Job ID = 1292888 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T11:55:55 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T11:55:55 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/sos/sra-pub-run-1/SRR8176703/SRR8176703.1' 2019-06-02T11:55:55 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR8176703', 'SEQUENCE', 'NAME' ).VDBManagerOpenDBRead() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 18,953,288 reads read : 37,906,576 reads written : 37,906,576 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: 00:21:03 18953288 reads; of these: 18953288 (100.00%) were paired; of these: 2421386 (12.78%) aligned concordantly 0 times 14046114 (74.11%) aligned concordantly exactly 1 time 2485788 (13.12%) aligned concordantly >1 times ---- 2421386 pairs aligned concordantly 0 times; of these: 1632114 (67.40%) aligned discordantly 1 time ---- 789272 pairs aligned 0 times concordantly or discordantly; of these: 1578544 mates make up the pairs; of these: 713072 (45.17%) aligned 0 times 437096 (27.69%) aligned exactly 1 time 428376 (27.14%) aligned >1 times 98.12% overall alignment rate Time searching: 00:21:03 Overall time: 00:21:03 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 284343 / 18149646 = 0.0157 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 @ Sun, 02 Jun 2019 21:42:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 21:42:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:42:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:42:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 21:42:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:42:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:42:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 21:42:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:42:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:42:14: 1000000 INFO @ Sun, 02 Jun 2019 21:42:16: 1000000 INFO @ Sun, 02 Jun 2019 21:42:16: 1000000 INFO @ Sun, 02 Jun 2019 21:42:22: 2000000 INFO @ Sun, 02 Jun 2019 21:42:27: 2000000 INFO @ Sun, 02 Jun 2019 21:42:27: 2000000 INFO @ Sun, 02 Jun 2019 21:42:30: 3000000 INFO @ Sun, 02 Jun 2019 21:42:36: 3000000 INFO @ Sun, 02 Jun 2019 21:42:37: 3000000 INFO @ Sun, 02 Jun 2019 21:42:37: 4000000 INFO @ Sun, 02 Jun 2019 21:42:44: 4000000 INFO @ Sun, 02 Jun 2019 21:42:45: 5000000 INFO @ Sun, 02 Jun 2019 21:42:47: 4000000 INFO @ Sun, 02 Jun 2019 21:42:52: 5000000 INFO @ Sun, 02 Jun 2019 21:42:53: 6000000 INFO @ Sun, 02 Jun 2019 21:42:57: 5000000 INFO @ Sun, 02 Jun 2019 21:43:01: 6000000 INFO @ Sun, 02 Jun 2019 21:43:02: 7000000 INFO @ Sun, 02 Jun 2019 21:43:08: 6000000 INFO @ Sun, 02 Jun 2019 21:43:10: 7000000 INFO @ Sun, 02 Jun 2019 21:43:10: 8000000 INFO @ Sun, 02 Jun 2019 21:43:19: 8000000 INFO @ Sun, 02 Jun 2019 21:43:19: 7000000 INFO @ Sun, 02 Jun 2019 21:43:19: 9000000 INFO @ Sun, 02 Jun 2019 21:43:27: 9000000 INFO @ Sun, 02 Jun 2019 21:43:27: 10000000 INFO @ Sun, 02 Jun 2019 21:43:29: 8000000 INFO @ Sun, 02 Jun 2019 21:43:35: 10000000 INFO @ Sun, 02 Jun 2019 21:43:36: 11000000 INFO @ Sun, 02 Jun 2019 21:43:39: 9000000 INFO @ Sun, 02 Jun 2019 21:43:43: 11000000 INFO @ Sun, 02 Jun 2019 21:43:44: 12000000 INFO @ Sun, 02 Jun 2019 21:43:49: 10000000 INFO @ Sun, 02 Jun 2019 21:43:51: 13000000 INFO @ Sun, 02 Jun 2019 21:43:52: 12000000 INFO @ Sun, 02 Jun 2019 21:43:59: 11000000 INFO @ Sun, 02 Jun 2019 21:43:59: 14000000 INFO @ Sun, 02 Jun 2019 21:44:00: 13000000 INFO @ Sun, 02 Jun 2019 21:44:07: 15000000 INFO @ Sun, 02 Jun 2019 21:44:08: 14000000 INFO @ Sun, 02 Jun 2019 21:44:08: 12000000 INFO @ Sun, 02 Jun 2019 21:44:15: 16000000 INFO @ Sun, 02 Jun 2019 21:44:16: 15000000 INFO @ Sun, 02 Jun 2019 21:44:18: 13000000 INFO @ Sun, 02 Jun 2019 21:44:23: 17000000 INFO @ Sun, 02 Jun 2019 21:44:24: 16000000 INFO @ Sun, 02 Jun 2019 21:44:28: 14000000 INFO @ Sun, 02 Jun 2019 21:44:30: 18000000 INFO @ Sun, 02 Jun 2019 21:44:32: 17000000 INFO @ Sun, 02 Jun 2019 21:44:37: 15000000 INFO @ Sun, 02 Jun 2019 21:44:38: 19000000 INFO @ Sun, 02 Jun 2019 21:44:40: 18000000 INFO @ Sun, 02 Jun 2019 21:44:46: 20000000 INFO @ Sun, 02 Jun 2019 21:44:47: 16000000 INFO @ Sun, 02 Jun 2019 21:44:49: 19000000 INFO @ Sun, 02 Jun 2019 21:44:54: 21000000 INFO @ Sun, 02 Jun 2019 21:44:57: 20000000 INFO @ Sun, 02 Jun 2019 21:44:57: 17000000 INFO @ Sun, 02 Jun 2019 21:45:02: 22000000 INFO @ Sun, 02 Jun 2019 21:45:05: 21000000 INFO @ Sun, 02 Jun 2019 21:45:07: 18000000 INFO @ Sun, 02 Jun 2019 21:45:10: 23000000 INFO @ Sun, 02 Jun 2019 21:45:13: 22000000 INFO @ Sun, 02 Jun 2019 21:45:17: 19000000 INFO @ Sun, 02 Jun 2019 21:45:18: 24000000 INFO @ Sun, 02 Jun 2019 21:45:21: 23000000 INFO @ Sun, 02 Jun 2019 21:45:25: 25000000 INFO @ Sun, 02 Jun 2019 21:45:26: 20000000 INFO @ Sun, 02 Jun 2019 21:45:29: 24000000 INFO @ Sun, 02 Jun 2019 21:45:33: 26000000 INFO @ Sun, 02 Jun 2019 21:45:36: 21000000 INFO @ Sun, 02 Jun 2019 21:45:37: 25000000 INFO @ Sun, 02 Jun 2019 21:45:41: 27000000 INFO @ Sun, 02 Jun 2019 21:45:46: 26000000 INFO @ Sun, 02 Jun 2019 21:45:46: 22000000 INFO @ Sun, 02 Jun 2019 21:45:49: 28000000 INFO @ Sun, 02 Jun 2019 21:45:54: 27000000 INFO @ Sun, 02 Jun 2019 21:45:56: 23000000 INFO @ Sun, 02 Jun 2019 21:45:56: 29000000 INFO @ Sun, 02 Jun 2019 21:46:02: 28000000 INFO @ Sun, 02 Jun 2019 21:46:04: 30000000 INFO @ Sun, 02 Jun 2019 21:46:06: 24000000 INFO @ Sun, 02 Jun 2019 21:46:10: 29000000 INFO @ Sun, 02 Jun 2019 21:46:12: 31000000 INFO @ Sun, 02 Jun 2019 21:46:16: 25000000 INFO @ Sun, 02 Jun 2019 21:46:18: 30000000 INFO @ Sun, 02 Jun 2019 21:46:20: 32000000 INFO @ Sun, 02 Jun 2019 21:46:26: 26000000 INFO @ Sun, 02 Jun 2019 21:46:26: 31000000 INFO @ Sun, 02 Jun 2019 21:46:27: 33000000 INFO @ Sun, 02 Jun 2019 21:46:34: 32000000 INFO @ Sun, 02 Jun 2019 21:46:35: 27000000 INFO @ Sun, 02 Jun 2019 21:46:35: 34000000 INFO @ Sun, 02 Jun 2019 21:46:42: 33000000 INFO @ Sun, 02 Jun 2019 21:46:43: 35000000 INFO @ Sun, 02 Jun 2019 21:46:44: 28000000 INFO @ Sun, 02 Jun 2019 21:46:50: 34000000 INFO @ Sun, 02 Jun 2019 21:46:51: 36000000 INFO @ Sun, 02 Jun 2019 21:46:54: 29000000 INFO @ Sun, 02 Jun 2019 21:46:56: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:46:56: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:46:56: #1 total tags in treatment: 16258296 INFO @ Sun, 02 Jun 2019 21:46:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:46:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:46:56: #1 tags after filtering in treatment: 14818675 INFO @ Sun, 02 Jun 2019 21:46:56: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 02 Jun 2019 21:46:56: #1 finished! INFO @ Sun, 02 Jun 2019 21:46:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:46:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:46:57: #2 number of paired peaks: 359 WARNING @ Sun, 02 Jun 2019 21:46:57: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Sun, 02 Jun 2019 21:46:57: start model_add_line... INFO @ Sun, 02 Jun 2019 21:46:57: start X-correlation... INFO @ Sun, 02 Jun 2019 21:46:57: end of X-cor INFO @ Sun, 02 Jun 2019 21:46:57: #2 finished! INFO @ Sun, 02 Jun 2019 21:46:57: #2 predicted fragment length is 146 bps INFO @ Sun, 02 Jun 2019 21:46:57: #2 alternative fragment length(s) may be 4,126,146 bps INFO @ Sun, 02 Jun 2019 21:46:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.20_model.r INFO @ Sun, 02 Jun 2019 21:46:57: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:46:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:46:58: 35000000 INFO @ Sun, 02 Jun 2019 21:47:03: 30000000 INFO @ Sun, 02 Jun 2019 21:47:06: 36000000 INFO @ Sun, 02 Jun 2019 21:47:11: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:47:11: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:47:11: #1 total tags in treatment: 16258296 INFO @ Sun, 02 Jun 2019 21:47:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:47:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:47:12: #1 tags after filtering in treatment: 14818675 INFO @ Sun, 02 Jun 2019 21:47:12: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 02 Jun 2019 21:47:12: #1 finished! INFO @ Sun, 02 Jun 2019 21:47:12: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:47:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:47:13: 31000000 INFO @ Sun, 02 Jun 2019 21:47:13: #2 number of paired peaks: 359 WARNING @ Sun, 02 Jun 2019 21:47:13: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Sun, 02 Jun 2019 21:47:13: start model_add_line... INFO @ Sun, 02 Jun 2019 21:47:13: start X-correlation... INFO @ Sun, 02 Jun 2019 21:47:13: end of X-cor INFO @ Sun, 02 Jun 2019 21:47:13: #2 finished! INFO @ Sun, 02 Jun 2019 21:47:13: #2 predicted fragment length is 146 bps INFO @ Sun, 02 Jun 2019 21:47:13: #2 alternative fragment length(s) may be 4,126,146 bps INFO @ Sun, 02 Jun 2019 21:47:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.05_model.r INFO @ Sun, 02 Jun 2019 21:47:13: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:47:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:47:22: 32000000 INFO @ Sun, 02 Jun 2019 21:47:31: 33000000 INFO @ Sun, 02 Jun 2019 21:47:36: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:47:40: 34000000 INFO @ Sun, 02 Jun 2019 21:47:49: 35000000 INFO @ Sun, 02 Jun 2019 21:47:52: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:47:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:47:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:47:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.20_summits.bed INFO @ Sun, 02 Jun 2019 21:47:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (213 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:47:58: 36000000 INFO @ Sun, 02 Jun 2019 21:48:04: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:48:04: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:48:04: #1 total tags in treatment: 16258296 INFO @ Sun, 02 Jun 2019 21:48:04: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:48:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:48:04: #1 tags after filtering in treatment: 14818675 INFO @ Sun, 02 Jun 2019 21:48:04: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 02 Jun 2019 21:48:04: #1 finished! INFO @ Sun, 02 Jun 2019 21:48:04: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:48:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:48:06: #2 number of paired peaks: 359 WARNING @ Sun, 02 Jun 2019 21:48:06: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Sun, 02 Jun 2019 21:48:06: start model_add_line... INFO @ Sun, 02 Jun 2019 21:48:06: start X-correlation... INFO @ Sun, 02 Jun 2019 21:48:06: end of X-cor INFO @ Sun, 02 Jun 2019 21:48:06: #2 finished! INFO @ Sun, 02 Jun 2019 21:48:06: #2 predicted fragment length is 146 bps INFO @ Sun, 02 Jun 2019 21:48:06: #2 alternative fragment length(s) may be 4,126,146 bps INFO @ Sun, 02 Jun 2019 21:48:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.10_model.r INFO @ Sun, 02 Jun 2019 21:48:06: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:48:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:48:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:48:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:48:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.05_summits.bed INFO @ Sun, 02 Jun 2019 21:48:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (438 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:48:44: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:49:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:49:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:49:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996818/SRX4996818.10_summits.bed INFO @ Sun, 02 Jun 2019 21:49:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (323 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。