Job ID = 1299411 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T09:05:40 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' 2019-06-03T09:05:40 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/sra20/SRR/001146/SRR1174430' 2019-06-03T09:05:40 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR1174430' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T09:05:40 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T09:39:31 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 ) 2019-06-03T09:53:42 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 : 29,965,807 reads read : 59,931,614 reads written : 59,931,614 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: 01:03:44 29965807 reads; of these: 29965807 (100.00%) were paired; of these: 10671674 (35.61%) aligned concordantly 0 times 13570795 (45.29%) aligned concordantly exactly 1 time 5723338 (19.10%) aligned concordantly >1 times ---- 10671674 pairs aligned concordantly 0 times; of these: 463149 (4.34%) aligned discordantly 1 time ---- 10208525 pairs aligned 0 times concordantly or discordantly; of these: 20417050 mates make up the pairs; of these: 19342995 (94.74%) aligned 0 times 591958 (2.90%) aligned exactly 1 time 482097 (2.36%) aligned >1 times 67.72% overall alignment rate Time searching: 01:03:44 Overall time: 01:03:44 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] 10224192 / 19732764 = 0.5181 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 20:24:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.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 20:24:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:24:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:24:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.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 20:24:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:24:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:24:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.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 20:24:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:24:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:24:46: 1000000 INFO @ Mon, 03 Jun 2019 20:24:47: 1000000 INFO @ Mon, 03 Jun 2019 20:24:48: 1000000 INFO @ Mon, 03 Jun 2019 20:24:54: 2000000 INFO @ Mon, 03 Jun 2019 20:24:56: 2000000 INFO @ Mon, 03 Jun 2019 20:24:57: 2000000 INFO @ Mon, 03 Jun 2019 20:25:02: 3000000 INFO @ Mon, 03 Jun 2019 20:25:04: 3000000 INFO @ Mon, 03 Jun 2019 20:25:06: 3000000 INFO @ Mon, 03 Jun 2019 20:25:09: 4000000 INFO @ Mon, 03 Jun 2019 20:25:13: 4000000 INFO @ Mon, 03 Jun 2019 20:25:15: 4000000 INFO @ Mon, 03 Jun 2019 20:25:17: 5000000 INFO @ Mon, 03 Jun 2019 20:25:22: 5000000 INFO @ Mon, 03 Jun 2019 20:25:25: 5000000 INFO @ Mon, 03 Jun 2019 20:25:25: 6000000 INFO @ Mon, 03 Jun 2019 20:25:31: 6000000 INFO @ Mon, 03 Jun 2019 20:25:33: 7000000 INFO @ Mon, 03 Jun 2019 20:25:34: 6000000 INFO @ Mon, 03 Jun 2019 20:25:39: 7000000 INFO @ Mon, 03 Jun 2019 20:25:40: 8000000 INFO @ Mon, 03 Jun 2019 20:25:43: 7000000 INFO @ Mon, 03 Jun 2019 20:25:48: 8000000 INFO @ Mon, 03 Jun 2019 20:25:48: 9000000 INFO @ Mon, 03 Jun 2019 20:25:53: 8000000 INFO @ Mon, 03 Jun 2019 20:25:56: 10000000 INFO @ Mon, 03 Jun 2019 20:25:57: 9000000 INFO @ Mon, 03 Jun 2019 20:26:02: 9000000 INFO @ Mon, 03 Jun 2019 20:26:04: 11000000 INFO @ Mon, 03 Jun 2019 20:26:05: 10000000 INFO @ Mon, 03 Jun 2019 20:26:11: 10000000 INFO @ Mon, 03 Jun 2019 20:26:12: 12000000 INFO @ Mon, 03 Jun 2019 20:26:14: 11000000 INFO @ Mon, 03 Jun 2019 20:26:20: 11000000 INFO @ Mon, 03 Jun 2019 20:26:21: 13000000 INFO @ Mon, 03 Jun 2019 20:26:22: 12000000 INFO @ Mon, 03 Jun 2019 20:26:29: 12000000 INFO @ Mon, 03 Jun 2019 20:26:29: 14000000 INFO @ Mon, 03 Jun 2019 20:26:31: 13000000 INFO @ Mon, 03 Jun 2019 20:26:38: 15000000 INFO @ Mon, 03 Jun 2019 20:26:38: 13000000 INFO @ Mon, 03 Jun 2019 20:26:40: 14000000 INFO @ Mon, 03 Jun 2019 20:26:46: 16000000 INFO @ Mon, 03 Jun 2019 20:26:48: 14000000 INFO @ Mon, 03 Jun 2019 20:26:49: 15000000 INFO @ Mon, 03 Jun 2019 20:26:54: 17000000 INFO @ Mon, 03 Jun 2019 20:26:57: 16000000 INFO @ Mon, 03 Jun 2019 20:26:58: 15000000 INFO @ Mon, 03 Jun 2019 20:27:03: 18000000 INFO @ Mon, 03 Jun 2019 20:27:06: 17000000 INFO @ Mon, 03 Jun 2019 20:27:07: 16000000 INFO @ Mon, 03 Jun 2019 20:27:10: 19000000 INFO @ Mon, 03 Jun 2019 20:27:14: 18000000 INFO @ Mon, 03 Jun 2019 20:27:14: 17000000 INFO @ Mon, 03 Jun 2019 20:27:18: 20000000 INFO @ Mon, 03 Jun 2019 20:27:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:27:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:27:19: #1 total tags in treatment: 9223358 INFO @ Mon, 03 Jun 2019 20:27:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:27:19: #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 20:27:19: #1 tags after filtering in treatment: 8572847 INFO @ Mon, 03 Jun 2019 20:27:19: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 20:27:19: #1 finished! INFO @ Mon, 03 Jun 2019 20:27:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:27:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:27:20: #2 number of paired peaks: 571 WARNING @ Mon, 03 Jun 2019 20:27:20: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Mon, 03 Jun 2019 20:27:20: start model_add_line... INFO @ Mon, 03 Jun 2019 20:27:20: start X-correlation... INFO @ Mon, 03 Jun 2019 20:27:20: end of X-cor INFO @ Mon, 03 Jun 2019 20:27:20: #2 finished! INFO @ Mon, 03 Jun 2019 20:27:20: #2 predicted fragment length is 108 bps INFO @ Mon, 03 Jun 2019 20:27:20: #2 alternative fragment length(s) may be 108 bps INFO @ Mon, 03 Jun 2019 20:27:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.05_model.r INFO @ Mon, 03 Jun 2019 20:27:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:27:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:27:22: 19000000 INFO @ Mon, 03 Jun 2019 20:27:22: 18000000 INFO @ Mon, 03 Jun 2019 20:27:29: 19000000 INFO @ Mon, 03 Jun 2019 20:27:30: 20000000 INFO @ Mon, 03 Jun 2019 20:27:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:27:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:27:31: #1 total tags in treatment: 9223358 INFO @ Mon, 03 Jun 2019 20:27:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:27:31: #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 20:27:31: #1 tags after filtering in treatment: 8572847 INFO @ Mon, 03 Jun 2019 20:27:31: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 20:27:31: #1 finished! INFO @ Mon, 03 Jun 2019 20:27:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:27:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:27:32: #2 number of paired peaks: 571 WARNING @ Mon, 03 Jun 2019 20:27:32: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Mon, 03 Jun 2019 20:27:32: start model_add_line... INFO @ Mon, 03 Jun 2019 20:27:32: start X-correlation... INFO @ Mon, 03 Jun 2019 20:27:32: end of X-cor INFO @ Mon, 03 Jun 2019 20:27:32: #2 finished! INFO @ Mon, 03 Jun 2019 20:27:32: #2 predicted fragment length is 108 bps INFO @ Mon, 03 Jun 2019 20:27:32: #2 alternative fragment length(s) may be 108 bps INFO @ Mon, 03 Jun 2019 20:27:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.10_model.r INFO @ Mon, 03 Jun 2019 20:27:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:27:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:27:37: 20000000 INFO @ Mon, 03 Jun 2019 20:27:38: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:27:38: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:27:38: #1 total tags in treatment: 9223358 INFO @ Mon, 03 Jun 2019 20:27:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:27:38: #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 20:27:38: #1 tags after filtering in treatment: 8572847 INFO @ Mon, 03 Jun 2019 20:27:38: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 20:27:38: #1 finished! INFO @ Mon, 03 Jun 2019 20:27:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:27:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:27:39: #2 number of paired peaks: 571 WARNING @ Mon, 03 Jun 2019 20:27:39: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Mon, 03 Jun 2019 20:27:39: start model_add_line... INFO @ Mon, 03 Jun 2019 20:27:39: start X-correlation... INFO @ Mon, 03 Jun 2019 20:27:39: end of X-cor INFO @ Mon, 03 Jun 2019 20:27:39: #2 finished! INFO @ Mon, 03 Jun 2019 20:27:39: #2 predicted fragment length is 108 bps INFO @ Mon, 03 Jun 2019 20:27:39: #2 alternative fragment length(s) may be 108 bps INFO @ Mon, 03 Jun 2019 20:27:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.20_model.r INFO @ Mon, 03 Jun 2019 20:27:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:27:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:27:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:27:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:27:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:27:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:27:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.05_summits.bed INFO @ Mon, 03 Jun 2019 20:27:59: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5322 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:28:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:28:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:28:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:28:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.10_summits.bed INFO @ Mon, 03 Jun 2019 20:28:10: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2174 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:28:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:28:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:28:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474577/SRX474577.20_summits.bed INFO @ Mon, 03 Jun 2019 20:28:18: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (787 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。