Job ID = 1295564 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T05:20:37 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' 2019-06-03T05:20:37 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/sra14/SRR/000991/SRR1015601' 2019-06-03T05:20:37 fasterq-dump.2.9.6 err: invalid accession 'SRR1015601' spots read : 27,999,413 reads read : 27,999,413 reads written : 27,999,413 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:15:58 27999413 reads; of these: 27999413 (100.00%) were unpaired; of these: 6356860 (22.70%) aligned 0 times 11238957 (40.14%) aligned exactly 1 time 10403596 (37.16%) aligned >1 times 77.30% overall alignment rate Time searching: 00:15:59 Overall time: 00:15:59 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] 11858611 / 21642553 = 0.5479 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 14:50:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.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 14:50:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:50:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:50:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.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 14:50:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:50:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:50:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.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 14:50:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:50:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:51:07: 1000000 INFO @ Mon, 03 Jun 2019 14:51:08: 1000000 INFO @ Mon, 03 Jun 2019 14:51:08: 1000000 INFO @ Mon, 03 Jun 2019 14:51:16: 2000000 INFO @ Mon, 03 Jun 2019 14:51:17: 2000000 INFO @ Mon, 03 Jun 2019 14:51:17: 2000000 INFO @ Mon, 03 Jun 2019 14:51:23: 3000000 INFO @ Mon, 03 Jun 2019 14:51:25: 3000000 INFO @ Mon, 03 Jun 2019 14:51:25: 3000000 INFO @ Mon, 03 Jun 2019 14:51:31: 4000000 INFO @ Mon, 03 Jun 2019 14:51:33: 4000000 INFO @ Mon, 03 Jun 2019 14:51:33: 4000000 INFO @ Mon, 03 Jun 2019 14:51:39: 5000000 INFO @ Mon, 03 Jun 2019 14:51:41: 5000000 INFO @ Mon, 03 Jun 2019 14:51:42: 5000000 INFO @ Mon, 03 Jun 2019 14:51:46: 6000000 INFO @ Mon, 03 Jun 2019 14:51:50: 6000000 INFO @ Mon, 03 Jun 2019 14:51:50: 6000000 INFO @ Mon, 03 Jun 2019 14:51:54: 7000000 INFO @ Mon, 03 Jun 2019 14:51:58: 7000000 INFO @ Mon, 03 Jun 2019 14:51:58: 7000000 INFO @ Mon, 03 Jun 2019 14:52:02: 8000000 INFO @ Mon, 03 Jun 2019 14:52:06: 8000000 INFO @ Mon, 03 Jun 2019 14:52:06: 8000000 INFO @ Mon, 03 Jun 2019 14:52:10: 9000000 INFO @ Mon, 03 Jun 2019 14:52:15: 9000000 INFO @ Mon, 03 Jun 2019 14:52:15: 9000000 INFO @ Mon, 03 Jun 2019 14:52:16: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 14:52:16: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 14:52:16: #1 total tags in treatment: 9783942 INFO @ Mon, 03 Jun 2019 14:52:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:52:16: #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 14:52:16: #1 tags after filtering in treatment: 9783942 INFO @ Mon, 03 Jun 2019 14:52:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:52:16: #1 finished! INFO @ Mon, 03 Jun 2019 14:52:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:52:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:52:18: #2 number of paired peaks: 2786 INFO @ Mon, 03 Jun 2019 14:52:18: start model_add_line... INFO @ Mon, 03 Jun 2019 14:52:18: start X-correlation... INFO @ Mon, 03 Jun 2019 14:52:18: end of X-cor INFO @ Mon, 03 Jun 2019 14:52:18: #2 finished! INFO @ Mon, 03 Jun 2019 14:52:18: #2 predicted fragment length is 26 bps INFO @ Mon, 03 Jun 2019 14:52:18: #2 alternative fragment length(s) may be 26 bps INFO @ Mon, 03 Jun 2019 14:52:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.05_model.r WARNING @ Mon, 03 Jun 2019 14:52:18: #2 Since the d (26) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:52:18: #2 You may need to consider one of the other alternative d(s): 26 WARNING @ Mon, 03 Jun 2019 14:52:18: #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 14:52:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:52:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:52:22: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 14:52:22: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 14:52:22: #1 total tags in treatment: 9783942 INFO @ Mon, 03 Jun 2019 14:52:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:52:22: #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 14:52:22: #1 tags after filtering in treatment: 9783942 INFO @ Mon, 03 Jun 2019 14:52:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:52:22: #1 finished! INFO @ Mon, 03 Jun 2019 14:52:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:52:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:52:22: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 14:52:22: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 14:52:22: #1 total tags in treatment: 9783942 INFO @ Mon, 03 Jun 2019 14:52:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:52:22: #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 14:52:22: #1 tags after filtering in treatment: 9783942 INFO @ Mon, 03 Jun 2019 14:52:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:52:22: #1 finished! INFO @ Mon, 03 Jun 2019 14:52:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:52:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:52:23: #2 number of paired peaks: 2786 INFO @ Mon, 03 Jun 2019 14:52:23: start model_add_line... INFO @ Mon, 03 Jun 2019 14:52:23: start X-correlation... INFO @ Mon, 03 Jun 2019 14:52:23: end of X-cor INFO @ Mon, 03 Jun 2019 14:52:23: #2 finished! INFO @ Mon, 03 Jun 2019 14:52:23: #2 predicted fragment length is 26 bps INFO @ Mon, 03 Jun 2019 14:52:23: #2 alternative fragment length(s) may be 26 bps INFO @ Mon, 03 Jun 2019 14:52:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.20_model.r WARNING @ Mon, 03 Jun 2019 14:52:23: #2 Since the d (26) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:52:23: #2 You may need to consider one of the other alternative d(s): 26 WARNING @ Mon, 03 Jun 2019 14:52:23: #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 14:52:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:52:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:52:23: #2 number of paired peaks: 2786 INFO @ Mon, 03 Jun 2019 14:52:23: start model_add_line... INFO @ Mon, 03 Jun 2019 14:52:24: start X-correlation... INFO @ Mon, 03 Jun 2019 14:52:24: end of X-cor INFO @ Mon, 03 Jun 2019 14:52:24: #2 finished! INFO @ Mon, 03 Jun 2019 14:52:24: #2 predicted fragment length is 26 bps INFO @ Mon, 03 Jun 2019 14:52:24: #2 alternative fragment length(s) may be 26 bps INFO @ Mon, 03 Jun 2019 14:52:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.10_model.r WARNING @ Mon, 03 Jun 2019 14:52:24: #2 Since the d (26) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:52:24: #2 You may need to consider one of the other alternative d(s): 26 WARNING @ Mon, 03 Jun 2019 14:52:24: #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 14:52:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:52:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:52:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:52:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:52:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:52:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:52:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:52:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.05_summits.bed INFO @ Mon, 03 Jun 2019 14:52:57: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (10294 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:53:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:53:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:53:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.20_summits.bed INFO @ Mon, 03 Jun 2019 14:53:02: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1671 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:53:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:53:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:53:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX367039/SRX367039.10_summits.bed INFO @ Mon, 03 Jun 2019 14:53:03: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5868 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。