Job ID = 2007874 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:34:49 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 : 184,858 reads read : 369,716 reads written : 369,716 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: 00:00:07 184858 reads; of these: 184858 (100.00%) were paired; of these: 13558 (7.33%) aligned concordantly 0 times 156845 (84.85%) aligned concordantly exactly 1 time 14455 (7.82%) aligned concordantly >1 times ---- 13558 pairs aligned concordantly 0 times; of these: 6712 (49.51%) aligned discordantly 1 time ---- 6846 pairs aligned 0 times concordantly or discordantly; of these: 13692 mates make up the pairs; of these: 10675 (77.97%) aligned 0 times 1490 (10.88%) aligned exactly 1 time 1527 (11.15%) aligned >1 times 97.11% overall alignment rate Time searching: 00:00:07 Overall time: 00:00:07 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] 545 / 177616 = 0.0031 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 16:36:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.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 16:36:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:36:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:37:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.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 16:37:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:37:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:37:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.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 16:37:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:37:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:37:02: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:37:02: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:37:02: #1 total tags in treatment: 170767 INFO @ Fri, 05 Jul 2019 16:37:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:37:02: #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 16:37:02: #1 tags after filtering in treatment: 168971 INFO @ Fri, 05 Jul 2019 16:37:02: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:37:02: #1 finished! INFO @ Fri, 05 Jul 2019 16:37:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:37:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:37:02: #2 number of paired peaks: 284 WARNING @ Fri, 05 Jul 2019 16:37:02: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Fri, 05 Jul 2019 16:37:02: start model_add_line... INFO @ Fri, 05 Jul 2019 16:37:02: start X-correlation... INFO @ Fri, 05 Jul 2019 16:37:02: end of X-cor INFO @ Fri, 05 Jul 2019 16:37:02: #2 finished! INFO @ Fri, 05 Jul 2019 16:37:02: #2 predicted fragment length is 192 bps INFO @ Fri, 05 Jul 2019 16:37:02: #2 alternative fragment length(s) may be 152,173,192,208,229,278 bps INFO @ Fri, 05 Jul 2019 16:37:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.05_model.r INFO @ Fri, 05 Jul 2019 16:37:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:37:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:37:02: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:37:02: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:37:02: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:37:02: #1 total tags in treatment: 170767 INFO @ Fri, 05 Jul 2019 16:37:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:37:02: #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 16:37:02: #1 tags after filtering in treatment: 168971 INFO @ Fri, 05 Jul 2019 16:37:02: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:37:02: #1 finished! INFO @ Fri, 05 Jul 2019 16:37:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:37:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:37:02: #2 number of paired peaks: 284 WARNING @ Fri, 05 Jul 2019 16:37:02: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Fri, 05 Jul 2019 16:37:02: start model_add_line... INFO @ Fri, 05 Jul 2019 16:37:02: start X-correlation... INFO @ Fri, 05 Jul 2019 16:37:02: end of X-cor INFO @ Fri, 05 Jul 2019 16:37:02: #2 finished! INFO @ Fri, 05 Jul 2019 16:37:02: #2 predicted fragment length is 192 bps INFO @ Fri, 05 Jul 2019 16:37:02: #2 alternative fragment length(s) may be 152,173,192,208,229,278 bps INFO @ Fri, 05 Jul 2019 16:37:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.10_model.r INFO @ Fri, 05 Jul 2019 16:37:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:37:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:37:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:37:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:37:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.05_summits.bed INFO @ Fri, 05 Jul 2019 16:37:02: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (165 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 16:37:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:37:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:37:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:37:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.10_summits.bed INFO @ Fri, 05 Jul 2019 16:37:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (55 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:37:03: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:37:03: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:37:03: #1 total tags in treatment: 170767 INFO @ Fri, 05 Jul 2019 16:37:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:37:03: #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 16:37:03: #1 tags after filtering in treatment: 168971 INFO @ Fri, 05 Jul 2019 16:37:03: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:37:03: #1 finished! INFO @ Fri, 05 Jul 2019 16:37:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:37:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:37:03: #2 number of paired peaks: 284 WARNING @ Fri, 05 Jul 2019 16:37:03: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Fri, 05 Jul 2019 16:37:03: start model_add_line... INFO @ Fri, 05 Jul 2019 16:37:03: start X-correlation... INFO @ Fri, 05 Jul 2019 16:37:03: end of X-cor INFO @ Fri, 05 Jul 2019 16:37:03: #2 finished! INFO @ Fri, 05 Jul 2019 16:37:03: #2 predicted fragment length is 192 bps INFO @ Fri, 05 Jul 2019 16:37:03: #2 alternative fragment length(s) may be 152,173,192,208,229,278 bps INFO @ Fri, 05 Jul 2019 16:37:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.20_model.r INFO @ Fri, 05 Jul 2019 16:37:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:37:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:37:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:37:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:37:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:37:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462413/ERX462413.20_summits.bed INFO @ Fri, 05 Jul 2019 16:37:04: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (15 records, 4 fields): 1 millis BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling