Job ID = 1295540 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T05:10:33 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' 2019-06-03T05:10:33 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/sra36/SRR/000990/SRR1013782' 2019-06-03T05:10:43 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1013782' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T05:10:43 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 17,312,277 reads read : 17,312,277 reads written : 17,312,277 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: 00:08:25 17312277 reads; of these: 17312277 (100.00%) were unpaired; of these: 687926 (3.97%) aligned 0 times 12172005 (70.31%) aligned exactly 1 time 4452346 (25.72%) aligned >1 times 96.03% overall alignment rate Time searching: 00:08:25 Overall time: 00:08:25 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] 1888670 / 16624351 = 0.1136 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 14:36:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.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 14:36:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:36:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:36:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.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 14:36:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:36:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:36:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.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 14:36:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:36:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:37:09: 1000000 INFO @ Mon, 03 Jun 2019 14:37:10: 1000000 INFO @ Mon, 03 Jun 2019 14:37:11: 1000000 INFO @ Mon, 03 Jun 2019 14:37:23: 2000000 INFO @ Mon, 03 Jun 2019 14:37:24: 2000000 INFO @ Mon, 03 Jun 2019 14:37:27: 2000000 INFO @ Mon, 03 Jun 2019 14:37:37: 3000000 INFO @ Mon, 03 Jun 2019 14:37:37: 3000000 INFO @ Mon, 03 Jun 2019 14:37:41: 3000000 INFO @ Mon, 03 Jun 2019 14:37:49: 4000000 INFO @ Mon, 03 Jun 2019 14:37:52: 4000000 INFO @ Mon, 03 Jun 2019 14:37:55: 4000000 INFO @ Mon, 03 Jun 2019 14:38:02: 5000000 INFO @ Mon, 03 Jun 2019 14:38:07: 5000000 INFO @ Mon, 03 Jun 2019 14:38:10: 5000000 INFO @ Mon, 03 Jun 2019 14:38:15: 6000000 INFO @ Mon, 03 Jun 2019 14:38:21: 6000000 INFO @ Mon, 03 Jun 2019 14:38:24: 6000000 INFO @ Mon, 03 Jun 2019 14:38:27: 7000000 INFO @ Mon, 03 Jun 2019 14:38:36: 7000000 INFO @ Mon, 03 Jun 2019 14:38:39: 7000000 INFO @ Mon, 03 Jun 2019 14:38:41: 8000000 INFO @ Mon, 03 Jun 2019 14:38:50: 8000000 INFO @ Mon, 03 Jun 2019 14:38:53: 9000000 INFO @ Mon, 03 Jun 2019 14:38:54: 8000000 INFO @ Mon, 03 Jun 2019 14:39:04: 9000000 INFO @ Mon, 03 Jun 2019 14:39:06: 10000000 INFO @ Mon, 03 Jun 2019 14:39:08: 9000000 INFO @ Mon, 03 Jun 2019 14:39:18: 10000000 INFO @ Mon, 03 Jun 2019 14:39:19: 11000000 INFO @ Mon, 03 Jun 2019 14:39:23: 10000000 INFO @ Mon, 03 Jun 2019 14:39:31: 11000000 INFO @ Mon, 03 Jun 2019 14:39:32: 12000000 INFO @ Mon, 03 Jun 2019 14:39:37: 11000000 INFO @ Mon, 03 Jun 2019 14:39:44: 12000000 INFO @ Mon, 03 Jun 2019 14:39:44: 13000000 INFO @ Mon, 03 Jun 2019 14:39:52: 12000000 INFO @ Mon, 03 Jun 2019 14:39:57: 14000000 INFO @ Mon, 03 Jun 2019 14:39:57: 13000000 INFO @ Mon, 03 Jun 2019 14:40:07: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 14:40:07: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 14:40:07: #1 total tags in treatment: 14735681 INFO @ Mon, 03 Jun 2019 14:40:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:40:07: #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 14:40:07: #1 tags after filtering in treatment: 14735681 INFO @ Mon, 03 Jun 2019 14:40:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:40:07: #1 finished! INFO @ Mon, 03 Jun 2019 14:40:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:40:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:40:07: 13000000 INFO @ Mon, 03 Jun 2019 14:40:09: #2 number of paired peaks: 186 WARNING @ Mon, 03 Jun 2019 14:40:09: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Mon, 03 Jun 2019 14:40:09: start model_add_line... INFO @ Mon, 03 Jun 2019 14:40:09: start X-correlation... INFO @ Mon, 03 Jun 2019 14:40:09: end of X-cor INFO @ Mon, 03 Jun 2019 14:40:09: #2 finished! INFO @ Mon, 03 Jun 2019 14:40:09: #2 predicted fragment length is 65 bps INFO @ Mon, 03 Jun 2019 14:40:09: #2 alternative fragment length(s) may be 65,503 bps INFO @ Mon, 03 Jun 2019 14:40:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.10_model.r WARNING @ Mon, 03 Jun 2019 14:40:09: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:40:09: #2 You may need to consider one