Job ID = 1295736 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T06:15:51 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' 2019-06-03T06:15:51 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/sra68/SRR/007410/SRR7588747' 2019-06-03T06:15:51 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_db_type().VDBManagerOpenDBRead( 'SRR7588747' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T06:15:51 fasterq-dump.2.9.6 err: invalid accession 'SRR7588747' spots read : 43,195,034 reads read : 86,390,068 reads written : 86,390,068 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: 02:39:45 43195034 reads; of these: 43195034 (100.00%) were paired; of these: 20318541 (47.04%) aligned concordantly 0 times 9444163 (21.86%) aligned concordantly exactly 1 time 13432330 (31.10%) aligned concordantly >1 times ---- 20318541 pairs aligned concordantly 0 times; of these: 7605 (0.04%) aligned discordantly 1 time ---- 20310936 pairs aligned 0 times concordantly or discordantly; of these: 40621872 mates make up the pairs; of these: 39293274 (96.73%) aligned 0 times 382287 (0.94%) aligned exactly 1 time 946311 (2.33%) aligned >1 times 54.52% overall alignment rate Time searching: 02:39:45 Overall time: 02:39:45 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 36 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 22620295 / 22727853 = 0.9953 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 19:38:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.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 19:38:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:38:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:38:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.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 19:38:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:38:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:38:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.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 19:38:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:38:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:38:57: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 19:39:00: 1000000 INFO @ Mon, 03 Jun 2019 19:39:04: 1000000 INFO @ Mon, 03 Jun 2019 19:39:08: #1 tag size is determined as 149 bps INFO @ Mon, 03 Jun 2019 19:39:08: #1 tag size = 149 INFO @ Mon, 03 Jun 2019 19:39:08: #1 total tags in treatment: 260793 INFO @ Mon, 03 Jun 2019 19:39:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:39:08: #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 19:39:08: #1 tags after filtering in treatment: 98849 INFO @ Mon, 03 Jun 2019 19:39:08: #1 Redundant rate of treatment: 0.62 INFO @ Mon, 03 Jun 2019 19:39:08: #1 finished! INFO @ Mon, 03 Jun 2019 19:39:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:39:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:39:08: #2 number of paired peaks: 4096 INFO @ Mon, 03 Jun 2019 19:39:08: start model_add_line... INFO @ Mon, 03 Jun 2019 19:39:08: start X-correlation... INFO @ Mon, 03 Jun 2019 19:39:08: end of X-cor INFO @ Mon, 03 Jun 2019 19:39:08: #2 finished! INFO @ Mon, 03 Jun 2019 19:39:08: #2 predicted fragment length is 212 bps INFO @ Mon, 03 Jun 2019 19:39:08: #2 alternative fragment length(s) may be 212 bps INFO @ Mon, 03 Jun 2019 19:39:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.10_model.r WARNING @ Mon, 03 Jun 2019 19:39:08: #2 Since the d (212) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:39:08: #2 You may need to consider one of the other alternative d(s): 212 WARNING @ Mon, 03 Jun 2019 19:39:08: #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 19:39:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:39:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:39:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:39:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:39:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:39:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.10_summits.bed INFO @ Mon, 03 Jun 2019 19:39:09: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (184 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:39:12: #1 tag size is determined as 149 bps INFO @ Mon, 03 Jun 2019 19:39:12: #1 tag size = 149 INFO @ Mon, 03 Jun 2019 19:39:12: #1 total tags in treatment: 260793 INFO @ Mon, 03 Jun 2019 19:39:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:39:12: #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 19:39:12: #1 tags after filtering in treatment: 98849 INFO @ Mon, 03 Jun 2019 19:39:12: #1 Redundant rate of treatment: 0.62 INFO @ Mon, 03 Jun 2019 19:39:12: #1 finished! INFO @ Mon, 03 Jun 2019 19:39:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:39:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:39:12: #2 number of paired peaks: 4096 INFO @ Mon, 03 Jun 2019 19:39:12: start model_add_line... INFO @ Mon, 03 Jun 2019 19:39:12: start X-correlation... INFO @ Mon, 03 Jun 2019 19:39:12: end of X-cor INFO @ Mon, 03 Jun 2019 19:39:12: #2 finished! INFO @ Mon, 03 Jun 2019 19:39:12: #2 predicted fragment length is 212 bps INFO @ Mon, 03 Jun 2019 19:39:12: #2 alternative fragment length(s) may be 212 bps INFO @ Mon, 03 Jun 2019 19:39:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.20_model.r WARNING @ Mon, 03 Jun 2019 19:39:12: #2 Since the d (212) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:39:12: #2 You may need to consider one of the other alternative d(s): 212 WARNING @ Mon, 03 Jun 2019 19:39:12: #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 19:39:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:39:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:39:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:39:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:39:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:39:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.20_summits.bed INFO @ Mon, 03 Jun 2019 19:39:12: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (72 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:39:19: #1 tag size is determined as 149 bps INFO @ Mon, 03 Jun 2019 19:39:19: #1 tag size = 149 INFO @ Mon, 03 Jun 2019 19:39:19: #1 total tags in treatment: 260793 INFO @ Mon, 03 Jun 2019 19:39:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:39:19: #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 19:39:19: #1 tags after filtering in treatment: 98849 INFO @ Mon, 03 Jun 2019 19:39:19: #1 Redundant rate of treatment: 0.62 INFO @ Mon, 03 Jun 2019 19:39:19: #1 finished! INFO @ Mon, 03 Jun 2019 19:39:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:39:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:39:19: #2 number of paired peaks: 4096 INFO @ Mon, 03 Jun 2019 19:39:19: start model_add_line... INFO @ Mon, 03 Jun 2019 19:39:19: start X-correlation... INFO @ Mon, 03 Jun 2019 19:39:19: end of X-cor INFO @ Mon, 03 Jun 2019 19:39:19: #2 finished! INFO @ Mon, 03 Jun 2019 19:39:19: #2 predicted fragment length is 212 bps INFO @ Mon, 03 Jun 2019 19:39:19: #2 alternative fragment length(s) may be 212 bps INFO @ Mon, 03 Jun 2019 19:39:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.05_model.r WARNING @ Mon, 03 Jun 2019 19:39:19: #2 Since the d (212) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:39:19: #2 You may need to consider one of the other alternative d(s): 212 WARNING @ Mon, 03 Jun 2019 19:39:19: #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 19:39:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:39:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:39:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:39:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:39:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:39:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4453995/SRX4453995.05_summits.bed INFO @ Mon, 03 Jun 2019 19:39:20: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (478 records, 4 fields): 3 millis CompletedMACS2peakCalling