Job ID = 1295462 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T04:50:31 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' 2019-06-03T04:50:31 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/SRR6292555/SRR6292555.1' 2019-06-03T04:50:31 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR6292555' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T04:50:32 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 25,172,797 reads read : 50,345,594 reads written : 50,345,594 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: 01:06:47 25172797 reads; of these: 25172797 (100.00%) were paired; of these: 2870219 (11.40%) aligned concordantly 0 times 14759522 (58.63%) aligned concordantly exactly 1 time 7543056 (29.97%) aligned concordantly >1 times ---- 2870219 pairs aligned concordantly 0 times; of these: 155730 (5.43%) aligned discordantly 1 time ---- 2714489 pairs aligned 0 times concordantly or discordantly; of these: 5428978 mates make up the pairs; of these: 4160444 (76.63%) aligned 0 times 646255 (11.90%) aligned exactly 1 time 622279 (11.46%) aligned >1 times 91.74% overall alignment rate Time searching: 01:06:47 Overall time: 01:06:47 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] 1371733 / 22383002 = 0.0613 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 15:34:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.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 15:34:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:34:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:34:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.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 15:34:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:34:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:34:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.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 15:34:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:34:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:34:37: 1000000 INFO @ Mon, 03 Jun 2019 15:34:38: 1000000 INFO @ Mon, 03 Jun 2019 15:34:38: 1000000 INFO @ Mon, 03 Jun 2019 15:34:43: 2000000 INFO @ Mon, 03 Jun 2019 15:34:45: 2000000 INFO @ Mon, 03 Jun 2019 15:34:45: 2000000 INFO @ Mon, 03 Jun 2019 15:34:50: 3000000 INFO @ Mon, 03 Jun 2019 15:34:53: 3000000 INFO @ Mon, 03 Jun 2019 15:34:53: 3000000 INFO @ Mon, 03 Jun 2019 15:34:56: 4000000 INFO @ Mon, 03 Jun 2019 15:35:01: 4000000 INFO @ Mon, 03 Jun 2019 15:35:01: 4000000 INFO @ Mon, 03 Jun 2019 15:35:02: 5000000 INFO @ Mon, 03 Jun 2019 15:35:09: 5000000 INFO @ Mon, 03 Jun 2019 15:35:09: 6000000 INFO @ Mon, 03 Jun 2019 15:35:09: 5000000 INFO @ Mon, 03 Jun 2019 15:35:15: 7000000 INFO @ Mon, 03 Jun 2019 15:35:16: 6000000 INFO @ Mon, 03 Jun 2019 15:35:17: 6000000 INFO @ Mon, 03 Jun 2019 15:35:21: 8000000 INFO @ Mon, 03 Jun 2019 15:35:24: 7000000 INFO @ Mon, 03 Jun 2019 15:35:24: 7000000 INFO @ Mon, 03 Jun 2019 15:35:27: 9000000 INFO @ Mon, 03 Jun 2019 15:35:32: 8000000 INFO @ Mon, 03 Jun 2019 15:35:32: 8000000 INFO @ Mon, 03 Jun 2019 15:35:34: 10000000 INFO @ Mon, 03 Jun 2019 15:35:39: 9000000 INFO @ Mon, 03 Jun 2019 15:35:40: 9000000 INFO @ Mon, 03 Jun 2019 15:35:40: 11000000 INFO @ Mon, 03 Jun 2019 15:35:47: 12000000 INFO @ Mon, 03 Jun 2019 15:35:47: 10000000 INFO @ Mon, 03 Jun 2019 15:35:48: 10000000 INFO @ Mon, 03 Jun 2019 15:35:53: 13000000 INFO @ Mon, 03 Jun 2019 15:35:55: 11000000 INFO @ Mon, 03 Jun 2019 15:35:56: 11000000 INFO @ Mon, 03 Jun 2019 15:35:59: 14000000 INFO @ Mon, 03 Jun 2019 15:36:02: 12000000 INFO @ Mon, 03 Jun 2019 15:36:03: 12000000 INFO @ Mon, 03 Jun 2019 15:36:06: 15000000 INFO @ Mon, 03 Jun 2019 15:36:10: 13000000 INFO @ Mon, 03 Jun 2019 15:36:11: 13000000 INFO @ Mon, 03 Jun 2019 15:36:12: 16000000 INFO @ Mon, 03 Jun 2019 15:36:18: 14000000 INFO @ Mon, 03 Jun 2019 15:36:19: 17000000 INFO @ Mon, 03 Jun 2019 15:36:19: 14000000 INFO @ Mon, 03 Jun 2019 15:36:25: 15000000 INFO @ Mon, 03 Jun 2019 15:36:25: 18000000 INFO @ Mon, 03 Jun 2019 15:36:27: 15000000 INFO @ Mon, 03 Jun 2019 15:36:32: 19000000 INFO @ Mon, 03 Jun 2019 15:36:33: 16000000 INFO @ Mon, 03 Jun 2019 15:36:34: 16000000 INFO @ Mon, 03 Jun 2019 