Job ID = 1294429 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T22:40:27 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' 2019-06-02T22:40:27 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/traces/sra12/SRR/000849/SRR869742' 2019-06-02T22:40:27 fasterq-dump.2.9.6 err: invalid accession 'SRR869742' spots read : 22,109,731 reads read : 22,109,731 reads written : 22,109,731 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: 00:00:01 Multiseed full-index search: 00:09:54 22109731 reads; of these: 22109731 (100.00%) were unpaired; of these: 1293742 (5.85%) aligned 0 times 13813324 (62.48%) aligned exactly 1 time 7002665 (31.67%) aligned >1 times 94.15% overall alignment rate Time searching: 00:09:55 Overall time: 00:09:55 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_rmdupse_core] 3520850 / 20815989 = 0.1691 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 08:10:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.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 08:10:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:10:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:10:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.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 08:10:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:10:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:10:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.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 08:10:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:10:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:10:31: 1000000 INFO @ Mon, 03 Jun 2019 08:10:31: 1000000 INFO @ Mon, 03 Jun 2019 08:10:35: 1000000 INFO @ Mon, 03 Jun 2019 08:10:41: 2000000 INFO @ Mon, 03 Jun 2019 08:10:41: 2000000 INFO @ Mon, 03 Jun 2019 08:10:47: 2000000 INFO @ Mon, 03 Jun 2019 08:10:49: 3000000 INFO @ Mon, 03 Jun 2019 08:10:50: 3000000 INFO @ Mon, 03 Jun 2019 08:10:58: 4000000 INFO @ Mon, 03 Jun 2019 08:10:59: 3000000 INFO @ Mon, 03 Jun 2019 08:10:59: 4000000 INFO @ Mon, 03 Jun 2019 08:11:07: 5000000 INFO @ Mon, 03 Jun 2019 08:11:08: 5000000 INFO @ Mon, 03 Jun 2019 08:11:10: 4000000 INFO @ Mon, 03 Jun 2019 08:11:15: 6000000 INFO @ Mon, 03 Jun 2019 08:11:16: 6000000 INFO @ Mon, 03 Jun 2019 08:11:21: 5000000 INFO @ Mon, 03 Jun 2019 08:11:23: 7000000 INFO @ Mon, 03 Jun 2019 08:11:25: 7000000 INFO @ Mon, 03 Jun 2019 08:11:33: 8000000 INFO @ Mon, 03 Jun 2019 08:11:33: 6000000 INFO @ Mon, 03 Jun 2019 08:11:34: 8000000 INFO @ Mon, 03 Jun 2019 08:11:43: 9000000 INFO @ Mon, 03 Jun 2019 08:11:43: 9000000 INFO @ Mon, 03 Jun 2019 08:11:45: 7000000 INFO @ Mon, 03 Jun 2019 08:11:51: 10000000 INFO @ Mon, 03 Jun 2019 08:11:51: 10000000 INFO @ Mon, 03 Jun 2019 08:11:58: 8000000 INFO @ Mon, 03 Jun 2019 08:12:01: 11000000 INFO @ Mon, 03 Jun 2019 08:12:02: 11000000 INFO @ Mon, 03 Jun 2019 08:12:09: 9000000 INFO @ Mon, 03 Jun 2019 08:12:10: 12000000 INFO @ Mon, 03 Jun 2019 08:12:10: 12000000 INFO @ Mon, 03 Jun 2019 08:12:18: 13000000 INFO @ Mon, 03 Jun 2019 08:12:19: 13000000 INFO @ Mon, 03 Jun 2019 08:12:21: 10000000 INFO @ Mon, 03 Jun 2019 08:12:27: 14000000 INFO @ Mon, 03 Jun 2019 08:12:28: 14000000 INFO @ Mon, 03 Jun 2019 08:12:32: 11000000 INFO @ Mon, 03 Jun 2019 08:12:35: 15000000 INFO @ Mon, 03 Jun 2019 08:12:36: 15000000 INFO @ Mon, 03 Jun 2019 08:12:43: 16000000 INFO @ Mon, 03 Jun 2019 08:12:44: 12000000 INFO @ Mon, 03 Jun 2019 08:12:45: 16000000 INFO @ Mon, 03 Jun 2019 08:12:54: 17000000 INFO @ Mon, 03 Jun 2019 08:12:55: 17000000 INFO @ Mon, 03 Jun 2019 08:12:56: 13000000 INFO @ Mon, 03 Jun 2019 08:12:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:12:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:12:57: #1 total tags in treatment: 17295139 INFO @ Mon, 03 Jun 2019 08:12:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:12:57: #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 08:12:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:12:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:12:57: #1 total tags in treatment: 17295139 INFO @ Mon, 03 Jun 2019 08:12:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:12:57: #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 08:12:58: #1 tags after filtering in treatment: 17295139 INFO @ Mon, 03 Jun 2019 08:12:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:12:58: #1 finished! INFO @ Mon, 03 Jun 2019 08:12:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:12:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:12:58: #1 tags after filtering in treatment: 17295139 INFO @ Mon, 03 Jun 2019 08:12:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:12:58: #1 finished! INFO @ Mon, 03 Jun 2019 