Job ID = 1292000 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T08:05:34 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' 2019-06-02T08:05:34 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/sra49/SRR/005663/SRR5799203' 2019-06-02T08:05:34 fasterq-dump.2.9.6 err: invalid accession 'SRR5799203' spots read : 28,765,215 reads read : 57,530,430 reads written : 57,530,430 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: 00:21:43 28765215 reads; of these: 28765215 (100.00%) were paired; of these: 11740968 (40.82%) aligned concordantly 0 times 14149984 (49.19%) aligned concordantly exactly 1 time 2874263 (9.99%) aligned concordantly >1 times ---- 11740968 pairs aligned concordantly 0 times; of these: 294685 (2.51%) aligned discordantly 1 time ---- 11446283 pairs aligned 0 times concordantly or discordantly; of these: 22892566 mates make up the pairs; of these: 22041165 (96.28%) aligned 0 times 585581 (2.56%) aligned exactly 1 time 265820 (1.16%) aligned >1 times 61.69% overall alignment rate Time searching: 00:21:43 Overall time: 00:21:43 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 12624191 / 17304779 = 0.7295 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 @ Sun, 02 Jun 2019 17:56:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 17:56:56: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:56:56: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:56:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 17:56:56: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:56:56: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:56:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 17:56:56: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:56:56: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:57:04: 1000000 INFO @ Sun, 02 Jun 2019 17:57:07: 1000000 INFO @ Sun, 02 Jun 2019 17:57:07: 1000000 INFO @ Sun, 02 Jun 2019 17:57:13: 2000000 INFO @ Sun, 02 Jun 2019 17:57:18: 2000000 INFO @ Sun, 02 Jun 2019 17:57:18: 2000000 INFO @ Sun, 02 Jun 2019 17:57:21: 3000000 INFO @ Sun, 02 Jun 2019 17:57:28: 3000000 INFO @ Sun, 02 Jun 2019 17:57:29: 3000000 INFO @ Sun, 02 Jun 2019 17:57:30: 4000000 INFO @ Sun, 02 Jun 2019 17:57:36: 4000000 INFO @ Sun, 02 Jun 2019 17:57:38: 5000000 INFO @ Sun, 02 Jun 2019 17:57:39: 4000000 INFO @ Sun, 02 Jun 2019 17:57:44: 5000000 INFO @ Sun, 02 Jun 2019 17:57:47: 6000000 INFO @ Sun, 02 Jun 2019 17:57:49: 5000000 INFO @ Sun, 02 Jun 2019 17:57:52: 6000000 INFO @ Sun, 02 Jun 2019 17:57:55: 7000000 INFO @ Sun, 02 Jun 2019 17:57:59: 6000000 INFO @ Sun, 02 Jun 2019 17:58:01: 7000000 INFO @ Sun, 02 Jun 2019 17:58:04: 8000000 INFO @ Sun, 02 Jun 2019 17:58:08: 7000000 INFO @ Sun, 02 Jun 2019 17:58:10: 8000000 INFO @ Sun, 02 Jun 2019 17:58:12: 9000000 INFO @ Sun, 02 Jun 2019 17:58:18: 8000000 INFO @ Sun, 02 Jun 2019 17:58:19: 9000000 INFO @ Sun, 02 Jun 2019 17:58:20: 10000000 INFO @ Sun, 02 Jun 2019 17:58:22: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:58:22: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:58:22: #1 total tags in treatment: 4593156 INFO @ Sun, 02 Jun 2019 17:58:22: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:58:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:58:22: #1 tags after filtering in treatment: 4121862 INFO @ Sun, 02 Jun 2019 17:58:22: #1 Redundant rate of treatment: 0.10 INFO @ Sun, 02 Jun 2019 17:58:22: #1 finished! INFO @ Sun, 02 Jun 2019 17:58:22: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:58:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:58:23: #2 number of paired peaks: 1658 INFO @ Sun, 02 Jun 2019 17:58:23: start model_add_line... INFO @ Sun, 02 Jun 2019 17:58:23: start X-correlation... INFO @ Sun, 02 Jun 2019 17:58:23: end of X-cor INFO @ Sun, 02 Jun 2019 17:58:23: #2 finished! INFO @ Sun, 02 Jun 2019 17:58:23: #2 predicted fragment length is 168 bps INFO @ Sun, 02 Jun 2019 17:58:23: #2 alternative fragment length(s) may be 4,168 bps INFO @ Sun, 02 Jun 2019 17:58:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.05_model.r INFO @ Sun, 02 Jun 2019 17:58:23: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:58:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:58:27: 9000000 INFO @ Sun, 02 Jun 2019 17:58:28: 10000000 INFO @ Sun, 02 Jun 2019 17:58:30: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:58:30: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:58:30: #1 total tags in treatment: 4593156 INFO @ Sun, 02 Jun 2019 17:58:30: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:58:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:58:30: #1 tags after filtering in treatment: 4121862 INFO @ Sun, 02 Jun 2019 17:58:30: #1 Redundant rate of treatment: 0.10 INFO @ Sun, 02 Jun 2019 17:58:30: #1 finished! INFO @ Sun, 02 Jun 2019 17:58:30: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:58:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:58:31: #2 number of paired peaks: 1658 INFO @ Sun, 02 Jun 2019 17:58:31: start model_add_line... INFO @ Sun, 02 Jun 2019 17:58:31: start X-correlation... INFO @ Sun, 02 Jun 2019 17:58:31: end of X-cor INFO @ Sun, 02 Jun 2019 17:58:31: #2 finished! INFO @ Sun, 02 Jun 2019 17:58:31: #2 predicted fragment length is 168 bps INFO @ Sun, 02 Jun 2019 17:58:31: #2 alternative fragment length(s) may be 4,168 bps INFO @ Sun, 02 Jun 2019 17:58:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.10_model.r INFO @ Sun, 02 Jun 2019 17:58:31: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:58:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:58:36: 10000000 INFO @ Sun, 02 Jun 2019 17:58:38: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:58:38: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:58:38: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:58:38: #1 total tags in treatment: 4593156 INFO @ Sun, 02 Jun 2019 17:58:38: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:58:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:58:38: #1 tags after filtering in treatment: 4121862 INFO @ Sun, 02 Jun 2019 17:58:38: #1 Redundant rate of treatment: 0.10 INFO @ Sun, 02 Jun 2019 17:58:38: #1 finished! INFO @ Sun, 02 Jun 2019 17:58:38: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:58:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:58:39: #2 number of paired peaks: 1658 INFO @ Sun, 02 Jun 2019 17:58:39: start model_add_line... INFO @ Sun, 02 Jun 2019 17:58:39: start X-correlation... INFO @ Sun, 02 Jun 2019 17:58:39: end of X-cor INFO @ Sun, 02 Jun 2019 17:58:39: #2 finished! INFO @ Sun, 02 Jun 2019 17:58:39: #2 predicted fragment length is 168 bps INFO @ Sun, 02 Jun 2019 17:58:39: #2 alternative fragment length(s) may be 4,168 bps INFO @ Sun, 02 Jun 2019 17:58:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.20_model.r INFO @ Sun, 02 Jun 2019 17:58:39: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:58:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:58:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:58:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:58:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.05_summits.bed INFO @ Sun, 02 Jun 2019 17:58:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1052 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:58:46: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:58:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:58:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:58:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.10_summits.bed INFO @ Sun, 02 Jun 2019 17:58:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (581 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:58:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:59:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:59:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:59:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978696/SRX2978696.20_summits.bed INFO @ Sun, 02 Jun 2019 17:59:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (308 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。