Job ID = 1294896 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T01:35:50 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' 2019-06-03T01:35:50 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/SRR870156' 2019-06-03T01:35:59 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR870156' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 16,539,414 reads read : 16,539,414 reads written : 16,539,414 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: 00:08:14 16539414 reads; of these: 16539414 (100.00%) were unpaired; of these: 698666 (4.22%) aligned 0 times 10319685 (62.39%) aligned exactly 1 time 5521063 (33.38%) aligned >1 times 95.78% overall alignment rate Time searching: 00:08:14 Overall time: 00:08:14 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] 2191973 / 15840748 = 0.1384 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 10:59:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.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 10:59:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:59:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:59:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.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 10:59:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:59:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:59:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.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 10:59:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:59:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:59:10: 1000000 INFO @ Mon, 03 Jun 2019 10:59:11: 1000000 INFO @ Mon, 03 Jun 2019 10:59:13: 1000000 INFO @ Mon, 03 Jun 2019 10:59:19: 2000000 INFO @ Mon, 03 Jun 2019 10:59:20: 2000000 INFO @ Mon, 03 Jun 2019 10:59:23: 2000000 INFO @ Mon, 03 Jun 2019 10:59:26: 3000000 INFO @ Mon, 03 Jun 2019 10:59:28: 3000000 INFO @ Mon, 03 Jun 2019 10:59:33: 3000000 INFO @ Mon, 03 Jun 2019 10:59:34: 4000000 INFO @ Mon, 03 Jun 2019 10:59:36: 4000000 INFO @ Mon, 03 Jun 2019 10:59:42: 5000000 INFO @ Mon, 03 Jun 2019 10:59:44: 4000000 INFO @ Mon, 03 Jun 2019 10:59:45: 5000000 INFO @ Mon, 03 Jun 2019 10:59:50: 6000000 INFO @ Mon, 03 Jun 2019 10:59:54: 6000000 INFO @ Mon, 03 Jun 2019 10:59:54: 5000000 INFO @ Mon, 03 Jun 2019 10:59:57: 7000000 INFO @ Mon, 03 Jun 2019 11:00:02: 7000000 INFO @ Mon, 03 Jun 2019 11:00:05: 8000000 INFO @ Mon, 03 Jun 2019 11:00:05: 6000000 INFO @ Mon, 03 Jun 2019 11:00:11: 8000000 INFO @ Mon, 03 Jun 2019 11:00:12: 9000000 INFO @ Mon, 03 Jun 2019 11:00:15: 7000000 INFO @ Mon, 03 Jun 2019 11:00:19: 9000000 INFO @ Mon, 03 Jun 2019 11:00:20: 10000000 INFO @ Mon, 03 Jun 2019 11:00:25: 8000000 INFO @ Mon, 03 Jun 2019 11:00:27: 11000000 INFO @ Mon, 03 Jun 2019 11:00:27: 10000000 INFO @ Mon, 03 Jun 2019 11:00:35: 12000000 INFO @ Mon, 03 Jun 2019 11:00:36: 9000000 INFO @ Mon, 03 Jun 2019 11:00:36: 11000000 INFO @ Mon, 03 Jun 2019 11:00:42: 13000000 INFO @ Mon, 03 Jun 2019 11:00:44: 12000000 INFO @ Mon, 03 Jun 2019 11:00:46: 10000000 INFO @ Mon, 03 Jun 2019 11:00:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:00:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:00:47: #1 total tags in treatment: 13648775 INFO @ Mon, 03 Jun 2019 11:00:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:00:47: #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 11:00:47: #1 tags after filtering in treatment: 13648775 INFO @ Mon, 03 Jun 2019 11:00:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:00:47: #1 finished! INFO @ Mon, 03 Jun 2019 11:00:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:00:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:00:49: #2 number of paired peaks: 401 WARNING @ Mon, 03 Jun 2019 11:00:49: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Mon, 03 Jun 2019 11:00:49: start model_add_line... INFO @ Mon, 03 Jun 2019 11:00:49: start X-correlation... INFO @ Mon, 03 Jun 2019 11:00:49: end of X-cor INFO @ Mon, 03 Jun 2019 11:00:49: #2 finished! INFO @ Mon, 03 Jun 2019 11:00:49: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 11:00:49: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 11:00:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.10_model.r WARNING @ Mon, 03 Jun 2019 11:00:49: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:00:49: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 11:00:49: #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 11:00:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:00:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:00:53: 13000000 INFO @ Mon, 03 Jun 2019 11:00:56: 11000000 INFO @ Mon, 03 Jun 2019 11:00:58: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:00:58: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:00:58: #1 total tags in treatment: 13648775 INFO @ Mon, 03 Jun 2019 11:00:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:00:58: #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 11:00:58: #1 tags after filtering in treatment: 13648775 INFO @ Mon, 03 Jun 2019 11:00:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:00:58: #1 finished! INFO @ Mon, 03 Jun 2019 11:00:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:00:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:01:00: #2 number of paired peaks: 401 WARNING @ Mon, 03 Jun 2019 11:01:00: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Mon, 03 Jun 2019 11:01:00: start model_add_line... INFO @ Mon, 03 Jun 2019 11:01:00: start X-correlation... INFO @ Mon, 03 Jun 2019 11:01:00: end of X-cor INFO @ Mon, 03 Jun 2019 11:01:00: #2 finished! INFO @ Mon, 03 Jun 2019 11:01:00: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 11:01:00: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 11:01:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.05_model.r WARNING @ Mon, 03 Jun 2019 11:01:00: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:01:00: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 11:01:00: #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 11:01:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:01:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:01:06: 12000000 INFO @ Mon, 03 Jun 2019 11:01:16: 13000000 INFO @ Mon, 03 Jun 2019 11:01:22: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:01:22: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:01:22: #1 total tags in treatment: 13648775 INFO @ Mon, 03 Jun 2019 11:01:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:01:22: #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 11:01:22: #1 tags after filtering in treatment: 13648775 INFO @ Mon, 03 Jun 2019 11:01:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:01:22: #1 finished! INFO @ Mon, 03 Jun 2019 11:01:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:01:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:01:24: #2 number of paired peaks: 401 WARNING @ Mon, 03 Jun 2019 11:01:24: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Mon, 03 Jun 2019 11:01:24: start model_add_line... INFO @ Mon, 03 Jun 2019 11:01:24: start X-correlation... INFO @ Mon, 03 Jun 2019 11:01:24: end of X-cor INFO @ Mon, 03 Jun 2019 11:01:24: #2 finished! INFO @ Mon, 03 Jun 2019 11:01:24: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 11:01:24: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 11:01:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.20_model.r WARNING @ Mon, 03 Jun 2019 11:01:24: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:01:24: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 11:01:24: #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 11:01:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:01:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:01:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:01:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:01:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:01:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:01:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.10_summits.bed INFO @ Mon, 03 Jun 2019 11:01:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1937 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:01:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:01:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:01:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.05_summits.bed INFO @ Mon, 03 Jun 2019 11:01:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2212 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:02:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:02:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:02:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:02:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287967/SRX287967.20_summits.bed INFO @ Mon, 03 Jun 2019 11:02:19: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1517 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。