Job ID = 1306964 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:01:08 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' 2019-06-03T13:01:08 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/sra18/SRR/001188/SRR1217237' 2019-06-03T13:01:17 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1217237' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 9,255,352 reads read : 9,255,352 reads written : 9,255,352 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: 00:04:33 9255352 reads; of these: 9255352 (100.00%) were unpaired; of these: 200672 (2.17%) aligned 0 times 5762348 (62.26%) aligned exactly 1 time 3292332 (35.57%) aligned >1 times 97.83% overall alignment rate Time searching: 00:04:33 Overall time: 00:04:33 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_rmdupse_core] 636063 / 9054680 = 0.0702 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 22:13:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.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 22:13:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:13:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:13:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.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 22:13:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:13:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:13:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.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 22:13:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:13:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:13:44: 1000000 INFO @ Mon, 03 Jun 2019 22:13:44: 1000000 INFO @ Mon, 03 Jun 2019 22:13:46: 1000000 INFO @ Mon, 03 Jun 2019 22:13:51: 2000000 INFO @ Mon, 03 Jun 2019 22:13:52: 2000000 INFO @ Mon, 03 Jun 2019 22:13:56: 2000000 INFO @ Mon, 03 Jun 2019 22:13:59: 3000000 INFO @ Mon, 03 Jun 2019 22:13:59: 3000000 INFO @ Mon, 03 Jun 2019 22:14:05: 3000000 INFO @ Mon, 03 Jun 2019 22:14:06: 4000000 INFO @ Mon, 03 Jun 2019 22:14:07: 4000000 INFO @ Mon, 03 Jun 2019 22:14:13: 5000000 INFO @ Mon, 03 Jun 2019 22:14:14: 4000000 INFO @ Mon, 03 Jun 2019 22:14:14: 5000000 INFO @ Mon, 03 Jun 2019 22:14:20: 6000000 INFO @ Mon, 03 Jun 2019 22:14:22: 6000000 INFO @ Mon, 03 Jun 2019 22:14:22: 5000000 INFO @ Mon, 03 Jun 2019 22:14:28: 7000000 INFO @ Mon, 03 Jun 2019 22:14:29: 7000000 INFO @ Mon, 03 Jun 2019 22:14:31: 6000000 INFO @ Mon, 03 Jun 2019 22:14:35: 8000000 INFO @ Mon, 03 Jun 2019 22:14:37: 8000000 INFO @ Mon, 03 Jun 2019 22:14:38: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:14:38: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:14:38: #1 total tags in treatment: 8418617 INFO @ Mon, 03 Jun 2019 22:14:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:14:38: #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 22:14:38: #1 tags after filtering in treatment: 8418617 INFO @ Mon, 03 Jun 2019 22:14:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:14:38: #1 finished! INFO @ Mon, 03 Jun 2019 22:14:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:14:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:14:39: 7000000 INFO @ Mon, 03 Jun 2019 22:14:39: #2 number of paired peaks: 1454 INFO @ Mon, 03 Jun 2019 22:14:39: start model_add_line... INFO @ Mon, 03 Jun 2019 22:14:39: start X-correlation... INFO @ Mon, 03 Jun 2019 22:14:39: end of X-cor INFO @ Mon, 03 Jun 2019 22:14:39: #2 finished! INFO @ Mon, 03 Jun 2019 22:14:39: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 22:14:39: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 03 Jun 2019 22:14:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.05_model.r WARNING @ Mon, 03 Jun 2019 22:14:39: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:14:39: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 03 Jun 2019 22:14:39: #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 22:14:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:14:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:14:40: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:14:40: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:14:40: #1 total tags in treatment: 8418617 INFO @ Mon, 03 Jun 2019 22:14:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:14:40: #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 22:14:40: #1 tags after filtering in treatment: 8418617 INFO @ Mon, 03 Jun 2019 22:14:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:14:40: #1 finished! INFO @ Mon, 03 Jun 2019 22:14:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:14:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:14:41: #2 number of paired peaks: 1454 INFO @ Mon, 03 Jun 2019 22:14:41: start model_add_line... INFO @ Mon, 03 Jun 2019 22:14:41: start X-correlation... INFO @ Mon, 03 Jun 2019 22:14:41: end of X-cor INFO @ Mon, 03 Jun 2019 22:14:41: #2 finished! INFO @ Mon, 03 Jun 2019 22:14:41: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 22:14:41: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 03 Jun 2019 22:14:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.10_model.r WARNING @ Mon, 03 Jun 2019 22:14:41: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:14:41: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 03 Jun 2019 22:14:41: #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 22:14:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:14:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:14:47: 8000000 INFO @ Mon, 03 Jun 2019 22:14:51: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:14:51: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:14:51: #1 total tags in treatment: 8418617 INFO @ Mon, 03 Jun 2019 22:14:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:14:51: #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 22:14:51: #1 tags after filtering in treatment: 8418617 INFO @ Mon, 03 Jun 2019 22:14:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:14:51: #1 finished! INFO @ Mon, 03 Jun 2019 22:14:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:14:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:14:52: #2 number of paired peaks: 1454 INFO @ Mon, 03 Jun 2019 22:14:52: start model_add_line... INFO @ Mon, 03 Jun 2019 22:14:52: start X-correlation... INFO @ Mon, 03 Jun 2019 22:14:52: end of X-cor INFO @ Mon, 03 Jun 2019 22:14:52: #2 finished! INFO @ Mon, 03 Jun 2019 22:14:52: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 22:14:52: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 03 Jun 2019 22:14:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.20_model.r WARNING @ Mon, 03 Jun 2019 22:14:52: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:14:52: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 03 Jun 2019 22:14:52: #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 22:14:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:14:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:15:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:15:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:15:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:15:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:15:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.05_summits.bed INFO @ Mon, 03 Jun 2019 22:15:16: Done! pass1 - making usageList (15 chroms): 2 millis INFO @ Mon, 03 Jun 2019 22:15:16: #3 Call peaks for each chromosome... pass2 - checking and writing primary data (3189 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:15:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:15:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:15:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.10_summits.bed INFO @ Mon, 03 Jun 2019 22:15:18: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (2101 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:15:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:15:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:15:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511132/SRX511132.20_summits.bed INFO @ Mon, 03 Jun 2019 22:15:28: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (941 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。