Job ID = 2007962 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:53:10 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 : 1,692,458 reads read : 3,384,916 reads written : 3,384,916 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: 00:02:13 1692458 reads; of these: 1692458 (100.00%) were paired; of these: 207517 (12.26%) aligned concordantly 0 times 1369241 (80.90%) aligned concordantly exactly 1 time 115700 (6.84%) aligned concordantly >1 times ---- 207517 pairs aligned concordantly 0 times; of these: 33905 (16.34%) aligned discordantly 1 time ---- 173612 pairs aligned 0 times concordantly or discordantly; of these: 347224 mates make up the pairs; of these: 319409 (91.99%) aligned 0 times 18337 (5.28%) aligned exactly 1 time 9478 (2.73%) aligned >1 times 90.56% overall alignment rate Time searching: 00:02:14 Overall time: 00:02:14 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] 210664 / 1513406 = 0.1392 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 17:02:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.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 17:02:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:02:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:02:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.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 17:02:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:02:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:02:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.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 17:02:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:02:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:02:19: 1000000 INFO @ Fri, 05 Jul 2019 17:02:21: 1000000 INFO @ Fri, 05 Jul 2019 17:02:25: 1000000 INFO @ Fri, 05 Jul 2019 17:02:33: 2000000 INFO @ Fri, 05 Jul 2019 17:02:34: 2000000 INFO @ Fri, 05 Jul 2019 17:02:39: 2000000 INFO @ Fri, 05 Jul 2019 17:02:40: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:02:40: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:02:40: #1 total tags in treatment: 1276539 INFO @ Fri, 05 Jul 2019 17:02:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:02:40: #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 17:02:40: #1 tags after filtering in treatment: 1221973 INFO @ Fri, 05 Jul 2019 17:02:40: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 17:02:40: #1 finished! INFO @ Fri, 05 Jul 2019 17:02:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:02:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:02:40: #2 number of paired peaks: 164 WARNING @ Fri, 05 Jul 2019 17:02:40: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 05 Jul 2019 17:02:40: start model_add_line... INFO @ Fri, 05 Jul 2019 17:02:40: start X-correlation... INFO @ Fri, 05 Jul 2019 17:02:40: end of X-cor INFO @ Fri, 05 Jul 2019 17:02:40: #2 finished! INFO @ Fri, 05 Jul 2019 17:02:40: #2 predicted fragment length is 180 bps INFO @ Fri, 05 Jul 2019 17:02:40: #2 alternative fragment length(s) may be 58,61,106,139,157,180,186,220,232,240,257,273,298,317,394,425,469,491,530,534,560 bps INFO @ Fri, 05 Jul 2019 17:02:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.10_model.r WARNING @ Fri, 05 Jul 2019 17:02:40: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:02:40: #2 You may need to consider one of the other alternative d(s): 58,61,106,139,157,180,186,220,232,240,257,273,298,317,394,425,469,491,530,534,560 WARNING @ Fri, 05 Jul 2019 17:02:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 17:02:40: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:02:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:02:43: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:02:43: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:02:43: #1 total tags in treatment: 1276539 INFO @ Fri, 05 Jul 2019 17:02:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:02:43: #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 17:02:43: #1 tags after filtering in treatment: 1221973 INFO @ Fri, 05 Jul 2019 17:02:43: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 17:02:43: #1 finished! INFO @ Fri, 05 Jul 2019 17:02:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:02:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:02:43: #2 number of paired peaks: 164 WARNING @ Fri, 05 Jul 2019 17:02:43: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 05 Jul 2019 17:02:43: start model_add_line... INFO @ Fri, 05 Jul 2019 17:02:43: start X-correlation... INFO @ Fri, 05 Jul 2019 17:02:43: end of X-cor INFO @ Fri, 05 Jul 2019 17:02:43: #2 finished! INFO @ Fri, 05 Jul 2019 17:02:43: #2 predicted fragment length is 180 bps INFO @ Fri, 05 Jul 2019 17:02:43: #2 alternative fragment length(s) may be 58,61,106,139,157,180,186,220,232,240,257,273,298,317,394,425,469,491,530,534,560 bps INFO @ Fri, 05 Jul 2019 17:02:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.05_model.r WARNING @ Fri, 05 Jul 2019 17:02:43: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:02:43: #2 You may need to consider one of the other alternative d(s): 58,61,106,139,157,180,186,220,232,240,257,273,298,317,394,425,469,491,530,534,560 WARNING @ Fri, 05 Jul 2019 17:02:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 17:02:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:02:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:02:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:02:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:02:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:02:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.10_summits.bed INFO @ Fri, 05 Jul 2019 17:02:45: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (16 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:02:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:02:48: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:02:48: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:02:48: #1 total tags in treatment: 1276539 INFO @ Fri, 05 Jul 2019 17:02:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:02:48: #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 17:02:48: #1 tags after filtering in treatment: 1221973 INFO @ Fri, 05 Jul 2019 17:02:48: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 17:02:48: #1 finished! INFO @ Fri, 05 Jul 2019 17:02:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:02:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:02:48: #2 number of paired peaks: 164 WARNING @ Fri, 05 Jul 2019 17:02:48: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 05 Jul 2019 17:02:48: start model_add_line... INFO @ Fri, 05 Jul 2019 17:02:48: start X-correlation... INFO @ Fri, 05 Jul 2019 17:02:48: end of X-cor INFO @ Fri, 05 Jul 2019 17:02:48: #2 finished! INFO @ Fri, 05 Jul 2019 17:02:48: #2 predicted fragment length is 180 bps INFO @ Fri, 05 Jul 2019 17:02:48: #2 alternative fragment length(s) may be 58,61,106,139,157,180,186,220,232,240,257,273,298,317,394,425,469,491,530,534,560 bps INFO @ Fri, 05 Jul 2019 17:02:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.20_model.r WARNING @ Fri, 05 Jul 2019 17:02:48: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:02:48: #2 You may need to consider one of the other alternative d(s): 58,61,106,139,157,180,186,220,232,240,257,273,298,317,394,425,469,491,530,534,560 WARNING @ Fri, 05 Jul 2019 17:02:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 17:02:48: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:02:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:02:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:02:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:02:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.05_summits.bed INFO @ Fri, 05 Jul 2019 17:02:49: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (51 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 17:02:51: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:02:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:02:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:02:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471753/ERX471753.20_summits.bed INFO @ Fri, 05 Jul 2019 17:02:53: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。