Job ID = 1295190 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T03:25:41 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' 2019-06-03T03:25:41 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/sra13/SRR/000925/SRR947614' 2019-06-03T03:25:50 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR947614' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T03:25:50 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 18,493,128 reads read : 18,493,128 reads written : 18,493,128 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: 00:07:47 18493128 reads; of these: 18493128 (100.00%) were unpaired; of these: 1124974 (6.08%) aligned 0 times 13121128 (70.95%) aligned exactly 1 time 4247026 (22.97%) aligned >1 times 93.92% overall alignment rate Time searching: 00:07:47 Overall time: 00:07:47 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 8 files... [bam_rmdupse_core] 1482337 / 17368154 = 0.0853 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 12:58:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.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 12:58:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:58:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:58:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.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 12:58:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:58:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:58:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.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 12:58:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:58:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:59:06: 1000000 INFO @ Mon, 03 Jun 2019 12:59:08: 1000000 INFO @ Mon, 03 Jun 2019 12:59:08: 1000000 INFO @ Mon, 03 Jun 2019 12:59:15: 2000000 INFO @ Mon, 03 Jun 2019 12:59:18: 2000000 INFO @ Mon, 03 Jun 2019 12:59:19: 2000000 INFO @ Mon, 03 Jun 2019 12:59:24: 3000000 INFO @ Mon, 03 Jun 2019 12:59:28: 3000000 INFO @ Mon, 03 Jun 2019 12:59:29: 3000000 INFO @ Mon, 03 Jun 2019 12:59:32: 4000000 INFO @ Mon, 03 Jun 2019 12:59:38: 4000000 INFO @ Mon, 03 Jun 2019 12:59:40: 4000000 INFO @ Mon, 03 Jun 2019 12:59:41: 5000000 INFO @ Mon, 03 Jun 2019 12:59:47: 5000000 INFO @ Mon, 03 Jun 2019 12:59:50: 5000000 INFO @ Mon, 03 Jun 2019 12:59:50: 6000000 INFO @ Mon, 03 Jun 2019 12:59:57: 6000000 INFO @ Mon, 03 Jun 2019 12:59:59: 7000000 INFO @ Mon, 03 Jun 2019 13:00:00: 6000000 INFO @ Mon, 03 Jun 2019 13:00:06: 7000000 INFO @ Mon, 03 Jun 2019 13:00:08: 8000000 INFO @ Mon, 03 Jun 2019 13:00:11: 7000000 INFO @ Mon, 03 Jun 2019 13:00:16: 8000000 INFO @ Mon, 03 Jun 2019 13:00:17: 9000000 INFO @ Mon, 03 Jun 2019 13:00:22: 8000000 INFO @ Mon, 03 Jun 2019 13:00:26: 9000000 INFO @ Mon, 03 Jun 2019 13:00:26: 10000000 INFO @ Mon, 03 Jun 2019 13:00:32: 9000000 INFO @ Mon, 03 Jun 2019 13:00:35: 10000000 INFO @ Mon, 03 Jun 2019 13:00:36: 11000000 INFO @ Mon, 03 Jun 2019 13:00:43: 10000000 INFO @ Mon, 03 Jun 2019 13:00:44: 11000000 INFO @ Mon, 03 Jun 2019 13:00:45: 12000000 INFO @ Mon, 03 Jun 2019 13:00:53: 12000000 INFO @ Mon, 03 Jun 2019 13:00:54: 11000000 INFO @ Mon, 03 Jun 2019 13:00:54: 13000000 INFO @ Mon, 03 Jun 2019 13:01:03: 13000000 INFO @ Mon, 03 Jun 2019 13:01:04: 14000000 INFO @ Mon, 03 Jun 2019 13:01:04: 12000000 INFO @ Mon, 03 Jun 2019 13:01:12: 14000000 INFO @ Mon, 03 Jun 2019 13:01:13: 15000000 INFO @ Mon, 03 Jun 2019 13:01:15: 13000000 INFO @ Mon, 03 Jun 2019 13:01:21: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:01:21: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:01:21: #1 total tags in treatment: 15885817 INFO @ Mon, 03 Jun 2019 13:01:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:01:21: #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 13:01:21: 15000000 INFO @ Mon, 03 Jun 2019 13:01:21: #1 tags after filtering in treatment: 15885817 INFO @ Mon, 03 Jun 2019 13:01:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:01:21: #1 finished! INFO @ Mon, 03 Jun 2019 13:01:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:01:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:01:22: #2 number of paired peaks: 160 WARNING @ Mon, 03 Jun 2019 13:01:22: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Mon, 03 Jun 2019 13:01:22: start model_add_line... INFO @ Mon, 03 Jun 2019 13:01:22: start X-correlation... INFO @ Mon, 03 Jun 2019 13:01:22: end of X-cor INFO @ Mon, 03 Jun 2019 13:01:22: #2 finished! INFO @ Mon, 03 Jun 2019 13:01:22: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 13:01:22: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 13:01:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.10_model.r WARNING @ Mon, 03 Jun 2019 