15:36:38: 20000000 INFO @ Mon, 03 Jun 2019 15:36:40: 17000000 INFO @ Mon, 03 Jun 2019 15:36:42: 17000000 INFO @ Mon, 03 Jun 2019 15:36:44: 21000000 INFO @ Mon, 03 Jun 2019 15:36:47: 18000000 INFO @ Mon, 03 Jun 2019 15:36:49: 18000000 INFO @ Mon, 03 Jun 2019 15:36:51: 22000000 INFO @ Mon, 03 Jun 2019 15:36:55: 19000000 INFO @ Mon, 03 Jun 2019 15:36:57: 19000000 INFO @ Mon, 03 Jun 2019 15:36:57: 23000000 INFO @ Mon, 03 Jun 2019 15:37:02: 20000000 INFO @ Mon, 03 Jun 2019 15:37:03: 24000000 INFO @ Mon, 03 Jun 2019 15:37:04: 20000000 INFO @ Mon, 03 Jun 2019 15:37:09: 21000000 INFO @ Mon, 03 Jun 2019 15:37:10: 25000000 INFO @ Mon, 03 Jun 2019 15:37:12: 21000000 INFO @ Mon, 03 Jun 2019 15:37:17: 22000000 INFO @ Mon, 03 Jun 2019 15:37:17: 26000000 INFO @ Mon, 03 Jun 2019 15:37:19: 22000000 INFO @ Mon, 03 Jun 2019 15:37:23: 23000000 INFO @ Mon, 03 Jun 2019 15:37:24: 27000000 INFO @ Mon, 03 Jun 2019 15:37:26: 23000000 INFO @ Mon, 03 Jun 2019 15:37:31: 28000000 INFO @ Mon, 03 Jun 2019 15:37:31: 24000000 INFO @ Mon, 03 Jun 2019 15:37:34: 24000000 INFO @ Mon, 03 Jun 2019 15:37:37: 29000000 INFO @ Mon, 03 Jun 2019 15:37:38: 25000000 INFO @ Mon, 03 Jun 2019 15:37:41: 25000000 INFO @ Mon, 03 Jun 2019 15:37:43: 30000000 INFO @ Mon, 03 Jun 2019 15:37:44: 26000000 INFO @ Mon, 03 Jun 2019 15:37:47: 26000000 INFO @ Mon, 03 Jun 2019 15:37:50: 31000000 INFO @ Mon, 03 Jun 2019 15:37:51: 27000000 INFO @ Mon, 03 Jun 2019 15:37:54: 27000000 INFO @ Mon, 03 Jun 2019 15:37:56: 32000000 INFO @ Mon, 03 Jun 2019 15:37:58: 28000000 INFO @ Mon, 03 Jun 2019 15:38:02: 28000000 INFO @ Mon, 03 Jun 2019 15:38:02: 33000000 INFO @ Mon, 03 Jun 2019 15:38:05: 29000000 INFO @ Mon, 03 Jun 2019 15:38:08: 34000000 INFO @ Mon, 03 Jun 2019 15:38:09: 29000000 INFO @ Mon, 03 Jun 2019 15:38:13: 30000000 INFO @ Mon, 03 Jun 2019 15:38:15: 35000000 INFO @ Mon, 03 Jun 2019 15:38:17: 30000000 INFO @ Mon, 03 Jun 2019 15:38:20: 31000000 INFO @ Mon, 03 Jun 2019 15:38:21: 36000000 INFO @ Mon, 03 Jun 2019 15:38:25: 31000000 INFO @ Mon, 03 Jun 2019 15:38:27: 37000000 INFO @ Mon, 03 Jun 2019 15:38:28: 32000000 INFO @ Mon, 03 Jun 2019 15:38:32: 32000000 INFO @ Mon, 03 Jun 2019 15:38:34: 38000000 INFO @ Mon, 03 Jun 2019 15:38:35: 33000000 INFO @ Mon, 03 Jun 2019 15:38:39: 33000000 INFO @ Mon, 03 Jun 2019 15:38:40: 39000000 INFO @ Mon, 03 Jun 2019 15:38:42: 34000000 INFO @ Mon, 03 Jun 2019 15:38:46: 40000000 INFO @ Mon, 03 Jun 2019 15:38:47: 34000000 INFO @ Mon, 03 Jun 2019 15:38:49: 35000000 INFO @ Mon, 03 Jun 2019 15:38:52: 41000000 INFO @ Mon, 03 Jun 2019 15:38:54: 35000000 INFO @ Mon, 03 Jun 2019 15:38:57: 36000000 INFO @ Mon, 03 Jun 2019 15:38:59: 42000000 INFO @ Mon, 03 Jun 2019 15:39:02: 36000000 INFO @ Mon, 03 Jun 2019 15:39:04: 37000000 INFO @ Mon, 03 Jun 2019 15:39:05: 43000000 INFO @ Mon, 03 Jun 2019 15:39:08: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:39:08: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:39:08: #1 total tags in treatment: 20932117 INFO @ Mon, 03 Jun 2019 15:39:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:39:08: #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 15:39:09: #1 tags after filtering in treatment: 18845030 INFO @ Mon, 03 Jun 2019 15:39:09: #1 Redundant rate of treatment: 0.10 INFO @ Mon, 03 Jun 2019 15:39:09: #1 finished! INFO @ Mon, 03 Jun 2019 15:39:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:39:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:39:09: 37000000 INFO @ Mon, 03 Jun 2019 15:39:10: #2 number of paired peaks: 1192 INFO @ Mon, 03 Jun 2019 15:39:10: start model_add_line... INFO @ Mon, 03 Jun 2019 15:39:11: start X-correlation... INFO @ Mon, 03 Jun 2019 15:39:11: end of X-cor INFO @ Mon, 03 Jun 2019 15:39:11: #2 finished! INFO @ Mon, 03 Jun 2019 15:39:11: #2 predicted fragment length is 159 bps INFO @ Mon, 03 Jun 2019 15:39:11: #2 alternative fragment length(s) may be 4,159 bps INFO @ Mon, 03 Jun 2019 15:39:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.10_model.r INFO @ Mon, 03 Jun 2019 15:39:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:39:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:39:11: 38000000 INFO @ Mon, 03 Jun 2019 15:39:17: 38000000 