Job ID = 2016547 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-07T06:48:38 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 9,675,664 reads read : 19,351,328 reads written : 19,351,328 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:16 9675664 reads; of these: 9675664 (100.00%) were paired; of these: 1459864 (15.09%) aligned concordantly 0 times 7024932 (72.60%) aligned concordantly exactly 1 time 1190868 (12.31%) aligned concordantly >1 times ---- 1459864 pairs aligned concordantly 0 times; of these: 400067 (27.40%) aligned discordantly 1 time ---- 1059797 pairs aligned 0 times concordantly or discordantly; of these: 2119594 mates make up the pairs; of these: 1844274 (87.01%) aligned 0 times 124672 (5.88%) aligned exactly 1 time 150648 (7.11%) aligned >1 times 90.47% overall alignment rate Time searching: 00:02:17 Overall time: 00:02:17 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_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] 5558165 / 8613490 = 0.6453 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, 07 Jul 2019 16:02:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.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 @ Sun, 07 Jul 2019 16:02:44: #1 read tag files... INFO @ Sun, 07 Jul 2019 16:02:44: #1 read treatment tags... INFO @ Sun, 07 Jul 2019 16:02:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.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 @ Sun, 07 Jul 2019 16:02:44: #1 read tag files... INFO @ Sun, 07 Jul 2019 16:02:44: #1 read treatment tags... INFO @ Sun, 07 Jul 2019 16:02:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.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 @ Sun, 07 Jul 2019 16:02:44: #1 read tag files... INFO @ Sun, 07 Jul 2019 16:02:44: #1 read treatment tags... INFO @ Sun, 07 Jul 2019 16:02:51: 1000000 INFO @ Sun, 07 Jul 2019 16:02:51: 1000000 INFO @ Sun, 07 Jul 2019 16:02:51: 1000000 INFO @ Sun, 07 Jul 2019 16:02:57: 2000000 INFO @ Sun, 07 Jul 2019 16:02:58: 2000000 INFO @ Sun, 07 Jul 2019 16:02:59: 2000000 INFO @ Sun, 07 Jul 2019 16:03:03: 3000000 INFO @ Sun, 07 Jul 2019 16:03:04: 3000000 INFO @ Sun, 07 Jul 2019 16:03:07: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 07 Jul 2019 16:03:09: 4000000 INFO @ Sun, 07 Jul 2019 16:03:11: 4000000 BigWig に変換しました。 INFO @ Sun, 07 Jul 2019 16:03:15: 4000000 INFO @ Sun, 07 Jul 2019 16:03:15: 5000000 INFO @ Sun, 07 Jul 2019 16:03:17: 5000000 INFO @ Sun, 07 Jul 2019 16:03:21: 6000000 INFO @ Sun, 07 Jul 2019 16:03:22: 5000000 INFO @ Sun, 07 Jul 2019 16:03:23: #1 tag size is determined as 51 bps INFO @ Sun, 07 Jul 2019 16:03:23: #1 tag size = 51 INFO @ Sun, 07 Jul 2019 16:03:23: #1 total tags in treatment: 2935305 INFO @ Sun, 07 Jul 2019 16:03:23: #1 user defined the maximum tags... INFO @ Sun, 07 Jul 2019 16:03:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Jul 2019 16:03:23: #1 tags after filtering in treatment: 1449850 INFO @ Sun, 07 Jul 2019 16:03:23: #1 Redundant rate of treatment: 0.51 INFO @ Sun, 07 Jul 2019 16:03:23: #1 finished! INFO @ Sun, 07 Jul 2019 16:03:23: #2 Build Peak Model... INFO @ Sun, 07 Jul 2019 16:03:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Jul 2019 16:03:23: #2 number of paired peaks: 1289 INFO @ Sun, 07 Jul 2019 16:03:23: start model_add_line... INFO @ Sun, 07 Jul 2019 16:03:23: start X-correlation... INFO @ Sun, 07 Jul 2019 16:03:24: 6000000 INFO @ Sun, 07 Jul 2019 16:03:24: end of X-cor INFO @ Sun, 07 Jul 2019 16:03:24: #2 finished! INFO @ Sun, 07 Jul 2019 16:03:24: #2 predicted fragment length is 278 bps INFO @ Sun, 07 Jul 2019 16:03:24: #2 alternative fragment length(s) may be 0,47,91,113,163,190,229,251,278,295,318,357 bps INFO @ Sun, 07 Jul 2019 16:03:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.20_model.r INFO @ Sun, 07 Jul 2019 16:03:24: #3 Call peaks... INFO @ Sun, 07 Jul 2019 16:03:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Jul 2019 16:03:26: #1 tag size is determined as 51 bps INFO @ Sun, 07 Jul 2019 16:03:26: #1 tag size = 51 INFO @ Sun, 07 Jul 2019 16:03:26: #1 total tags in treatment: 2935305 INFO @ Sun, 07 Jul 2019 16:03:26: #1 user defined the maximum tags... INFO @ Sun, 07 Jul 2019 16:03:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Jul 2019 16:03:26: #1 tags after filtering in treatment: 1449850 INFO @ Sun, 07 Jul 2019 16:03:26: #1 Redundant rate of treatment: 0.51 INFO @ Sun, 07 Jul 2019 16:03:26: #1 finished! INFO @ Sun, 07 Jul 2019 16:03:26: #2 Build Peak Model... INFO @ Sun, 07 Jul 2019 16:03:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Jul 2019 16:03:27: #2 number of paired peaks: 1289 INFO @ Sun, 07 Jul 2019 16:03:27: start model_add_line... INFO @ Sun, 07 Jul 2019 16:03:27: start X-correlation... INFO @ Sun, 07 Jul 2019 16:03:27: end of X-cor INFO @ Sun, 07 Jul 2019 16:03:27: #2 finished! INFO @ Sun, 07 Jul 2019 16:03:27: #2 predicted fragment length is 278 bps INFO @ Sun, 07 Jul 2019 16:03:27: #2 alternative fragment length(s) may be 0,47,91,113,163,190,229,251,278,295,318,357 bps INFO @ Sun, 07 Jul 2019 16:03:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.10_model.r INFO @ Sun, 07 Jul 2019 16:03:27: #3 Call peaks... INFO @ Sun, 07 Jul 2019 16:03:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Jul 2019 16:03:30: 6000000 INFO @ Sun, 07 Jul 2019 16:03:33: #1 tag size is determined as 51 bps INFO @ Sun, 07 Jul 2019 16:03:33: #1 tag size = 51 INFO @ Sun, 07 Jul 2019 16:03:33: #1 total tags in treatment: 2935305 INFO @ Sun, 07 Jul 2019 16:03:33: #1 user defined the maximum tags... INFO @ Sun, 07 Jul 2019 16:03:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Jul 2019 16:03:33: #1 tags after filtering in treatment: 1449850 INFO @ Sun, 07 Jul 2019 16:03:33: #1 Redundant rate of treatment: 0.51 INFO @ Sun, 07 Jul 2019 16:03:33: #1 finished! INFO @ Sun, 07 Jul 2019 16:03:33: #2 Build Peak Model... INFO @ Sun, 07 Jul 2019 16:03:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Jul 2019 16:03:33: #2 number of paired peaks: 1289 INFO @ Sun, 07 Jul 2019 16:03:33: start model_add_line... INFO @ Sun, 07 Jul 2019 16:03:33: start X-correlation... INFO @ Sun, 07 Jul 2019 16:03:33: end of X-cor INFO @ Sun, 07 Jul 2019 16:03:33: #2 finished! INFO @ Sun, 07 Jul 2019 16:03:33: #2 predicted fragment length is 278 bps INFO @ Sun, 07 Jul 2019 16:03:33: #2 alternative fragment length(s) may be 0,47,91,113,163,190,229,251,278,295,318,357 bps INFO @ Sun, 07 Jul 2019 16:03:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.05_model.r INFO @ Sun, 07 Jul 2019 16:03:33: #3 Call peaks... INFO @ Sun, 07 Jul 2019 16:03:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Jul 2019 16:03:39: #3 Call peaks for each chromosome... INFO @ Sun, 07 Jul 2019 16:03:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.20_peaks.xls INFO @ Sun, 07 Jul 2019 16:03:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.20_peaks.narrowPeak INFO @ Sun, 07 Jul 2019 16:03:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.20_summits.bed INFO @ Sun, 07 Jul 2019 16:03:40: Done! INFO @ Sun, 07 Jul 2019 16:03:41: #3 Call peaks for each chromosome... pass1 - making usageList (17 chroms): 4 millis pass2 - checking and writing primary data (192 records, 4 fields): 87 millis INFO @ Sun, 07 Jul 2019 16:03:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.10_peaks.xls INFO @ Sun, 07 Jul 2019 16:03:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.10_peaks.narrowPeak INFO @ Sun, 07 Jul 2019 16:03:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.10_summits.bed INFO @ Sun, 07 Jul 2019 16:03:43: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (309 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sun, 07 Jul 2019 16:03:48: #3 Call peaks for each chromosome... INFO @ Sun, 07 Jul 2019 16:03:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.05_peaks.xls INFO @ Sun, 07 Jul 2019 16:03:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.05_peaks.narrowPeak INFO @ Sun, 07 Jul 2019 16:03:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339853/SRX2339853.05_summits.bed INFO @ Sun, 07 Jul 2019 16:03:49: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (363 records, 4 fields): 3 millis CompletedMACS2peakCalling