08:12:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:12:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:12:59: #2 number of paired peaks: 198 WARNING @ Mon, 03 Jun 2019 08:12:59: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Mon, 03 Jun 2019 08:12:59: start model_add_line... INFO @ Mon, 03 Jun 2019 08:12:59: start X-correlation... INFO @ Mon, 03 Jun 2019 08:12:59: end of X-cor INFO @ Mon, 03 Jun 2019 08:12:59: #2 finished! INFO @ Mon, 03 Jun 2019 08:12:59: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 08:12:59: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 08:12:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.20_model.r INFO @ Mon, 03 Jun 2019 08:12:59: #2 number of paired peaks: 198 WARNING @ Mon, 03 Jun 2019 08:12:59: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Mon, 03 Jun 2019 08:12:59: start model_add_line... WARNING @ Mon, 03 Jun 2019 08:12:59: #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 08:12:59: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 08:12:59: #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 08:12:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:12:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:12:59: start X-correlation... INFO @ Mon, 03 Jun 2019 08:12:59: end of X-cor INFO @ Mon, 03 Jun 2019 08:12:59: #2 finished! INFO @ Mon, 03 Jun 2019 08:12:59: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 08:12:59: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 08:12:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.10_model.r WARNING @ Mon, 03 Jun 2019 08:12:59: #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 08:12:59: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 08:12:59: #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 08:12:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:12:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:13:08: 14000000 INFO @ Mon, 03 Jun 2019 08:13:19: 15000000 INFO @ Mon, 03 Jun 2019 08:13:30: 16000000 INFO @ Mon, 03 Jun 2019 08:13:41: 17000000 INFO @ Mon, 03 Jun 2019 08:13:44: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:13:44: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:13:44: #1 total tags in treatment: 17295139 INFO @ Mon, 03 Jun 2019 08:13:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:13:44: #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 08:13:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:13:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:13:45: #1 tags after filtering in treatment: 17295139 INFO @ Mon, 03 Jun 2019 08:13:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:13:45: #1 finished! INFO @ Mon, 03 Jun 2019 08:13:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:13:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:13:46: #2 number of paired peaks: 198 WARNING @ Mon, 03 Jun 2019 08:13:46: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Mon, 03 Jun 2019 08:13:46: start model_add_line... INFO @ Mon, 03 Jun 2019 08:13:46: start X-correlation... INFO @ Mon, 03 Jun 2019 08:13:46: end of X-cor INFO @ Mon, 03 Jun 2019 08:13:46: #2 finished! INFO @ Mon, 03 Jun 2019 08:13:46: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 08:13:46: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 08:13:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.05_model.r WARNING @ Mon, 03 Jun 2019 08:13:46: #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 08:13:46: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 08:13:46: #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 08:13:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:13:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:14:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:14:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:14:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.20_summits.bed INFO @ Mon, 03 Jun 2019 08:14:06: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1369 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:14:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:14:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:14:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.10_summits.bed INFO @ Mon, 03 Jun 2019 08:14:06: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1821 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:14:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:14:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:14:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:14:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287599/SRX287599.05_summits.bed INFO @ Mon, 03 Jun 2019 08:14:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2221 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。