Job ID = 1307206 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:05:44 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' 2019-06-03T13:05:44 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/sos/sra-pub-run-2/SRR8433313/SRR8433313.1' 2019-06-03T13:05:44 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR8433313' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 15,830,776 reads read : 31,661,552 reads written : 15,830,776 reads 0-length : 15,830,776 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: 00:05:46 15830776 reads; of these: 15830776 (100.00%) were unpaired; of these: 233014 (1.47%) aligned 0 times 14534843 (91.81%) aligned exactly 1 time 1062919 (6.71%) aligned >1 times 98.53% overall alignment rate Time searching: 00:05:46 Overall time: 00:05:46 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] 7315174 / 15597762 = 0.4690 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 22:23:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.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 22:23:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:23:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:23:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.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 22:23:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:23:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:24:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.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 22:24:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:24:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:24:08: 1000000 INFO @ Mon, 03 Jun 2019 22:24:09: 1000000 INFO @ Mon, 03 Jun 2019 22:24:12: 1000000 INFO @ Mon, 03 Jun 2019 22:24:16: 2000000 INFO @ Mon, 03 Jun 2019 22:24:17: 2000000 INFO @ Mon, 03 Jun 2019 22:24:23: 2000000 INFO @ Mon, 03 Jun 2019 22:24:24: 3000000 INFO @ Mon, 03 Jun 2019 22:24:25: 3000000 INFO @ Mon, 03 Jun 2019 22:24:32: 4000000 INFO @ Mon, 03 Jun 2019 22:24:32: 4000000 INFO @ Mon, 03 Jun 2019 22:24:33: 3000000 INFO @ Mon, 03 Jun 2019 22:24:40: 5000000 INFO @ Mon, 03 Jun 2019 22:24:40: 5000000 INFO @ Mon, 03 Jun 2019 22:24:43: 4000000 INFO @ Mon, 03 Jun 2019 22:24:47: 6000000 INFO @ Mon, 03 Jun 2019 22:24:48: 6000000 INFO @ Mon, 03 Jun 2019 22:24:53: 5000000 INFO @ Mon, 03 Jun 2019 22:24:55: 7000000 INFO @ Mon, 03 Jun 2019 22:24:56: 7000000 INFO @ Mon, 03 Jun 2019 22:25:02: 8000000 INFO @ Mon, 03 Jun 2019 22:25:03: 6000000 INFO @ Mon, 03 Jun 2019 22:25:03: 8000000 INFO @ Mon, 03 Jun 2019 22:25:04: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 22:25:04: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 22:25:04: #1 total tags in treatment: 8282588 INFO @ Mon, 03 Jun 2019 22:25:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:25:04: #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 22:25:04: #1 tags after filtering in treatment: 8282588 INFO @ Mon, 03 Jun 2019 22:25:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:25:04: #1 finished! INFO @ Mon, 03 Jun 2019 22:25:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:25:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:25:06: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 22:25:06: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 22:25:06: #1 total tags in treatment: 8282588 INFO @ Mon, 03 Jun 2019 22:25:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:25:06: #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 22:25:06: #1 tags after filtering in treatment: 8282588 INFO @ Mon, 03 Jun 2019 22:25:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:25:06: #1 finished! INFO @ Mon, 03 Jun 2019 22:25:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:25:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:25:06: #2 number of paired peaks: 12316 INFO @ Mon, 03 Jun 2019 22:25:06: start model_add_line... INFO @ Mon, 03 Jun 2019 22:25:06: start X-correlation... INFO @ Mon, 03 Jun 2019 22:25:06: end of X-cor INFO @ Mon, 03 Jun 2019 22:25:06: #2 finished! INFO @ Mon, 03 Jun 2019 22:25:06: #2 predicted fragment length is 123 bps INFO @ Mon, 03 Jun 2019 22:25:06: #2 alternative fragment length(s) may be 123 bps INFO @ Mon, 03 Jun 2019 22:25:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.05_model.r WARNING @ Mon, 03 Jun 2019 22:25:06: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:25:06: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Mon, 03 Jun 2019 22:25:06: #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 22:25:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:25:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:25:08: #2 number of paired peaks: 12316 INFO @ Mon, 03 Jun 2019 22:25:08: start model_add_line... INFO @ Mon, 03 Jun 2019 22:25:08: start X-correlation... INFO @ Mon, 03 Jun 2019 22:25:08: end of X-cor INFO @ Mon, 03 Jun 2019 22:25:08: #2 finished! INFO @ Mon, 03 Jun 2019 22:25:08: #2 predicted fragment length is 123 bps INFO @ Mon, 03 Jun 2019 22:25:08: #2 alternative fragment length(s) may be 123 bps INFO @ Mon, 03 Jun 2019 22:25:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.10_model.r WARNING @ Mon, 03 Jun 2019 22:25:08: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:25:08: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Mon, 03 Jun 2019 22:25:08: #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 22:25:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:25:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:25:12: 7000000 INFO @ Mon, 03 Jun 2019 22:25:22: 8000000 INFO @ Mon, 03 Jun 2019 22:25:25: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 22:25:25: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 22:25:25: #1 total tags in treatment: 8282588 INFO @ Mon, 03 Jun 2019 22:25:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:25:25: #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 22:25:25: #1 tags after filtering in treatment: 8282588 INFO @ Mon, 03 Jun 2019 22:25:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:25:25: #1 finished! INFO @ Mon, 03 Jun 2019 22:25:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:25:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:25:27: #2 number of paired peaks: 12316 INFO @ Mon, 03 Jun 2019 22:25:27: start model_add_line... INFO @ Mon, 03 Jun 2019 22:25:28: start X-correlation... INFO @ Mon, 03 Jun 2019 22:25:28: end of X-cor INFO @ Mon, 03 Jun 2019 22:25:28: #2 finished! INFO @ Mon, 03 Jun 2019 22:25:28: #2 predicted fragment length is 123 bps INFO @ Mon, 03 Jun 2019 22:25:28: #2 alternative fragment length(s) may be 123 bps INFO @ Mon, 03 Jun 2019 22:25:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.20_model.r WARNING @ Mon, 03 Jun 2019 22:25:28: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:25:28: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Mon, 03 Jun 2019 22:25:28: #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 22:25:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:25:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:25:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:25:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:25:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:25:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:25:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.05_summits.bed INFO @ Mon, 03 Jun 2019 22:25:44: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8991 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:25:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:25:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:25:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.10_summits.bed INFO @ Mon, 03 Jun 2019 22:25:45: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8414 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 22:25:57: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 22:26:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:26:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:26:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5241032/SRX5241032.20_summits.bed INFO @ Mon, 03 Jun 2019 22:26:08: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (7474 records, 4 fields): 14 millis CompletedMACS2peakCalling