Job ID = 5790870 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T22:58:07 fasterq-dump.2.9.6 fatal: SIGNAL - Segmentation fault spots read : 503,290 reads read : 1,006,580 reads written : 503,290 reads 0-length : 503,290 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: 00:00:06 503290 reads; of these: 503290 (100.00%) were unpaired; of these: 165 (0.03%) aligned 0 times 463241 (92.04%) aligned exactly 1 time 39884 (7.92%) aligned >1 times 99.97% overall alignment rate Time searching: 00:00:06 Overall time: 00:00:06 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_rmdupse_core] 32011 / 503125 = 0.0636 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 08:00:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.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 @ Wed, 22 Apr 2020 08:00:26: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:00:26: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:00:30: #1 tag size is determined as 76 bps INFO @ Wed, 22 Apr 2020 08:00:30: #1 tag size = 76 INFO @ Wed, 22 Apr 2020 08:00:30: #1 total tags in treatment: 471114 INFO @ Wed, 22 Apr 2020 08:00:30: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:00:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:00:30: #1 tags after filtering in treatment: 471114 INFO @ Wed, 22 Apr 2020 08:00:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:00:30: #1 finished! INFO @ Wed, 22 Apr 2020 08:00:30: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:00:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:00:30: #2 number of paired peaks: 270 WARNING @ Wed, 22 Apr 2020 08:00:30: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Wed, 22 Apr 2020 08:00:30: start model_add_line... INFO @ Wed, 22 Apr 2020 08:00:30: start X-correlation... INFO @ Wed, 22 Apr 2020 08:00:30: end of X-cor INFO @ Wed, 22 Apr 2020 08:00:30: #2 finished! INFO @ Wed, 22 Apr 2020 08:00:30: #2 predicted fragment length is 213 bps INFO @ Wed, 22 Apr 2020 08:00:30: #2 alternative fragment length(s) may be 191,213 bps INFO @ Wed, 22 Apr 2020 08:00:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.05_model.r INFO @ Wed, 22 Apr 2020 08:00:30: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:00:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:00:31: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:00:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:00:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:00:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.05_summits.bed INFO @ Wed, 22 Apr 2020 08:00:32: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (423 records, 4 fields): 2 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 08:00:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.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 @ Wed, 22 Apr 2020 08:00:56: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:00:56: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:01:04: #1 tag size is determined as 76 bps INFO @ Wed, 22 Apr 2020 08:01:04: #1 tag size = 76 INFO @ Wed, 22 Apr 2020 08:01:04: #1 total tags in treatment: 471114 INFO @ Wed, 22 Apr 2020 08:01:04: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:01:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:01:04: #1 tags after filtering in treatment: 471114 INFO @ Wed, 22 Apr 2020 08:01:04: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:01:04: #1 finished! INFO @ Wed, 22 Apr 2020 08:01:04: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:01:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:01:04: #2 number of paired peaks: 270 WARNING @ Wed, 22 Apr 2020 08:01:04: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Wed, 22 Apr 2020 08:01:04: start model_add_line... INFO @ Wed, 22 Apr 2020 08:01:04: start X-correlation... INFO @ Wed, 22 Apr 2020 08:01:04: end of X-cor INFO @ Wed, 22 Apr 2020 08:01:04: #2 finished! INFO @ Wed, 22 Apr 2020 08:01:04: #2 predicted fragment length is 213 bps INFO @ Wed, 22 Apr 2020 08:01:04: #2 alternative fragment length(s) may be 191,213 bps INFO @ Wed, 22 Apr 2020 08:01:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.10_model.r INFO @ Wed, 22 Apr 2020 08:01:04: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:01:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:01:05: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:01:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:01:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:01:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.10_summits.bed INFO @ Wed, 22 Apr 2020 08:01:06: Done! pass1 - making usageList (16 chroms): 22 millis pass2 - checking and writing primary data (292 records, 4 fields): 34 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 08:01:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.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 @ Wed, 22 Apr 2020 08:01:26: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:01:26: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:01:29: #1 tag size is determined as 76 bps INFO @ Wed, 22 Apr 2020 08:01:29: #1 tag size = 76 INFO @ Wed, 22 Apr 2020 08:01:29: #1 total tags in treatment: 471114 INFO @ Wed, 22 Apr 2020 08:01:29: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:01:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:01:29: #1 tags after filtering in treatment: 471114 INFO @ Wed, 22 Apr 2020 08:01:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:01:29: #1 finished! INFO @ Wed, 22 Apr 2020 08:01:29: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:01:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:01:29: #2 number of paired peaks: 270 WARNING @ Wed, 22 Apr 2020 08:01:29: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Wed, 22 Apr 2020 08:01:29: start model_add_line... INFO @ Wed, 22 Apr 2020 08:01:29: start X-correlation... INFO @ Wed, 22 Apr 2020 08:01:29: end of X-cor INFO @ Wed, 22 Apr 2020 08:01:29: #2 finished! INFO @ Wed, 22 Apr 2020 08:01:29: #2 predicted fragment length is 213 bps INFO @ Wed, 22 Apr 2020 08:01:29: #2 alternative fragment length(s) may be 191,213 bps INFO @ Wed, 22 Apr 2020 08:01:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.20_model.r INFO @ Wed, 22 Apr 2020 08:01:29: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:01:29: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 08:01:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 08:01:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:01:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:01:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5550808/SRX5550808.20_summits.bed INFO @ Wed, 22 Apr 2020 08:01:32: Done! pass1 - making usageList (16 chroms): 7 millis pass2 - checking and writing primary data (158 records, 4 fields): 3 millis CompletedMACS2peakCalling