Job ID = 2010528 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:05:02 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-05T14:05:02 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 20,668,887 reads read : 41,337,774 reads written : 41,337,774 rm: cannot remove ‘[DSE]RR*’: 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: 00:08:52 20668887 reads; of these: 20668887 (100.00%) were paired; of these: 15329692 (74.17%) aligned concordantly 0 times 3713784 (17.97%) aligned concordantly exactly 1 time 1625411 (7.86%) aligned concordantly >1 times ---- 15329692 pairs aligned concordantly 0 times; of these: 52475 (0.34%) aligned discordantly 1 time ---- 15277217 pairs aligned 0 times concordantly or discordantly; of these: 30554434 mates make up the pairs; of these: 29911079 (97.89%) aligned 0 times 345727 (1.13%) aligned exactly 1 time 297628 (0.97%) aligned >1 times 27.64% overall alignment rate Time searching: 00:08:52 Overall time: 00:08:52 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 8 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 chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 2892929 / 5385346 = 0.5372 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 @ Fri, 05 Jul 2019 23:25:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 23:25:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:25:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:25:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 23:25:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:25:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:25:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 23:25:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:25:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:25:43: 1000000 INFO @ Fri, 05 Jul 2019 23:25:45: 1000000 INFO @ Fri, 05 Jul 2019 23:25:45: 1000000 INFO @ Fri, 05 Jul 2019 23:25:51: 2000000 INFO @ Fri, 05 Jul 2019 23:25:52: 2000000 INFO @ Fri, 05 Jul 2019 23:25:55: 2000000 INFO @ Fri, 05 Jul 2019 23:25:58: 3000000 INFO @ Fri, 05 Jul 2019 23:26:00: 3000000 INFO @ Fri, 05 Jul 2019 23:26:04: 3000000 INFO @ Fri, 05 Jul 2019 23:26:06: 4000000 INFO @ Fri, 05 Jul 2019 23:26:08: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:26:13: 4000000 INFO @ Fri, 05 Jul 2019 23:26:13: 5000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:26:15: 5000000 INFO @ Fri, 05 Jul 2019 23:26:18: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:26:18: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:26:18: #1 total tags in treatment: 2464265 INFO @ Fri, 05 Jul 2019 23:26:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:26:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:26:18: #1 tags after filtering in treatment: 1212476 INFO @ Fri, 05 Jul 2019 23:26:18: #1 Redundant rate of treatment: 0.51 INFO @ Fri, 05 Jul 2019 23:26:18: #1 finished! INFO @ Fri, 05 Jul 2019 23:26:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:26:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:26:19: #2 number of paired peaks: 1079 INFO @ Fri, 05 Jul 2019 23:26:19: start model_add_line... INFO @ Fri, 05 Jul 2019 23:26:19: start X-correlation... INFO @ Fri, 05 Jul 2019 23:26:19: end of X-cor INFO @ Fri, 05 Jul 2019 23:26:19: #2 finished! INFO @ Fri, 05 Jul 2019 23:26:19: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 23:26:19: #2 alternative fragment length(s) may be 0,97,106,109,132,155,179 bps INFO @ Fri, 05 Jul 2019 23:26:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.05_model.r INFO @ Fri, 05 Jul 2019 23:26:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:26:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:26:20: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:26:20: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:26:20: #1 total tags in treatment: 2464265 INFO @ Fri, 05 Jul 2019 23:26:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:26:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:26:20: #1 tags after filtering in treatment: 1212476 INFO @ Fri, 05 Jul 2019 23:26:20: #1 Redundant rate of treatment: 0.51 INFO @ Fri, 05 Jul 2019 23:26:20: #1 finished! INFO @ Fri, 05 Jul 2019 23:26:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:26:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:26:20: #2 number of paired peaks: 1079 INFO @ Fri, 05 Jul 2019 23:26:20: start model_add_line... INFO @ Fri, 05 Jul 2019 23:26:20: start X-correlation... INFO @ Fri, 05 Jul 2019 23:26:20: end of X-cor INFO @ Fri, 05 Jul 2019 23:26:20: #2 finished! INFO @ Fri, 05 Jul 2019 23:26:20: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 23:26:20: #2 alternative fragment length(s) may be 0,97,106,109,132,155,179 bps INFO @ Fri, 05 Jul 2019 23:26:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.20_model.r INFO @ Fri, 05 Jul 2019 23:26:20: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:26:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:26:21: 5000000 INFO @ Fri, 05 Jul 2019 23:26:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:26:26: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:26:26: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:26:26: #1 total tags in treatment: 2464265 INFO @ Fri, 05 Jul 2019 23:26:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:26:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:26:26: #1 tags after filtering in treatment: 1212476 INFO @ Fri, 05 Jul 2019 23:26:26: #1 Redundant rate of treatment: 0.51 INFO @ Fri, 05 Jul 2019 23:26:26: #1 finished! INFO @ Fri, 05 Jul 2019 23:26:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:26:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:26:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:26:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:26:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.05_summits.bed INFO @ Fri, 05 Jul 2019 23:26:26: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (488 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 23:26:27: #2 number of paired peaks: 1079 INFO @ Fri, 05 Jul 2019 23:26:27: start model_add_line... INFO @ Fri, 05 Jul 2019 23:26:27: start X-correlation... INFO @ Fri, 05 Jul 2019 23:26:27: end of X-cor INFO @ Fri, 05 Jul 2019 23:26:27: #2 finished! INFO @ Fri, 05 Jul 2019 23:26:27: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 23:26:27: #2 alternative fragment length(s) may be 0,97,106,109,132,155,179 bps INFO @ Fri, 05 Jul 2019 23:26:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.10_model.r INFO @ Fri, 05 Jul 2019 23:26:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:26:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:26:27: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:26:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:26:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:26:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.20_summits.bed INFO @ Fri, 05 Jul 2019 23:26:28: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (273 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:26:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:26:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:27:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:27:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381231/SRX381231.10_summits.bed INFO @ Fri, 05 Jul 2019 23:27:08: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (393 records, 4 fields): 4 millis CompletedMACS2peakCalling