Job ID = 6528345 SRX = SRX5360597 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:50:25 prefetch.2.10.7: 1) Downloading 'SRR8559073'... 2020-06-29T14:50:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:50:50 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:50:50 prefetch.2.10.7: 'SRR8559073' is valid 2020-06-29T14:50:50 prefetch.2.10.7: 1) 'SRR8559073' was downloaded successfully Read 1183934 spots for SRR8559073/SRR8559073.sra Written 1183934 spots for SRR8559073/SRR8559073.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: 00:00:01 Multiseed full-index search: 00:00:14 1183934 reads; of these: 1183934 (100.00%) were unpaired; of these: 450830 (38.08%) aligned 0 times 700970 (59.21%) aligned exactly 1 time 32134 (2.71%) aligned >1 times 61.92% overall alignment rate Time searching: 00:00:15 Overall time: 00:00:15 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] 554723 / 733104 = 0.7567 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 23:52:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.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 23:52:03: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:52:03: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:52:04: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:52:04: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:52:04: #1 total tags in treatment: 178381 INFO @ Mon, 29 Jun 2020 23:52:04: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:52:04: #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 23:52:04: #1 tags after filtering in treatment: 178380 INFO @ Mon, 29 Jun 2020 23:52:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:52:04: #1 finished! INFO @ Mon, 29 Jun 2020 23:52:04: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:52:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:52:04: #2 number of paired peaks: 143 WARNING @ Mon, 29 Jun 2020 23:52:04: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Mon, 29 Jun 2020 23:52:04: start model_add_line... INFO @ Mon, 29 Jun 2020 23:52:04: start X-correlation... INFO @ Mon, 29 Jun 2020 23:52:04: end of X-cor INFO @ Mon, 29 Jun 2020 23:52:04: #2 finished! INFO @ Mon, 29 Jun 2020 23:52:04: #2 predicted fragment length is 50 bps INFO @ Mon, 29 Jun 2020 23:52:04: #2 alternative fragment length(s) may be 50,377,479,498,520 bps INFO @ Mon, 29 Jun 2020 23:52:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.05_model.r WARNING @ Mon, 29 Jun 2020 23:52:04: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:52:04: #2 You may need to consider one of the other alternative d(s): 50,377,479,498,520 WARNING @ Mon, 29 Jun 2020 23:52:04: #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 23:52:04: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:52:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:52:04: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:52:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:52:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:52:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.05_summits.bed INFO @ Mon, 29 Jun 2020 23:52:04: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (161 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 23:52:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.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 23:52:33: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:52:33: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:52:34: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:52:34: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:52:34: #1 total tags in treatment: 178381 INFO @ Mon, 29 Jun 2020 23:52:34: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:52:34: #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 23:52:34: #1 tags after filtering in treatment: 178380 INFO @ Mon, 29 Jun 2020 23:52:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:52:34: #1 finished! INFO @ Mon, 29 Jun 2020 23:52:34: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:52:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:52:34: #2 number of paired peaks: 143 WARNING @ Mon, 29 Jun 2020 23:52:34: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Mon, 29 Jun 2020 23:52:34: start model_add_line... INFO @ Mon, 29 Jun 2020 23:52:34: start X-correlation... INFO @ Mon, 29 Jun 2020 23:52:34: end of X-cor INFO @ Mon, 29 Jun 2020 23:52:34: #2 finished! INFO @ Mon, 29 Jun 2020 23:52:34: #2 predicted fragment length is 50 bps INFO @ Mon, 29 Jun 2020 23:52:34: #2 alternative fragment length(s) may be 50,377,479,498,520 bps INFO @ Mon, 29 Jun 2020 23:52:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.10_model.r WARNING @ Mon, 29 Jun 2020 23:52:34: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:52:34: #2 You may need to consider one of the other alternative d(s): 50,377,479,498,520 WARNING @ Mon, 29 Jun 2020 23:52:34: #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 23:52:34: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:52:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:52:34: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:52:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:52:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:52:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.10_summits.bed INFO @ Mon, 29 Jun 2020 23:52:34: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (119 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 23:53:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.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 23:53:03: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:53:03: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:53:04: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:53:04: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:53:04: #1 total tags in treatment: 178381 INFO @ Mon, 29 Jun 2020 23:53:04: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:53:04: #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 23:53:04: #1 tags after filtering in treatment: 178380 INFO @ Mon, 29 Jun 2020 23:53:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:53:04: #1 finished! INFO @ Mon, 29 Jun 2020 23:53:04: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:53:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:53:04: #2 number of paired peaks: 143 WARNING @ Mon, 29 Jun 2020 23:53:04: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Mon, 29 Jun 2020 23:53:04: start model_add_line... INFO @ Mon, 29 Jun 2020 23:53:04: start X-correlation... INFO @ Mon, 29 Jun 2020 23:53:04: end of X-cor INFO @ Mon, 29 Jun 2020 23:53:04: #2 finished! INFO @ Mon, 29 Jun 2020 23:53:04: #2 predicted fragment length is 50 bps INFO @ Mon, 29 Jun 2020 23:53:04: #2 alternative fragment length(s) may be 50,377,479,498,520 bps INFO @ Mon, 29 Jun 2020 23:53:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.20_model.r WARNING @ Mon, 29 Jun 2020 23:53:04: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:53:04: #2 You may need to consider one of the other alternative d(s): 50,377,479,498,520 WARNING @ Mon, 29 Jun 2020 23:53:04: #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 23:53:04: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:53:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:53:04: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:53:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:53:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:53:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360597/SRX5360597.20_summits.bed INFO @ Mon, 29 Jun 2020 23:53:04: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (73 records, 4 fields): 1 millis CompletedMACS2peakCalling