Job ID = 2590957 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-12T15:18:13 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 ) 2019-08-12T15:18:15 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-08-12T15:18:15 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-08-12T15:18:15 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 24,470,040 reads read : 48,940,080 reads written : 48,940,080 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: 00:48:53 24470040 reads; of these: 24470040 (100.00%) were paired; of these: 6458275 (26.39%) aligned concordantly 0 times 13193310 (53.92%) aligned concordantly exactly 1 time 4818455 (19.69%) aligned concordantly >1 times ---- 6458275 pairs aligned concordantly 0 times; of these: 977962 (15.14%) aligned discordantly 1 time ---- 5480313 pairs aligned 0 times concordantly or discordantly; of these: 10960626 mates make up the pairs; of these: 9514907 (86.81%) aligned 0 times 661809 (6.04%) aligned exactly 1 time 783910 (7.15%) aligned >1 times 80.56% overall alignment rate Time searching: 00:48:53 Overall time: 00:48:53 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] 2506895 / 18842296 = 0.1330 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 01:30:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.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 01:30:35: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:30:35: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:30:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.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 01:30:36: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:30:36: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:30:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.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 01:30:37: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:30:37: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:30:43: 1000000 INFO @ Tue, 13 Aug 2019 01:30:44: 1000000 INFO @ Tue, 13 Aug 2019 01:30:45: 1000000 INFO @ Tue, 13 Aug 2019 01:30:51: 2000000 INFO @ Tue, 13 Aug 2019 01:30:52: 2000000 INFO @ Tue, 13 Aug 2019 01:30:53: 2000000 INFO @ Tue, 13 Aug 2019 01:30:59: 3000000 INFO @ Tue, 13 Aug 2019 01:31:00: 3000000 INFO @ Tue, 13 Aug 2019 01:31:01: 3000000 INFO @ Tue, 13 Aug 2019 01:31:07: 4000000 INFO @ Tue, 13 Aug 2019 01:31:09: 4000000 INFO @ Tue, 13 Aug 2019 01:31:10: 4000000 INFO @ Tue, 13 Aug 2019 01:31:15: 5000000 INFO @ Tue, 13 Aug 2019 01:31:17: 5000000 INFO @ Tue, 13 Aug 2019 01:31:18: 5000000 INFO @ Tue, 13 Aug 2019 01:31:24: 6000000 INFO @ Tue, 13 Aug 2019 01:31:25: 6000000 INFO @ Tue, 13 Aug 2019 01:31:26: 6000000 INFO @ Tue, 13 Aug 2019 01:31:32: 7000000 INFO @ Tue, 13 Aug 2019 01:31:33: 7000000 INFO @ Tue, 13 Aug 2019 01:31:34: 7000000 INFO @ Tue, 13 Aug 2019 01:31:40: 8000000 INFO @ Tue, 13 Aug 2019 01:31:41: 8000000 INFO @ Tue, 13 Aug 2019 01:31:42: 8000000 INFO @ Tue, 13 Aug 2019 01:31:48: 9000000 INFO @ Tue, 13 Aug 2019 01:31:50: 9000000 INFO @ Tue, 13 Aug 2019 01:31:51: 9000000 INFO @ Tue, 13 Aug 2019 01:31:56: 10000000 INFO @ Tue, 13 Aug 2019 01:31:58: 10000000 INFO @ Tue, 13 Aug 2019 01:31:59: 10000000 INFO @ Tue, 13 Aug 2019 01:32:04: 11000000 INFO @ Tue, 13 Aug 2019 01:32:06: 11000000 INFO @ Tue, 13 Aug 2019 01:32:07: 11000000 INFO @ Tue, 13 Aug 2019 01:32:12: 12000000 INFO @ Tue, 13 Aug 2019 01:32:14: 12000000 INFO @ Tue, 13 Aug 2019 01:32:15: 12000000 INFO @ Tue, 13 Aug 2019 01:32:20: 13000000 INFO @ Tue, 13 Aug 2019 01:32:22: 13000000 INFO @ Tue, 13 Aug 2019 01:32:23: 13000000 INFO @ Tue, 13 Aug 2019 01:32:28: 14000000 INFO @ Tue, 13 Aug 2019 01:32:31: 14000000 INFO @ Tue, 13 Aug 2019 01:32:32: 14000000 INFO @ Tue, 13 Aug 2019 01:32:36: 15000000 INFO @ Tue, 13 Aug 2019 01:32:39: 15000000 INFO @ Tue, 13 Aug 2019 01:32:40: 15000000 INFO @ Tue, 13 Aug 2019 01:32:45: 16000000 INFO @ Tue, 13 Aug 2019 01:32:47: 16000000 INFO @ Tue, 13 Aug 2019 01:32:48: 16000000 INFO @ Tue, 13 Aug 2019 01:32:53: 17000000 INFO @ Tue, 13 Aug 2019 01:32:55: 17000000 INFO @ Tue, 13 Aug 2019 01:32:56: 17000000 INFO @ Tue, 13 Aug 2019 01:33:01: 18000000 INFO @ Tue, 13 Aug 2019 01:33:03: 18000000 INFO @ Tue, 13 Aug 2019 01:33:04: 18000000 INFO @ Tue, 13 Aug 2019 01:33:09: 19000000 INFO @ Tue, 13 Aug 2019 01:33:11: 19000000 INFO @ Tue, 13 Aug 2019 01:33:12: 19000000 INFO @ Tue, 13 Aug 2019 01:33:17: 20000000 INFO @ Tue, 13 Aug 2019 01:33:20: 20000000 INFO @ Tue, 13 Aug 2019 01:33:21: 20000000 INFO @ Tue, 13 Aug 2019 01:33:25: 21000000 INFO @ Tue, 13 Aug 2019 01:33:28: 21000000 INFO @ Tue, 13 Aug 2019 01:33:29: 21000000 INFO @ Tue, 13 Aug 2019 01:33:33: 22000000 INFO @ Tue, 13 Aug 2019 01:33:36: 22000000 INFO @ Tue, 13 Aug 2019 01:33:37: 22000000 INFO @ Tue, 13 Aug 2019 01:33:41: 23000000 INFO @ Tue, 13 Aug 2019 01:33:44: 23000000 INFO @ Tue, 13 Aug 2019 01:33:45: 23000000 INFO @ Tue, 13 Aug 2019 01:33:49: 24000000 INFO @ Tue, 13 Aug 2019 01:33:52: 24000000 INFO @ Tue, 13 Aug 2019 01:33:53: 24000000 INFO @ Tue, 13 Aug 2019 01:33:57: 25000000 INFO @ Tue, 13 Aug 2019 01:34:00: 25000000 INFO @ Tue, 13 Aug 2019 01:34:01: 25000000 INFO @ Tue, 13 Aug 2019 01:34:05: 26000000 INFO @ Tue, 13 Aug 2019 01:34:08: 26000000 INFO @ Tue, 13 Aug 2019 01:34:10: 26000000 INFO @ Tue, 13 Aug 2019 01:34:13: 27000000 INFO @ Tue, 13 Aug 2019 01:34:17: 27000000 INFO @ Tue, 13 Aug 2019 01:34:18: 27000000 INFO @ Tue, 13 Aug 2019 01:34:22: 28000000 INFO @ Tue, 13 Aug 2019 01:34:25: 28000000 INFO @ Tue, 13 Aug 2019 01:34:26: 28000000 INFO @ Tue, 13 Aug 2019 01:34:30: 29000000 INFO @ Tue, 13 Aug 2019 01:34:33: 29000000 INFO @ Tue, 13 Aug 2019 01:34:34: 29000000 INFO @ Tue, 13 Aug 2019 01:34:38: 30000000 INFO @ Tue, 13 Aug 2019 01:34:41: 30000000 INFO @ Tue, 13 Aug 2019 01:34:42: 30000000 INFO @ Tue, 13 Aug 2019 01:34:46: 31000000 INFO @ Tue, 13 Aug 2019 01:34:49: 31000000 INFO @ Tue, 13 Aug 2019 01:34:50: 31000000 INFO @ Tue, 13 Aug 2019 01:34:54: 32000000 INFO @ Tue, 13 Aug 2019 01:34:57: 32000000 INFO @ Tue, 13 Aug 2019 01:34:58: 32000000 INFO @ Tue, 13 Aug 2019 01:35:01: 33000000 INFO @ Tue, 13 Aug 2019 01:35:05: 33000000 INFO @ Tue, 13 Aug 2019 01:35:06: 33000000 INFO @ Tue, 13 Aug 2019 01:35:09: 34000000 INFO @ Tue, 13 Aug 2019 01:35:13: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 01:35:13: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 01:35:13: #1 total tags in treatment: 15600065 INFO @ Tue, 13 Aug 2019 01:35:13: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:35:13: #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 01:35:13: 34000000 INFO @ Tue, 13 Aug 2019 01:35:13: #1 tags after filtering in treatment: 12878821 INFO @ Tue, 13 Aug 2019 01:35:13: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 13 Aug 2019 01:35:13: #1 finished! INFO @ Tue, 13 Aug 2019 01:35:13: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:35:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:35:14: 34000000 INFO @ Tue, 13 Aug 2019 01:35:14: #2 number of paired peaks: 272 WARNING @ Tue, 13 Aug 2019 01:35:14: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Tue, 13 Aug 2019 01:35:14: start model_add_line... INFO @ Tue, 13 Aug 2019 01:35:14: start X-correlation... INFO @ Tue, 13 Aug 2019 01:35:14: end of X-cor INFO @ Tue, 13 Aug 2019 01:35:14: #2 finished! INFO @ Tue, 13 Aug 2019 01:35:14: #2 predicted fragment length is 109 bps INFO @ Tue, 13 Aug 2019 01:35:14: #2 alternative fragment length(s) may be 1,65,109 bps INFO @ Tue, 13 Aug 2019 01:35:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.05_model.r INFO @ Tue, 13 Aug 2019 01:35:14: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:35:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:35:16: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 01:35:16: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 01:35:16: #1 total tags in