Job ID = 1293943 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T18:25:27 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' 2019-06-02T18:25:27 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-2/SRR503390/SRR503390.1' 2019-06-02T18:25:32 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' 2019-06-02T18:25:32 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-2/SRR503390/SRR503390.1' 2019-06-02T18:25:32 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR503390' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T18:25:32 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 20,984,151 reads read : 41,968,302 reads written : 41,968,302 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: 01:23:53 20984151 reads; of these: 20984151 (100.00%) were paired; of these: 9023404 (43.00%) aligned concordantly 0 times 3221875 (15.35%) aligned concordantly exactly 1 time 8738872 (41.65%) aligned concordantly >1 times ---- 9023404 pairs aligned concordantly 0 times; of these: 227104 (2.52%) aligned discordantly 1 time ---- 8796300 pairs aligned 0 times concordantly or discordantly; of these: 17592600 mates make up the pairs; of these: 14576414 (82.86%) aligned 0 times 1876999 (10.67%) aligned exactly 1 time 1139187 (6.48%) aligned >1 times 65.27% overall alignment rate Time searching: 01:23:53 Overall time: 01:23:53 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 12 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] 1541081 / 11963066 = 0.1288 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 05:05:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.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 05:05:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:05:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:05:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.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 05:05:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:05:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:05:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.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 05:05:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:05:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:05:10: 1000000 INFO @ Mon, 03 Jun 2019 05:05:10: 1000000 INFO @ Mon, 03 Jun 2019 05:05:11: 1000000 INFO @ Mon, 03 Jun 2019 05:05:19: 2000000 INFO @ Mon, 03 Jun 2019 05:05:19: 2000000 INFO @ Mon, 03 Jun 2019 05:05:20: 2000000 INFO @ Mon, 03 Jun 2019 05:05:27: 3000000 INFO @ Mon, 03 Jun 2019 05:05:27: 3000000 INFO @ Mon, 03 Jun 2019 05:05:29: 3000000 INFO @ Mon, 03 Jun 2019 05:05:35: 4000000 INFO @ Mon, 03 Jun 2019 05:05:36: 4000000 INFO @ Mon, 03 Jun 2019 05:05:38: 4000000 INFO @ Mon, 03 Jun 2019 05:05:44: 5000000 INFO @ Mon, 03 Jun 2019 05:05:44: 5000000 INFO @ Mon, 03 Jun 2019 05:05:47: 5000000 INFO @ Mon, 03 Jun 2019 05:05:52: 6000000 INFO @ Mon, 03 Jun 2019 05:05:52: 6000000 INFO @ Mon, 03 Jun 2019 05:05:56: 6000000 INFO @ Mon, 03 Jun 2019 05:06:00: 7000000 INFO @ Mon, 03 Jun 2019 05:06:01: 7000000 INFO @ Mon, 03 Jun 2019 05:06:05: 7000000 INFO @ Mon, 03 Jun 2019 05:06:08: 8000000 INFO @ Mon, 03 Jun 2019 05:06:09: 8000000 INFO @ Mon, 03 Jun 2019 05:06:14: 8000000 INFO @ Mon, 03 Jun 2019 05:06:17: 9000000 INFO @ Mon, 03 Jun 2019 05:06:18: 9000000 INFO @ Mon, 03 Jun 2019 05:06:23: 9000000 INFO @ Mon, 03 Jun 2019 05:06:26: 10000000 INFO @ Mon, 03 Jun 2019 05:06:26: 10000000 INFO @ Mon, 03 Jun 2019 05:06:32: 10000000 INFO @ Mon, 03 Jun 2019 05:06:35: 11000000 INFO @ Mon, 03 Jun 2019 05:06:35: 11000000 INFO @ Mon, 03 Jun 2019 05:06:40: 11000000 INFO @ Mon, 03 Jun 2019 05:06:43: 12000000 INFO @ Mon, 03 Jun 2019 05:06:44: 12000000 INFO @ Mon, 03 Jun 2019 05:06:49: 12000000 INFO @ Mon, 03 Jun 2019 05:06:51: 13000000 INFO @ Mon, 03 Jun 2019 05:06:53: 13000000 INFO @ Mon, 03 Jun 2019 05:06:57: 13000000 INFO @ Mon, 03 Jun 2019 05:06:59: 14000000 INFO @ Mon, 03 Jun 2019 05:07:01: 14000000 INFO @ Mon, 03 Jun 2019 05:07:06: 14000000 INFO @ Mon, 03 Jun 2019 05:07:07: 15000000 INFO @ Mon, 03 Jun 2019 05:07:10: 15000000 INFO @ Mon, 03 Jun 2019 05:07:15: 15000000 INFO @ Mon, 03 Jun 2019 05:07:15: 16000000 INFO @ Mon, 03 Jun 2019 05:07:19: 16000000 INFO @ Mon, 03 Jun 2019 05:07:23: 17000000 INFO @ Mon, 03 Jun 2019 05:07:23: 16000000 INFO @ Mon, 03 Jun 2019 05:07:27: 17000000 INFO @ Mon, 03 Jun 2019 05:07:31: 18000000 INFO @ Mon, 03 Jun 2019 05:07:32: 17000000 INFO @ Mon, 03 Jun 2019 05:07:35: 18000000 INFO @ Mon, 03 Jun 2019 05:07:38: 19000000 INFO @ Mon, 03 Jun 2019 05:07:41: 18000000 INFO @ Mon, 03 Jun 2019 05:07:44: 19000000 INFO @ Mon, 03 Jun 2019 05:07:46: 20000000 INFO @ Mon, 03 Jun 2019 05:07:50: 19000000 INFO @ Mon, 03 Jun 2019 05:07:53: 20000000 INFO @ Mon, 03 Jun 2019 05:07:54: 21000000 INFO @ Mon, 03 Jun 2019 05:07:59: 20000000 INFO @ Mon, 03 Jun 2019 05:08:01: 21000000 INFO @ Mon, 03 Jun 2019 05:08:02: 22000000 INFO @ Mon, 03 Jun 2019 05:08:07: 21000000 INFO @ Mon, 03 Jun 2019 05:08:10: 22000000 INFO @ Mon, 03 Jun 2019 05:08:10: 23000000 INFO @ Mon, 03 Jun 2019 05:08:16: 22000000 INFO @ Mon, 03 Jun 2019 05:08:18: 24000000 INFO @ Mon, 03 Jun 2019 05:08:18: 23000000 INFO @ Mon, 03 Jun 2019 05:08:20: #1 tag size is determined as 45 bps INFO @ Mon, 03 Jun 2019 05:08:20: #1 tag size = 45 INFO @ Mon, 03 Jun 2019 05:08:20: #1 total tags in treatment: 10422622 INFO @ Mon, 03 Jun 2019 05:08:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:08:20: #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 05:08:21: #1 tags after filtering in treatment: 7481866 INFO @ Mon, 03 Jun 2019 05:08:21: #1 Redundant rate of treatment: 0.28 INFO @ Mon, 03 Jun 2019 05:08:21: #1 finished! INFO @ Mon, 03 Jun 2019 05:08:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:08:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:08:22: #2 number of paired peaks: 2310 INFO @ Mon, 03 Jun 2019 05:08:22: start model_add_line... INFO @ Mon, 03 Jun 2019 05:08:22: start X-correlation... INFO @ Mon, 03 Jun 2019 05:08:22: end of X-cor INFO @ Mon, 03 Jun 2019 05:08:22: #2 finished! INFO @ Mon, 03 Jun 2019 05:08:22: #2 predicted fragment length is 85 bps INFO @ Mon, 03 Jun 2019 05:08:22: #2 alternative fragment length(s) may be 85 bps INFO @ Mon, 03 Jun 2019 05:08:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.05_model.r WARNING @ Mon, 03 Jun 2019 05:08:22: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:08:22: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Mon, 03 Jun 2019 05:08:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:08:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:08:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:08:24: 23000000 INFO @ Mon, 03 Jun 2019 05:08:26: 24000000 INFO @ Mon, 03 Jun 2019 05:08:29: #1 tag size is determined as 45 bps INFO @ Mon, 03 Jun 2019 05:08:29: #1 tag size = 45 INFO @ Mon, 03 Jun 2019 05:08:29: #1 total tags in treatment: 10422622 INFO @ Mon, 03 Jun 2019 05:08:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:08:29: #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 05:08:29: #1 tags after filtering in treatment: 7481866 INFO @ Mon, 03 Jun 2019 05:08:29: #1 Redundant rate of treatment: 0.28 INFO @ Mon, 03 Jun 2019 05:08:29: #1 finished! INFO @ Mon, 03 Jun 2019 05:08:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:08:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:08:30: #2 number of paired peaks: 2310 INFO @ Mon, 03 Jun 2019 05:08:30: start model_add_line... INFO @ Mon, 03 Jun 2019 05:08:30: start X-correlation... INFO @ Mon, 03 Jun 2019 05:08:30: end of X-cor INFO @ Mon, 03 Jun 2019 05:08:30: #2 finished! INFO @ Mon, 03 Jun 2019 05:08:30: #2 predicted fragment length is 85 bps INFO @ Mon, 03 Jun 2019 05:08:30: #2 alternative fragment length(s) may be 85 bps INFO @ Mon, 03 Jun 2019 05:08:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.20_model.r WARNING @ Mon, 03 Jun 2019 05:08:30: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:08:30: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Mon, 03 Jun 2019 05:08:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:08:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:08:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:08:33: 24000000 INFO @ Mon, 03 Jun 2019 05:08:36: #1 tag size is determined as 45 bps INFO @ Mon, 03 Jun 2019 05:08:36: #1 tag size = 45 INFO @ Mon, 03 Jun 2019 05:08:36: #1 total tags in treatment: 10422622 INFO @ Mon, 03 Jun 2019 05:08:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:08:36: #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 05:08:36: #1 tags after filtering in treatment: 7481866 INFO @ Mon, 03 Jun 2019 05:08:36: #1 Redundant rate of treatment: 0.28 INFO @ Mon, 03 Jun 2019 05:08:36: #1 finished! INFO @ Mon, 03 Jun 2019 05:08:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:08:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:08:37: #2 number of paired peaks: 2310 INFO @ Mon, 03 Jun 2019 05:08:37: start model_add_line... INFO @ Mon, 03 Jun 2019 05:08:37: start X-correlation... INFO @ Mon, 03 Jun 2019 05:08:37: end of X-cor INFO @ Mon, 03 Jun 2019 05:08:37: #2 finished! INFO @ Mon, 03 Jun 2019 05:08:37: #2 predicted fragment length is 85 bps INFO @ Mon, 03 Jun 2019 05:08:37: #2 alternative fragment length(s) may be 85 bps INFO @ Mon, 03 Jun 2019 05:08:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.10_model.r WARNING @ Mon, 03 Jun 2019 05:08:37: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:08:37: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Mon, 03 Jun 2019 05:08:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:08:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:08:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:08:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:08:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:09:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:09:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:09:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:09:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.05_summits.bed INFO @ Mon, 03 Jun 2019 05:09:01: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (8634 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:09:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:09:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:09:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.20_summits.bed INFO @ Mon, 03 Jun 2019 05:09:07: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1255 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:09:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:09:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:09:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX151218/SRX151218.10_summits.bed INFO @ Mon, 03 Jun 2019 05:09:13: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (3025 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。