13:01:22: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:01:22: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 13:01:22: #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 13:01:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:01:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:01:25: 14000000 INFO @ Mon, 03 Jun 2019 13:01:29: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:01:29: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:01:29: #1 total tags in treatment: 15885817 INFO @ Mon, 03 Jun 2019 13:01:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:01:29: #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 13:01:29: #1 tags after filtering in treatment: 15885817 INFO @ Mon, 03 Jun 2019 13:01:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:01:29: #1 finished! INFO @ Mon, 03 Jun 2019 13:01:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:01:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:01:30: #2 number of paired peaks: 160 WARNING @ Mon, 03 Jun 2019 13:01:30: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Mon, 03 Jun 2019 13:01:30: start model_add_line... INFO @ Mon, 03 Jun 2019 13:01:30: start X-correlation... INFO @ Mon, 03 Jun 2019 13:01:30: end of X-cor INFO @ Mon, 03 Jun 2019 13:01:30: #2 finished! INFO @ Mon, 03 Jun 2019 13:01:30: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 13:01:30: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 13:01:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.20_model.r WARNING @ Mon, 03 Jun 2019 13:01:30: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:01:30: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 13:01:30: #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 13:01:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:01:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:01:34: 15000000 INFO @ Mon, 03 Jun 2019 13:01:43: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:01:43: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:01:43: #1 total tags in treatment: 15885817 INFO @ Mon, 03 Jun 2019 13:01:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:01:43: #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 13:01:43: #1 tags after filtering in treatment: 15885817 INFO @ Mon, 03 Jun 2019 13:01:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:01:43: #1 finished! INFO @ Mon, 03 Jun 2019 13:01:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:01:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:01:45: #2 number of paired peaks: 160 WARNING @ Mon, 03 Jun 2019 13:01:45: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Mon, 03 Jun 2019 13:01:45: start model_add_line... INFO @ Mon, 03 Jun 2019 13:01:45: start X-correlation... INFO @ Mon, 03 Jun 2019 13:01:45: end of X-cor INFO @ Mon, 03 Jun 2019 13:01:45: #2 finished! INFO @ Mon, 03 Jun 2019 13:01:45: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 13:01:45: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 13:01:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.05_model.r WARNING @ Mon, 03 Jun 2019 13:01:45: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:01:45: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 13:01:45: #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 13:01:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:01:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:02:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:02:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:02:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.10_peaks.xls INFO @ Mon, 03 Jun 2019 13:02:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:02:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.10_summits.bed INFO @ Mon, 03 Jun 2019 13:02:24: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1596 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:02:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:02:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.20_peaks.xls INFO @ Mon, 03 Jun 2019 13:02:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:02:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.20_summits.bed INFO @ Mon, 03 Jun 2019 13:02:32: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1053 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:02:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.05_peaks.xls INFO @ Mon, 03 Jun 2019 13:02:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:02:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331377/SRX331377.05_summits.bed INFO @ Mon, 03 Jun 2019 13:02:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1969 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。