Job ID = 1301234 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:40:57 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' 2019-06-03T10:40:57 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/sra17/SRR/001160/SRR1187965' 2019-06-03T10:40:57 fasterq-dump.2.9.6 err: invalid accession 'SRR1187965' spots read : 27,157,073 reads read : 27,157,073 reads written : 27,157,073 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: 00:09:51 27157073 reads; of these: 27157073 (100.00%) were unpaired; of these: 2656608 (9.78%) aligned 0 times 16815937 (61.92%) aligned exactly 1 time 7684528 (28.30%) aligned >1 times 90.22% overall alignment rate Time searching: 00:09:51 Overall time: 00:09:51 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] 14216517 / 24500465 = 0.5803 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 20:11:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.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 20:11:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:11:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:11:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.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 20:11:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.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 20:11:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:11:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:11:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:11:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:11:50: 1000000 INFO @ Mon, 03 Jun 2019 20:11:50: 1000000 INFO @ Mon, 03 Jun 2019 20:11:51: 1000000 INFO @ Mon, 03 Jun 2019 20:11:58: 2000000 INFO @ Mon, 03 Jun 2019 20:11:58: 2000000 INFO @ Mon, 03 Jun 2019 20:11:58: 2000000 INFO @ Mon, 03 Jun 2019 20:12:05: 3000000 INFO @ Mon, 03 Jun 2019 20:12:05: 3000000 INFO @ Mon, 03 Jun 2019 20:12:05: 3000000 INFO @ Mon, 03 Jun 2019 20:12:12: 4000000 INFO @ Mon, 03 Jun 2019 20:12:12: 4000000 INFO @ Mon, 03 Jun 2019 20:12:12: 4000000 INFO @ Mon, 03 Jun 2019 20:12:18: 5000000 INFO @ Mon, 03 Jun 2019 20:12:19: 5000000 INFO @ Mon, 03 Jun 2019 20:12:20: 5000000 INFO @ Mon, 03 Jun 2019 20:12:25: 6000000 INFO @ Mon, 03 Jun 2019 20:12:26: 6000000 INFO @ Mon, 03 Jun 2019 20:12:28: 6000000 INFO @ Mon, 03 Jun 2019 20:12:31: 7000000 INFO @ Mon, 03 Jun 2019 20:12:33: 7000000 INFO @ Mon, 03 Jun 2019 20:12:35: 7000000 INFO @ Mon, 03 Jun 2019 20:12:37: 8000000 INFO @ Mon, 03 Jun 2019 20:12:39: 8000000 INFO @ Mon, 03 Jun 2019 20:12:43: 8000000 INFO @ Mon, 03 Jun 2019 20:12:44: 9000000 INFO @ Mon, 03 Jun 2019 20:12:46: 9000000 INFO @ Mon, 03 Jun 2019 20:12:51: 10000000 INFO @ Mon, 03 Jun 2019 20:12:51: 9000000 INFO @ Mon, 03 Jun 2019 20:12:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:12:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:12:53: #1 total tags in treatment: 10283948 INFO @ Mon, 03 Jun 2019 20:12:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:12:53: #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 20:12:53: #1 tags after filtering in treatment: 10283948 INFO @ Mon, 03 Jun 2019 20:12:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:12:53: #1 finished! INFO @ Mon, 03 Jun 2019 20:12:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:12:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:12:53: 10000000 INFO @ Mon, 03 Jun 2019 20:12:54: #2 number of paired peaks: 1051 INFO @ Mon, 03 Jun 2019 20:12:54: start model_add_line... INFO @ Mon, 03 Jun 2019 20:12:54: start X-correlation... INFO @ Mon, 03 Jun 2019 20:12:54: end of X-cor INFO @ Mon, 03 Jun 2019 20:12:54: #2 finished! INFO @ Mon, 03 Jun 2019 20:12:54: #2 predicted fragment length is 61 bps INFO @ Mon, 03 Jun 2019 20:12:54: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 03 Jun 2019 20:12:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.05_model.r WARNING @ Mon, 03 Jun 2019 20:12:54: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:12:54: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 03 Jun 2019 20:12:54: #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 20:12:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:12:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:12:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:12:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:12:55: #1 total tags in treatment: 10283948 INFO @ Mon, 03 Jun 2019 20:12:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:12:55: #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 20:12:55: #1 tags after filtering in treatment: 10283948 INFO @ Mon, 03 Jun 2019 20:12:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:12:55: #1 finished! INFO @ Mon, 03 Jun 2019 20:12:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:12:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:12:56: #2 number of paired peaks: 1051 INFO @ Mon, 03 Jun 2019 20:12:56: start model_add_line... INFO @ Mon, 03 Jun 2019 20:12:57: start X-correlation... INFO @ Mon, 03 Jun 2019 20:12:57: end of X-cor INFO @ Mon, 03 Jun 2019 20:12:57: #2 finished! INFO @ Mon, 03 Jun 2019 20:12:57: #2 predicted fragment length is 61 bps INFO @ Mon, 03 Jun 2019 20:12:57: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 03 Jun 2019 20:12:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.10_model.r WARNING @ Mon, 03 Jun 2019 20:12:57: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:12:57: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 03 Jun 2019 20:12:57: #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 20:12:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:12:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:12:58: 10000000 INFO @ Mon, 03 Jun 2019 20:13:01: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:13:01: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:13:01: #1 total tags in treatment: 10283948 INFO @ Mon, 03 Jun 2019 20:13:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:13:01: #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 20:13:01: #1 tags after filtering in treatment: 10283948 INFO @ Mon, 03 Jun 2019 20:13:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:13:01: #1 finished! INFO @ Mon, 03 Jun 2019 20:13:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:13:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:13:02: #2 number of paired peaks: 1051 INFO @ Mon, 03 Jun 2019 20:13:02: start model_add_line... INFO @ Mon, 03 Jun 2019 20:13:02: start X-correlation... INFO @ Mon, 03 Jun 2019 20:13:02: end of X-cor INFO @ Mon, 03 Jun 2019 20:13:02: #2 finished! INFO @ Mon, 03 Jun 2019 20:13:02: #2 predicted fragment length is 61 bps INFO @ Mon, 03 Jun 2019 20:13:02: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 03 Jun 2019 20:13:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.20_model.r WARNING @ Mon, 03 Jun 2019 20:13:02: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:13:02: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 03 Jun 2019 20:13:02: #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 20:13:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:13:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:13:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:13:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:13:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:13:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:13:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:13:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.05_summits.bed INFO @ Mon, 03 Jun 2019 20:13:38: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5712 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:13:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:13:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:13:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.10_summits.bed INFO @ Mon, 03 Jun 2019 20:13:40: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2504 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:13:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:13:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:13:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485207/SRX485207.20_summits.bed INFO @ Mon, 03 Jun 2019 20:13:45: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1354 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。