Job ID = 2009910 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T11:39:09 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 : 4,037,633 reads read : 8,075,266 reads written : 8,075,266 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: 00:03:07 4037633 reads; of these: 4037633 (100.00%) were paired; of these: 1026755 (25.43%) aligned concordantly 0 times 2268007 (56.17%) aligned concordantly exactly 1 time 742871 (18.40%) aligned concordantly >1 times ---- 1026755 pairs aligned concordantly 0 times; of these: 30186 (2.94%) aligned discordantly 1 time ---- 996569 pairs aligned 0 times concordantly or discordantly; of these: 1993138 mates make up the pairs; of these: 1838895 (92.26%) aligned 0 times 97319 (4.88%) aligned exactly 1 time 56924 (2.86%) aligned >1 times 77.23% overall alignment rate Time searching: 00:03:07 Overall time: 00:03:07 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] 181583 / 3034466 = 0.0598 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 20:48:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.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 20:48:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:48:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:48:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.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 20:48:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:48:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:48:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.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 20:48:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:48:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:48:48: 1000000 INFO @ Fri, 05 Jul 2019 20:48:48: 1000000 INFO @ Fri, 05 Jul 2019 20:48:50: 1000000 INFO @ Fri, 05 Jul 2019 20:48:54: 2000000 INFO @ Fri, 05 Jul 2019 20:48:54: 2000000 INFO @ Fri, 05 Jul 2019 20:48:57: 2000000 INFO @ Fri, 05 Jul 2019 20:49:01: 3000000 INFO @ Fri, 05 Jul 2019 20:49:01: 3000000 INFO @ Fri, 05 Jul 2019 20:49:03: 3000000 INFO @ Fri, 05 Jul 2019 20:49:07: 4000000 INFO @ Fri, 05 Jul 2019 20:49:08: 4000000 INFO @ Fri, 05 Jul 2019 20:49:10: 4000000 INFO @ Fri, 05 Jul 2019 20:49:13: 5000000 INFO @ Fri, 05 Jul 2019 20:49:15: 5000000 INFO @ Fri, 05 Jul 2019 20:49:16: 5000000 INFO @ Fri, 05 Jul 2019 20:49:18: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:49:18: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:49:18: #1 total tags in treatment: 2829598 INFO @ Fri, 05 Jul 2019 20:49:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:49:18: #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 20:49:18: #1 tags after filtering in treatment: 1548116 INFO @ Fri, 05 Jul 2019 20:49:18: #1 Redundant rate of treatment: 0.45 INFO @ Fri, 05 Jul 2019 20:49:18: #1 finished! INFO @ Fri, 05 Jul 2019 20:49:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:49:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:49:18: #2 number of paired peaks: 864 WARNING @ Fri, 05 Jul 2019 20:49:18: Fewer paired peaks (864) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 864 pairs to build model! INFO @ Fri, 05 Jul 2019 20:49:18: start model_add_line... INFO @ Fri, 05 Jul 2019 20:49:18: start X-correlation... INFO @ Fri, 05 Jul 2019 20:49:18: end of X-cor INFO @ Fri, 05 Jul 2019 20:49:18: #2 finished! INFO @ Fri, 05 Jul 2019 20:49:18: #2 predicted fragment length is 152 bps INFO @ Fri, 05 Jul 2019 20:49:18: #2 alternative fragment length(s) may be 2,152 bps INFO @ Fri, 05 Jul 2019 20:49:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.10_model.r INFO @ Fri, 05 Jul 2019 20:49:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:49:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:49:21: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:49:21: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:49:21: #1 total tags in treatment: 2829598 INFO @ Fri, 05 Jul 2019 20:49:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:49:21: #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 20:49:21: #1 tags after filtering in treatment: 1548116 INFO @ Fri, 05 Jul 2019 20:49:21: #1 Redundant rate of treatment: 0.45 INFO @ Fri, 05 Jul 2019 20:49:21: #1 finished! INFO @ Fri, 05 Jul 2019 20:49:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:49:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:49:21: #2 number of paired peaks: 864 WARNING @ Fri, 05 Jul 2019 20:49:21: Fewer paired peaks (864) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 864 pairs to build model! INFO @ Fri, 05 Jul 2019 20:49:21: start model_add_line... INFO @ Fri, 05 Jul 2019 20:49:21: start X-correlation... INFO @ Fri, 05 Jul 2019 20:49:21: end of X-cor INFO @ Fri, 05 Jul 2019 20:49:21: #2 finished! INFO @ Fri, 05 Jul 2019 20:49:21: #2 predicted fragment length is 152 bps INFO @ Fri, 05 Jul 2019 20:49:21: #2 alternative fragment length(s) may be 2,152 bps INFO @ Fri, 05 Jul 2019 20:49:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.05_model.r INFO @ Fri, 05 Jul 2019 20:49:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:49:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:49:22: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:49:22: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:49:22: #1 total tags in treatment: 2829598 INFO @ Fri, 05 Jul 2019 20:49:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:49:22: #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 20:49:22: #1 tags after filtering in treatment: 1548116 INFO @ Fri, 05 Jul 2019 20:49:22: #1 Redundant rate of treatment: 0.45 INFO @ Fri, 05 Jul 2019 20:49:22: #1 finished! INFO @ Fri, 05 Jul 2019 20:49:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:49:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:49:22: #2 number of paired peaks: 864 WARNING @ Fri, 05 Jul 2019 20:49:22: Fewer paired peaks (864) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 864 pairs to build model! INFO @ Fri, 05 Jul 2019 20:49:22: start model_add_line... INFO @ Fri, 05 Jul 2019 20:49:23: start X-correlation... INFO @ Fri, 05 Jul 2019 20:49:23: end of X-cor INFO @ Fri, 05 Jul 2019 20:49:23: #2 finished! INFO @ Fri, 05 Jul 2019 20:49:23: #2 predicted fragment length is 152 bps INFO @ Fri, 05 Jul 2019 20:49:23: #2 alternative fragment length(s) may be 2,152 bps INFO @ Fri, 05 Jul 2019 20:49:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.20_model.r INFO @ Fri, 05 Jul 2019 20:49:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:49:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:49:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:49:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.10_peaks.xls INFO @ Fri, 05 Jul 2019 20:49:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:49:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.10_summits.bed INFO @ Fri, 05 Jul 2019 20:49:28: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (578 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 20:49:29: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:49:30: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:49:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.05_peaks.xls INFO @ Fri, 05 Jul 2019 20:49:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:49:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.05_summits.bed INFO @ Fri, 05 Jul 2019 20:49:30: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (724 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:49:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.20_peaks.xls INFO @ Fri, 05 Jul 2019 20:49:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:49:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339847/SRX2339847.20_summits.bed INFO @ Fri, 05 Jul 2019 20:49:32: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (423 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。