of the other alternative d(s): 65,503 WARNING @ Mon, 03 Jun 2019 14:40:09: #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 14:40:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:40:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:40:10: 14000000 INFO @ Mon, 03 Jun 2019 14:40:20: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 14:40:20: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 14:40:20: #1 total tags in treatment: 14735681 INFO @ Mon, 03 Jun 2019 14:40:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:40:20: #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 14:40:20: #1 tags after filtering in treatment: 14735681 INFO @ Mon, 03 Jun 2019 14:40:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:40:20: #1 finished! INFO @ Mon, 03 Jun 2019 14:40:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:40:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:40:23: #2 number of paired peaks: 186 WARNING @ Mon, 03 Jun 2019 14:40:23: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Mon, 03 Jun 2019 14:40:23: start model_add_line... INFO @ Mon, 03 Jun 2019 14:40:23: start X-correlation... INFO @ Mon, 03 Jun 2019 14:40:23: end of X-cor INFO @ Mon, 03 Jun 2019 14:40:23: #2 finished! INFO @ Mon, 03 Jun 2019 14:40:23: #2 predicted fragment length is 65 bps INFO @ Mon, 03 Jun 2019 14:40:23: #2 alternative fragment length(s) may be 65,503 bps INFO @ Mon, 03 Jun 2019 14:40:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.20_model.r WARNING @ Mon, 03 Jun 2019 14:40:23: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:40:23: #2 You may need to consider one of the other alternative d(s): 65,503 WARNING @ Mon, 03 Jun 2019 14:40:23: #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 14:40:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:40:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:40:23: 14000000 INFO @ Mon, 03 Jun 2019 14:40:34: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 14:40:34: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 14:40:34: #1 total tags in treatment: 14735681 INFO @ Mon, 03 Jun 2019 14:40:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:40:34: #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 14:40:35: #1 tags after filtering in treatment: 14735681 INFO @ Mon, 03 Jun 2019 14:40:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:40:35: #1 finished! INFO @ Mon, 03 Jun 2019 14:40:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:40:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:40:37: #2 number of paired peaks: 186 WARNING @ Mon, 03 Jun 2019 14:40:37: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Mon, 03 Jun 2019 14:40:37: start model_add_line... INFO @ Mon, 03 Jun 2019 14:40:37: start X-correlation... INFO @ Mon, 03 Jun 2019 14:40:37: end of X-cor INFO @ Mon, 03 Jun 2019 14:40:37: #2 finished! INFO @ Mon, 03 Jun 2019 14:40:37: #2 predicted fragment length is 65 bps INFO @ Mon, 03 Jun 2019 14:40:37: #2 alternative fragment length(s) may be 65,503 bps INFO @ Mon, 03 Jun 2019 14:40:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.05_model.r WARNING @ Mon, 03 Jun 2019 14:40:37: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:40:37: #2 You may need to consider one of the other alternative d(s): 65,503 WARNING @ Mon, 03 Jun 2019 14:40:37: #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 14:40:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:40:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:41:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:41:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:41:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:41:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:41:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:41:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.10_summits.bed INFO @ Mon, 03 Jun 2019 14:41:38: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3639 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:41:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:41:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:41:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.20_summits.bed INFO @ Mon, 03 Jun 2019 14:41:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1858 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:42:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:42:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:42:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX365704/SRX365704.05_summits.bed INFO @ Mon, 03 Jun 2019 14:42:05: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6861 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。