Job ID = 1295090 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T02:35:45 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' 2019-06-03T02:35:45 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/000905/SRR927103' 2019-06-03T02:35:45 fasterq-dump.2.9.6 err: invalid accession 'SRR927103' spots read : 18,249,589 reads read : 18,249,589 reads written : 18,249,589 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: 00:07:21 18249589 reads; of these: 18249589 (100.00%) were unpaired; of these: 976504 (5.35%) aligned 0 times 13034904 (71.43%) aligned exactly 1 time 4238181 (23.22%) aligned >1 times 94.65% overall alignment rate Time searching: 00:07:21 Overall time: 00:07:21 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] 1666558 / 17273085 = 0.0965 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 11:59:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.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 11:59:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:59:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:59:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.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 11:59:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:59:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:59:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.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 11:59:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:59:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:59:21: 1000000 INFO @ Mon, 03 Jun 2019 11:59:23: 1000000 INFO @ Mon, 03 Jun 2019 11:59:25: 1000000 INFO @ Mon, 03 Jun 2019 11:59:29: 2000000 INFO @ Mon, 03 Jun 2019 11:59:31: 2000000 INFO @ Mon, 03 Jun 2019 11:59:35: 2000000 INFO @ Mon, 03 Jun 2019 11:59:36: 3000000 INFO @ Mon, 03 Jun 2019 11:59:39: 3000000 INFO @ Mon, 03 Jun 2019 11:59:44: 4000000 INFO @ Mon, 03 Jun 2019 11:59:45: 3000000 INFO @ Mon, 03 Jun 2019 11:59:48: 4000000 INFO @ Mon, 03 Jun 2019 11:59:51: 5000000 INFO @ Mon, 03 Jun 2019 11:59:55: 4000000 INFO @ Mon, 03 Jun 2019 11:59:56: 5000000 INFO @ Mon, 03 Jun 2019 11:59:59: 6000000 INFO @ Mon, 03 Jun 2019 12:00:04: 6000000 INFO @ Mon, 03 Jun 2019 12:00:04: 5000000 INFO @ Mon, 03 Jun 2019 12:00:07: 7000000 INFO @ Mon, 03 Jun 2019 12:00:12: 7000000 INFO @ Mon, 03 Jun 2019 12:00:14: 6000000 INFO @ Mon, 03 Jun 2019 12:00:14: 8000000 INFO @ Mon, 03 Jun 2019 12:00:21: 8000000 INFO @ Mon, 03 Jun 2019 12:00:22: 9000000 INFO @ Mon, 03 Jun 2019 12:00:24: 7000000 INFO @ Mon, 03 Jun 2019 12:00:29: 9000000 INFO @ Mon, 03 Jun 2019 12:00:29: 10000000 INFO @ Mon, 03 Jun 2019 12:00:34: 8000000 INFO @ Mon, 03 Jun 2019 12:00:37: 11000000 INFO @ Mon, 03 Jun 2019 12:00:37: 10000000 INFO @ Mon, 03 Jun 2019 12:00:43: 9000000 INFO @ Mon, 03 Jun 2019 12:00:44: 12000000 INFO @ Mon, 03 Jun 2019 12:00:46: 11000000 INFO @ Mon, 03 Jun 2019 12:00:52: 13000000 INFO @ Mon, 03 Jun 2019 12:00:53: 10000000 INFO @ Mon, 03 Jun 2019 12:00:54: 12000000 INFO @ Mon, 03 Jun 2019 12:01:00: 14000000 INFO @ Mon, 03 Jun 2019 12:01:02: 13000000 INFO @ Mon, 03 Jun 2019 12:01:04: 11000000 INFO @ Mon, 03 Jun 2019 12:01:07: 15000000 INFO @ Mon, 03 Jun 2019 12:01:11: 14000000 INFO @ Mon, 03 Jun 2019 12:01:12: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:01:12: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:01:12: #1 total tags in treatment: 15606527 INFO @ Mon, 03 Jun 2019 12:01:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:01:12: #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 12:01:12: #1 tags after filtering in treatment: 15606527 INFO @ Mon, 03 Jun 2019 12:01:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:01:12: #1 finished! INFO @ Mon, 03 Jun 2019 12:01:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:01:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:01:14: #2 number of paired peaks: 161 WARNING @ Mon, 03 Jun 2019 12:01:14: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Mon, 03 Jun 2019 12:01:14: start model_add_line... INFO @ Mon, 03 Jun 2019 12:01:14: start X-correlation... INFO @ Mon, 03 Jun 2019 12:01:14: end of X-cor INFO @ Mon, 03 Jun 2019 12:01:14: #2 finished! INFO @ Mon, 03 Jun 2019 12:01:14: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 12:01:14: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 12:01:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.20_model.r WARNING @ Mon, 03 Jun 2019 12:01:14: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:01:14: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 12:01:14: #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 12:01:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:01:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:01:14: 12000000 INFO @ Mon, 03 Jun 2019 12:01:20: 15000000 INFO @ Mon, 03 Jun 2019 12:01:25: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:01:25: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:01:25: #1 total tags in treatment: 15606527 INFO @ Mon, 03 Jun 2019 12:01:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:01:25: #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 12:01:25: #1 tags after filtering in treatment: 15606527 INFO @ Mon, 03 Jun 2019 12:01:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:01:25: #1 finished! INFO @ Mon, 03 Jun 2019 12:01:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:01:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:01:25: 13000000 INFO @ Mon, 03 Jun 2019 12:01:26: #2 number of paired peaks: 161 WARNING @ Mon, 03 Jun 2019 12:01:26: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Mon, 03 Jun 2019 12:01:26: start model_add_line... INFO @ Mon, 03 Jun 2019 12:01:26: start X-correlation... INFO @ Mon, 03 Jun 2019 12:01:26: end of X-cor INFO @ Mon, 03 Jun 2019 12:01:26: #2 finished! INFO @ Mon, 03 Jun 2019 12:01:26: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 12:01:26: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 12:01:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.10_model.r WARNING @ Mon, 03 Jun 2019 12:01:26: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:01:26: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 12:01:26: #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 12:01:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:01:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:01:35: 14000000 INFO @ Mon, 03 Jun 2019 12:01:45: 15000000 INFO @ Mon, 03 Jun 2019 12:01:51: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:01:51: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:01:51: #1 total tags in treatment: 15606527 INFO @ Mon, 03 Jun 2019 12:01:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:01:51: #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 12:01:51: #1 tags after filtering in treatment: 15606527 INFO @ Mon, 03 Jun 2019 12:01:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:01:51: #1 finished! INFO @ Mon, 03 Jun 2019 12:01:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:01:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:01:52: #2 number of paired peaks: 161 WARNING @ Mon, 03 Jun 2019 12:01:52: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Mon, 03 Jun 2019 12:01:52: start model_add_line... INFO @ Mon, 03 Jun 2019 12:01:53: start X-correlation... INFO @ Mon, 03 Jun 2019 12:01:53: end of X-cor INFO @ Mon, 03 Jun 2019 12:01:53: #2 finished! INFO @ Mon, 03 Jun 2019 12:01:53: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 12:01:53: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 12:01:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.05_model.r WARNING @ Mon, 03 Jun 2019 12:01:53: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:01:53: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 12:01:53: #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 12:01:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:01:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:01:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:02:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:02:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:02:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:02:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.20_summits.bed INFO @ Mon, 03 Jun 2019 12:02:14: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1147 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:02:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:02:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:02:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.10_summits.bed INFO @ Mon, 03 Jun 2019 12:02:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1615 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:02:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:02:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:02:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:02:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318787/SRX318787.05_summits.bed INFO @ Mon, 03 Jun 2019 12:02:53: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1893 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。