INFO @ Mon, 03 Jun 2019 15:39:19: 39000000 INFO @ Mon, 03 Jun 2019 15:39:24: 39000000 INFO @ Mon, 03 Jun 2019 15:39:26: 40000000 INFO @ Mon, 03 Jun 2019 15:39:31: 40000000 INFO @ Mon, 03 Jun 2019 15:39:33: 41000000 INFO @ Mon, 03 Jun 2019 15:39:39: 41000000 INFO @ Mon, 03 Jun 2019 15:39:41: 42000000 INFO @ Mon, 03 Jun 2019 15:39:46: 42000000 INFO @ Mon, 03 Jun 2019 15:39:48: 43000000 INFO @ Mon, 03 Jun 2019 15:39:51: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:39:51: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:39:51: #1 total tags in treatment: 20932117 INFO @ Mon, 03 Jun 2019 15:39:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:39:51: #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 15:39:52: #1 tags after filtering in treatment: 18845030 INFO @ Mon, 03 Jun 2019 15:39:52: #1 Redundant rate of treatment: 0.10 INFO @ Mon, 03 Jun 2019 15:39:52: #1 finished! INFO @ Mon, 03 Jun 2019 15:39:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:39:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:39:54: #2 number of paired peaks: 1192 INFO @ Mon, 03 Jun 2019 15:39:54: start model_add_line... INFO @ Mon, 03 Jun 2019 15:39:54: start X-correlation... INFO @ Mon, 03 Jun 2019 15:39:54: end of X-cor INFO @ Mon, 03 Jun 2019 15:39:54: #2 finished! INFO @ Mon, 03 Jun 2019 15:39:54: #2 predicted fragment length is 159 bps INFO @ Mon, 03 Jun 2019 15:39:54: #2 alternative fragment length(s) may be 4,159 bps INFO @ Mon, 03 Jun 2019 15:39:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.05_model.r INFO @ Mon, 03 Jun 2019 15:39:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:39:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:39:54: 43000000 INFO @ Mon, 03 Jun 2019 15:39:57: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:39:57: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:39:57: #1 total tags in treatment: 20932117 INFO @ Mon, 03 Jun 2019 15:39:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:39:57: #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 15:39:58: #1 tags after filtering in treatment: 18845030 INFO @ Mon, 03 Jun 2019 15:39:58: #1 Redundant rate of treatment: 0.10 INFO @ Mon, 03 Jun 2019 15:39:58: #1 finished! INFO @ Mon, 03 Jun 2019 15:39:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:39:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:40:00: #2 number of paired peaks: 1192 INFO @ Mon, 03 Jun 2019 15:40:00: start model_add_line... INFO @ Mon, 03 Jun 2019 15:40:00: start X-correlation... INFO @ Mon, 03 Jun 2019 15:40:00: end of X-cor INFO @ Mon, 03 Jun 2019 15:40:00: #2 finished! INFO @ Mon, 03 Jun 2019 15:40:00: #2 predicted fragment length is 159 bps INFO @ Mon, 03 Jun 2019 15:40:00: #2 alternative fragment length(s) may be 4,159 bps INFO @ Mon, 03 Jun 2019 15:40:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.20_model.r INFO @ Mon, 03 Jun 2019 15:40:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:40:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:40:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:40:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:40:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:40:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.10_summits.bed INFO @ Mon, 03 Jun 2019 15:40:29: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1954 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:40:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:40:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:41:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:41:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:41:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.05_summits.bed INFO @ Mon, 03 Jun 2019 15:41:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3126 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:41:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:41:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:41:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393666/SRX3393666.20_summits.bed INFO @ Mon, 03 Jun 2019 15:41:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1081 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。