:17:59: 6000000 INFO @ Tue, 13 Aug 2019 01:18:02: 7000000 INFO @ Tue, 13 Aug 2019 01:18:06: 7000000 INFO @ Tue, 13 Aug 2019 01:18:09: 7000000 INFO @ Tue, 13 Aug 2019 01:18:11: 8000000 INFO @ Tue, 13 Aug 2019 01:18:16: 8000000 INFO @ Tue, 13 Aug 2019 01:18:18: 8000000 INFO @ Tue, 13 Aug 2019 01:18:19: 9000000 INFO @ Tue, 13 Aug 2019 01:18:25: 9000000 INFO @ Tue, 13 Aug 2019 01:18:27: 9000000 INFO @ Tue, 13 Aug 2019 01:18:28: 10000000 INFO @ Tue, 13 Aug 2019 01:18:35: 10000000 INFO @ Tue, 13 Aug 2019 01:18:36: 11000000 INFO @ Tue, 13 Aug 2019 01:18:37: 10000000 INFO @ Tue, 13 Aug 2019 01:18:44: 11000000 INFO @ Tue, 13 Aug 2019 01:18:45: 12000000 INFO @ Tue, 13 Aug 2019 01:18:46: 11000000 INFO @ Tue, 13 Aug 2019 01:18:53: 13000000 INFO @ Tue, 13 Aug 2019 01:18:53: 12000000 INFO @ Tue, 13 Aug 2019 01:18:56: 12000000 INFO @ Tue, 13 Aug 2019 01:19:01: 14000000 INFO @ Tue, 13 Aug 2019 01:19:03: 13000000 INFO @ Tue, 13 Aug 2019 01:19:05: 13000000 INFO @ Tue, 13 Aug 2019 01:19:10: 15000000 INFO @ Tue, 13 Aug 2019 01:19:12: 14000000 INFO @ Tue, 13 Aug 2019 01:19:14: 14000000 INFO @ Tue, 13 Aug 2019 01:19:18: 16000000 INFO @ Tue, 13 Aug 2019 01:19:22: 15000000 INFO @ Tue, 13 Aug 2019 01:19:24: 15000000 INFO @ Tue, 13 Aug 2019 01:19:27: 17000000 INFO @ Tue, 13 Aug 2019 01:19:31: 16000000 INFO @ Tue, 13 Aug 2019 01:19:33: 16000000 INFO @ Tue, 13 Aug 2019 01:19:35: 18000000 INFO @ Tue, 13 Aug 2019 01:19:40: 17000000 INFO @ Tue, 13 Aug 2019 01:19:42: 17000000 INFO @ Tue, 13 Aug 2019 01:19:44: 19000000 INFO @ Tue, 13 Aug 2019 01:19:50: 18000000 INFO @ Tue, 13 Aug 2019 01:19:52: 18000000 INFO @ Tue, 13 Aug 2019 01:19:52: 20000000 INFO @ Tue, 13 Aug 2019 01:19:59: 19000000 INFO @ Tue, 13 Aug 2019 01:20:01: 21000000 INFO @ Tue, 13 Aug 2019 01:20:01: 19000000 INFO @ Tue, 13 Aug 2019 01:20:08: 20000000 INFO @ Tue, 13 Aug 2019 01:20:09: 22000000 INFO @ Tue, 13 Aug 2019 01:20:11: 20000000 INFO @ Tue, 13 Aug 2019 01:20:17: 23000000 INFO @ Tue, 13 Aug 2019 01:20:18: 21000000 INFO @ Tue, 13 Aug 2019 01:20:20: 21000000 INFO @ Tue, 13 Aug 2019 01:20:26: 24000000 INFO @ Tue, 13 Aug 2019 01:20:27: 22000000 INFO @ Tue, 13 Aug 2019 01:20:29: 22000000 INFO @ Tue, 13 Aug 2019 01:20:34: 25000000 INFO @ Tue, 13 Aug 2019 01:20:36: 23000000 INFO @ Tue, 13 Aug 2019 01:20:38: 23000000 INFO @ Tue, 13 Aug 2019 01:20:43: 26000000 INFO @ Tue, 13 Aug 2019 01:20:46: 24000000 INFO @ Tue, 13 Aug 2019 01:20:48: 24000000 INFO @ Tue, 13 Aug 2019 01:20:51: 27000000 INFO @ Tue, 13 Aug 2019 01:20:55: 25000000 INFO @ Tue, 13 Aug 2019 01:20:57: 25000000 INFO @ Tue, 13 Aug 2019 01:21:00: 28000000 INFO @ Tue, 13 Aug 2019 01:21:04: 26000000 INFO @ Tue, 13 Aug 2019 01:21:06: 26000000 INFO @ Tue, 13 Aug 2019 01:21:08: 29000000 INFO @ Tue, 13 Aug 2019 01:21:13: 27000000 INFO @ Tue, 13 Aug 2019 01:21:15: 27000000 INFO @ Tue, 13 Aug 2019 01:21:16: 30000000 INFO @ Tue, 13 Aug 2019 01:21:23: 28000000 INFO @ Tue, 13 Aug 2019 01:21:25: 28000000 INFO @ Tue, 13 Aug 2019 01:21:25: 31000000 INFO @ Tue, 13 Aug 2019 01:21:32: 29000000 INFO @ Tue, 13 Aug 2019 01:21:33: 32000000 INFO @ Tue, 13 Aug 2019 01:21:34: 29000000 INFO @ Tue, 13 Aug 2019 01:21:41: 30000000 INFO @ Tue, 13 Aug 2019 01:21:42: 33000000 INFO @ Tue, 13 Aug 2019 01:21:43: 30000000 INFO @ Tue, 13 Aug 2019 01:21:50: 34000000 INFO @ Tue, 13 Aug 2019 01:21:50: 31000000 INFO @ Tue, 13 Aug 2019 01:21:52: 31000000 INFO @ Tue, 13 Aug 2019 01:21:58: 35000000 INFO @ Tue, 13 Aug 2019 01:22:00: 32000000 INFO @ Tue, 13 Aug 2019 01:22:02: 32000000 INFO @ Tue, 13 Aug 2019 01:22:07: 36000000 INFO @ Tue, 13 Aug 2019 01:22:09: 33000000 INFO @ Tue, 13 Aug 2019 01:22:11: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 01:22:11: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 01:22:11: #1 total tags in treatment: 17501772 INFO @ Tue, 13 Aug 2019 01:22:11: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:22:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 01:22:11: 33000000 INFO @ Tue, 13 Aug 2019 01:22:11: #1 tags after filtering in treatment: 13452972 INFO @ Tue, 13 Aug 2019 01:22:11: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 13 Aug 2019 01:22:11: #1 finished! INFO @ Tue, 13 Aug 2019 01:22:11: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:22:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:22:12: #2 number of paired peaks: 340 WARNING @ Tue, 13 Aug 2019 01:22:12: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Tue, 13 Aug 2019 01:22:12: start model_add_line... INFO @ Tue, 13 Aug 2019 01:22:12: start X-correlation... INFO @ Tue, 13 Aug 2019 01:22:12: end of X-cor INFO @ Tue, 13 Aug 2019 01:22:12: #2 finished! INFO @ Tue, 13 Aug 2019 01:22:12: #2 predicted fragment length is 111 