treatment: 15600065 INFO @ Tue, 13 Aug 2019 01:35:16: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:35:16: #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 01:35:17: #1 tags after filtering in treatment: 12878821 INFO @ Tue, 13 Aug 2019 01:35:17: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 13 Aug 2019 01:35:17: #1 finished! INFO @ Tue, 13 Aug 2019 01:35:17: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:35:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:35:17: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 01:35:17: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 01:35:17: #1 total tags in treatment: 15600065 INFO @ Tue, 13 Aug 2019 01:35:17: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:35:17: #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 01:35:18: #1 tags after filtering in treatment: 12878821 INFO @ Tue, 13 Aug 2019 01:35:18: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 13 Aug 2019 01:35:18: #1 finished! INFO @ Tue, 13 Aug 2019 01:35:18: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:35:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:35:18: #2 number of paired peaks: 272 WARNING @ Tue, 13 Aug 2019 01:35:18: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Tue, 13 Aug 2019 01:35:18: start model_add_line... INFO @ Tue, 13 Aug 2019 01:35:18: start X-correlation... INFO @ Tue, 13 Aug 2019 01:35:18: end of X-cor INFO @ Tue, 13 Aug 2019 01:35:18: #2 finished! INFO @ Tue, 13 Aug 2019 01:35:18: #2 predicted fragment length is 109 bps INFO @ Tue, 13 Aug 2019 01:35:18: #2 alternative fragment length(s) may be 1,65,109 bps INFO @ Tue, 13 Aug 2019 01:35:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.10_model.r INFO @ Tue, 13 Aug 2019 01:35:18: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:35:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:35:19: #2 number of paired peaks: 272 WARNING @ Tue, 13 Aug 2019 01:35:19: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Tue, 13 Aug 2019 01:35:19: start model_add_line... INFO @ Tue, 13 Aug 2019 01:35:19: start X-correlation... INFO @ Tue, 13 Aug 2019 01:35:19: end of X-cor INFO @ Tue, 13 Aug 2019 01:35:19: #2 finished! INFO @ Tue, 13 Aug 2019 01:35:19: #2 predicted fragment length is 109 bps INFO @ Tue, 13 Aug 2019 01:35:19: #2 alternative fragment length(s) may be 1,65,109 bps INFO @ Tue, 13 Aug 2019 01:35:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.20_model.r INFO @ Tue, 13 Aug 2019 01:35:19: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:35:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:35:49: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:35:53: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:35:54: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:36:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.05_peaks.xls INFO @ Tue, 13 Aug 2019 01:36:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:36:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.05_summits.bed INFO @ Tue, 13 Aug 2019 01:36:07: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2251 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 01:36:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.10_peaks.xls INFO @ Tue, 13 Aug 2019 01:36:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:36:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.10_summits.bed INFO @ Tue, 13 Aug 2019 01:36:10: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (553 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 01:36:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.20_peaks.xls INFO @ Tue, 13 Aug 2019 01:36:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:36:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5865773/SRX5865773.20_summits.bed INFO @ Tue, 13 Aug 2019 01:36:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (213 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。