Job ID = 6528339 SRX = SRX5360593 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:44:09 prefetch.2.10.7: 1) Downloading 'SRR8559069'... 2020-06-29T14:44:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:44:27 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:44:27 prefetch.2.10.7: 'SRR8559069' is valid 2020-06-29T14:44:27 prefetch.2.10.7: 1) 'SRR8559069' was downloaded successfully Read 1173188 spots for SRR8559069/SRR8559069.sra Written 1173188 spots for SRR8559069/SRR8559069.sra 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: 00:00:11 1173188 reads; of these: 1173188 (100.00%) were unpaired; of these: 440597 (37.56%) aligned 0 times 711361 (60.63%) aligned exactly 1 time 21230 (1.81%) aligned >1 times 62.44% overall alignment rate Time searching: 00:00:11 Overall time: 00:00:11 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 651714 / 732591 = 0.8896 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 @ Mon, 29 Jun 2020 23:45:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 29 Jun 2020 23:45:37: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:45:37: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:45:37: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:45:37: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:45:37: #1 total tags in treatment: 80877 INFO @ Mon, 29 Jun 2020 23:45:37: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:45:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:45:37: #1 tags after filtering in treatment: 80875 INFO @ Mon, 29 Jun 2020 23:45:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:45:37: #1 finished! INFO @ Mon, 29 Jun 2020 23:45:37: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:45:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:45:37: #2 number of paired peaks: 118 WARNING @ Mon, 29 Jun 2020 23:45:37: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Mon, 29 Jun 2020 23:45:37: start model_add_line... INFO @ Mon, 29 Jun 2020 23:45:37: start X-correlation... INFO @ Mon, 29 Jun 2020 23:45:37: end of X-cor INFO @ Mon, 29 Jun 2020 23:45:37: #2 finished! INFO @ Mon, 29 Jun 2020 23:45:37: #2 predicted fragment length is 56 bps INFO @ Mon, 29 Jun 2020 23:45:37: #2 alternative fragment length(s) may be 56,318,403,432,462,542,568 bps INFO @ Mon, 29 Jun 2020 23:45:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.05_model.r WARNING @ Mon, 29 Jun 2020 23:45:37: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:45:37: #2 You may need to consider one of the other alternative d(s): 56,318,403,432,462,542,568 WARNING @ Mon, 29 Jun 2020 23:45:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:45:37: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:45:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:45:37: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:45:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:45:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:45:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.05_summits.bed INFO @ Mon, 29 Jun 2020 23:45:37: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (145 records, 4 fields): 1 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 @ Mon, 29 Jun 2020 23:46:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 29 Jun 2020 23:46:07: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:46:07: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:46:07: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:46:07: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:46:07: #1 total tags in treatment: 80877 INFO @ Mon, 29 Jun 2020 23:46:07: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:46:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:46:07: #1 tags after filtering in treatment: 80875 INFO @ Mon, 29 Jun 2020 23:46:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:46:07: #1 finished! INFO @ Mon, 29 Jun 2020 23:46:07: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:46:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:46:07: #2 number of paired peaks: 118 WARNING @ Mon, 29 Jun 2020 23:46:07: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Mon, 29 Jun 2020 23:46:07: start model_add_line... INFO @ Mon, 29 Jun 2020 23:46:07: start X-correlation... INFO @ Mon, 29 Jun 2020 23:46:07: end of X-cor INFO @ Mon, 29 Jun 2020 23:46:07: #2 finished! INFO @ Mon, 29 Jun 2020 23:46:07: #2 predicted fragment length is 56 bps INFO @ Mon, 29 Jun 2020 23:46:07: #2 alternative fragment length(s) may be 56,318,403,432,462,542,568 bps INFO @ Mon, 29 Jun 2020 23:46:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.10_model.r WARNING @ Mon, 29 Jun 2020 23:46:07: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:46:07: #2 You may need to consider one of the other alternative d(s): 56,318,403,432,462,542,568 WARNING @ Mon, 29 Jun 2020 23:46:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:46:07: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:46:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:46:07: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:46:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:46:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:46:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.10_summits.bed INFO @ Mon, 29 Jun 2020 23:46:07: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (102 records, 4 fields): 1 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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:46:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 29 Jun 2020 23:46:37: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:46:37: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:46:37: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:46:37: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:46:37: #1 total tags in treatment: 80877 INFO @ Mon, 29 Jun 2020 23:46:37: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:46:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:46:37: #1 tags after filtering in treatment: 80875 INFO @ Mon, 29 Jun 2020 23:46:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:46:37: #1 finished! INFO @ Mon, 29 Jun 2020 23:46:37: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:46:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:46:37: #2 number of paired peaks: 118 WARNING @ Mon, 29 Jun 2020 23:46:37: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Mon, 29 Jun 2020 23:46:37: start model_add_line... INFO @ Mon, 29 Jun 2020 23:46:37: start X-correlation... INFO @ Mon, 29 Jun 2020 23:46:37: end of X-cor INFO @ Mon, 29 Jun 2020 23:46:37: #2 finished! INFO @ Mon, 29 Jun 2020 23:46:37: #2 predicted fragment length is 56 bps INFO @ Mon, 29 Jun 2020 23:46:37: #2 alternative fragment length(s) may be 56,318,403,432,462,542,568 bps INFO @ Mon, 29 Jun 2020 23:46:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.20_model.r WARNING @ Mon, 29 Jun 2020 23:46:37: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:46:37: #2 You may need to consider one of the other alternative d(s): 56,318,403,432,462,542,568 WARNING @ Mon, 29 Jun 2020 23:46:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:46:37: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:46:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:46:37: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:46:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:46:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:46:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360593/SRX5360593.20_summits.bed INFO @ Mon, 29 Jun 2020 23:46:37: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (47 records, 4 fields): 1 millis CompletedMACS2peakCalling