bps INFO @ Tue, 13 Aug 2019 01:22:12: #2 alternative fragment length(s) may be 37,89,111,122,464,506 bps INFO @ Tue, 13 Aug 2019 01:22:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.10_model.r INFO @ Tue, 13 Aug 2019 01:22:12: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:22:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:22:18: 34000000 INFO @ Tue, 13 Aug 2019 01:22:20: 34000000 INFO @ Tue, 13 Aug 2019 01:22:27: 35000000 INFO @ Tue, 13 Aug 2019 01:22:29: 35000000 INFO @ Tue, 13 Aug 2019 01:22:36: 36000000 INFO @ Tue, 13 Aug 2019 01:22:38: 36000000 INFO @ Tue, 13 Aug 2019 01:22:40: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 01:22:40: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 01:22:40: #1 total tags in treatment: 17501772 INFO @ Tue, 13 Aug 2019 01:22:40: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:22:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 01:22:41: #1 tags after filtering in treatment: 13452972 INFO @ Tue, 13 Aug 2019 01:22:41: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 13 Aug 2019 01:22:41: #1 finished! INFO @ Tue, 13 Aug 2019 01:22:41: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:22:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:22:42: #2 number of paired peaks: 340 WARNING @ Tue, 13 Aug 2019 01:22:42: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Tue, 13 Aug 2019 01:22:42: start model_add_line... INFO @ Tue, 13 Aug 2019 01:22:42: start X-correlation... INFO @ Tue, 13 Aug 2019 01:22:42: end of X-cor INFO @ Tue, 13 Aug 2019 01:22:42: #2 finished! INFO @ Tue, 13 Aug 2019 01:22:42: #2 predicted fragment length is 111 bps INFO @ Tue, 13 Aug 2019 01:22:42: #2 alternative fragment length(s) may be 37,89,111,122,464,506 bps INFO @ Tue, 13 Aug 2019 01:22:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.05_model.r INFO @ Tue, 13 Aug 2019 01:22:42: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:22:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:22:42: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 01:22:42: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 01:22:42: #1 total tags in treatment: 17501772 INFO @ Tue, 13 Aug 2019 01:22:42: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:22:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 01:22:42: #1 tags after filtering in treatment: 13452972 INFO @ Tue, 13 Aug 2019 01:22:42: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 13 Aug 2019 01:22:42: #1 finished! INFO @ Tue, 13 Aug 2019 01:22:42: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:22:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:22:44: #2 number of paired peaks: 340 WARNING @ Tue, 13 Aug 2019 01:22:44: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Tue, 13 Aug 2019 01:22:44: start model_add_line... INFO @ Tue, 13 Aug 2019 01:22:44: start X-correlation... INFO @ Tue, 13 Aug 2019 01:22:44: end of X-cor INFO @ Tue, 13 Aug 2019 01:22:44: #2 finished! INFO @ Tue, 13 Aug 2019 01:22:44: #2 predicted fragment length is 111 bps INFO @ Tue, 13 Aug 2019 01:22:44: #2 alternative fragment length(s) may be 37,89,111,122,464,506 bps INFO @ Tue, 13 Aug 2019 01:22:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.20_model.r INFO @ Tue, 13 Aug 2019 01:22:44: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:22:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:22:49: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:23:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.10_peaks.xls INFO @ Tue, 13 Aug 2019 01:23:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:23:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.10_summits.bed INFO @ Tue, 13 Aug 2019 01:23:06: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (434 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 01:23:19: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:23:20: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:23:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.05_peaks.xls INFO @ Tue, 13 Aug 2019 01:23:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:23:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.05_summits.bed INFO @ Tue, 13 Aug 2019 01:23:37: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2110 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 01:23:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.20_peaks.xls INFO @ Tue, 13 Aug 2019 01:23:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:23:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5865779/SRX5865779.20_summits.bed INFO @ Tue, 13 Aug 2019 01:23:39: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (106 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。