Job ID = 1294918 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T01:40:25 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' 2019-06-03T01:40:25 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/traces/sra11/SRR/000849/SRR870178' 2019-06-03T01:40:29 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' 2019-06-03T01:40:29 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/traces/sra11/SRR/000849/SRR870178' 2019-06-03T01:40:29 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR870178' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T01:40:29 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 14,011,618 reads read : 14,011,618 reads written : 14,011,618 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: 00:03:41 14011618 reads; of these: 14011618 (100.00%) were unpaired; of these: 1086367 (7.75%) aligned 0 times 11928880 (85.14%) aligned exactly 1 time 996371 (7.11%) aligned >1 times 92.25% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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 8 files... [bam_rmdupse_core] 1066722 / 12925251 = 0.0825 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 11:03:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.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 11:03:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:03:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:03:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.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 11:03:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:03:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:03:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.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 11:03:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:03:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:03:45: 1000000 INFO @ Mon, 03 Jun 2019 11:03:45: 1000000 INFO @ Mon, 03 Jun 2019 11:03:46: 1000000 INFO @ Mon, 03 Jun 2019 11:03:55: 2000000 INFO @ Mon, 03 Jun 2019 11:03:56: 2000000 INFO @ Mon, 03 Jun 2019 11:03:57: 2000000 INFO @ Mon, 03 Jun 2019 11:04:06: 3000000 INFO @ Mon, 03 Jun 2019 11:04:07: 3000000 INFO @ Mon, 03 Jun 2019 11:04:08: 3000000 INFO @ Mon, 03 Jun 2019 11:04:16: 4000000 INFO @ Mon, 03 Jun 2019 11:04:18: 4000000 INFO @ Mon, 03 Jun 2019 11:04:19: 4000000 INFO @ Mon, 03 Jun 2019 11:04:26: 5000000 INFO @ Mon, 03 Jun 2019 11:04:30: 5000000 INFO @ Mon, 03 Jun 2019 11:04:31: 5000000 INFO @ Mon, 03 Jun 2019 11:04:36: 6000000 INFO @ Mon, 03 Jun 2019 11:04:41: 6000000 INFO @ Mon, 03 Jun 2019 11:04:42: 6000000 INFO @ Mon, 03 Jun 2019 11:04:47: 7000000 INFO @ Mon, 03 Jun 2019 11:04:51: 7000000 INFO @ Mon, 03 Jun 2019 11:04:53: 7000000 INFO @ Mon, 03 Jun 2019 11:04:58: 8000000 INFO @ Mon, 03 Jun 2019 11:05:01: 8000000 INFO @ Mon, 03 Jun 2019 11:05:04: 8000000 INFO @ Mon, 03 Jun 2019 11:05:08: 9000000 INFO @ Mon, 03 Jun 2019 11:05:12: 9000000 INFO @ Mon, 03 Jun 2019 11:05:14: 9000000 INFO @ Mon, 03 Jun 2019 11:05:18: 10000000 INFO @ Mon, 03 Jun 2019 11:05:22: 10000000 INFO @ Mon, 03 Jun 2019 11:05:26: 10000000 INFO @ Mon, 03 Jun 2019 11:05:29: 11000000 INFO @ Mon, 03 Jun 2019 11:05:33: 11000000 INFO @ Mon, 03 Jun 2019 11:05:37: 11000000 INFO @ Mon, 03 Jun 2019 11:05:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:05:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:05:37: #1 total tags in treatment: 11858529 INFO @ Mon, 03 Jun 2019 11:05:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:05:37: #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 11:05:38: #1 tags after filtering in treatment: 11858529 INFO @ Mon, 03 Jun 2019 11:05:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:05:38: #1 finished! INFO @ Mon, 03 Jun 2019 11:05:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:05:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:05:39: #2 number of paired peaks: 334 WARNING @ Mon, 03 Jun 2019 11:05:39: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Mon, 03 Jun 2019 11:05:39: start model_add_line... INFO @ Mon, 03 Jun 2019 11:05:39: start X-correlation... INFO @ Mon, 03 Jun 2019 11:05:39: end of X-cor INFO @ Mon, 03 Jun 2019 11:05:39: #2 finished! INFO @ Mon, 03 Jun 2019 11:05:39: #2 predicted fragment length is 200 bps INFO @ Mon, 03 Jun 2019 11:05:39: #2 alternative fragment length(s) may be 200 bps INFO @ Mon, 03 Jun 2019 11:05:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.10_model.r INFO @ Mon, 03 Jun 2019 11:05:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:05:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:05:42: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:05:42: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:05:42: #1 total tags in treatment: 11858529 INFO @ Mon, 03 Jun 2019 11:05:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:05:42: #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 11:05:42: #1 tags after filtering in treatment: 11858529 INFO @ Mon, 03 Jun 2019 11:05:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:05:42: #1 finished! INFO @ Mon, 03 Jun 2019 11:05:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:05:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:05:43: #2 number of paired peaks: 334 WARNING @ Mon, 03 Jun 2019 11:05:43: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Mon, 03 Jun 2019 11:05:43: start model_add_line... INFO @ Mon, 03 Jun 2019 11:05:43: start X-correlation... INFO @ Mon, 03 Jun 2019 11:05:43: end of X-cor INFO @ Mon, 03 Jun 2019 11:05:43: #2 finished! INFO @ Mon, 03 Jun 2019 11:05:43: #2 predicted fragment length is 200 bps INFO @ Mon, 03 Jun 2019 11:05:43: #2 alternative fragment length(s) may be 200 bps INFO @ Mon, 03 Jun 2019 11:05:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.05_model.r INFO @ Mon, 03 Jun 2019 11:05:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:05:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:05:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:05:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:05:46: #1 total tags in treatment: 11858529 INFO @ Mon, 03 Jun 2019 11:05:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:05:46: #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 11:05:46: #1 tags after filtering in treatment: 11858529 INFO @ Mon, 03 Jun 2019 11:05:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:05:46: #1 finished! INFO @ Mon, 03 Jun 2019 11:05:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:05:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:05:47: #2 number of paired peaks: 334 WARNING @ Mon, 03 Jun 2019 11:05:47: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Mon, 03 Jun 2019 11:05:47: start model_add_line... INFO @ Mon, 03 Jun 2019 11:05:47: start X-correlation... INFO @ Mon, 03 Jun 2019 11:05:47: end of X-cor INFO @ Mon, 03 Jun 2019 11:05:47: #2 finished! INFO @ Mon, 03 Jun 2019 11:05:47: #2 predicted fragment length is 200 bps INFO @ Mon, 03 Jun 2019 11:05:47: #2 alternative fragment length(s) may be 200 bps INFO @ Mon, 03 Jun 2019 11:05:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.20_model.r INFO @ Mon, 03 Jun 2019 11:05:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:05:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:06:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:06:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:06:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:06:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:06:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:06:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.10_summits.bed INFO @ Mon, 03 Jun 2019 11:06:31: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2019 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:06:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:06:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:06:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.05_summits.bed INFO @ Mon, 03 Jun 2019 11:06:35: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4264 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:06:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:06:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:06:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287989/SRX287989.20_summits.bed INFO @ Mon, 03 Jun 2019 11:06:40: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (532 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。