Job ID = 6454099 SRX = SRX181441 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:57:04 prefetch.2.10.7: 1) Downloading 'SRR548178'... 2020-06-21T08:57:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:58:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:58:33 prefetch.2.10.7: 'SRR548178' is valid 2020-06-21T08:58:33 prefetch.2.10.7: 1) 'SRR548178' was downloaded successfully Read 8233797 spots for SRR548178/SRR548178.sra Written 8233797 spots for SRR548178/SRR548178.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: 00:01:09 8233797 reads; of these: 8233797 (100.00%) were unpaired; of these: 4478295 (54.39%) aligned 0 times 3372564 (40.96%) aligned exactly 1 time 382938 (4.65%) aligned >1 times 45.61% overall alignment rate Time searching: 00:01:09 Overall time: 00:01:09 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 2858764 / 3755502 = 0.7612 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 @ Sun, 21 Jun 2020 18:01:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.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 @ Sun, 21 Jun 2020 18:01:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:01:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:01:17: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:01:17: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:01:17: #1 total tags in treatment: 896738 INFO @ Sun, 21 Jun 2020 18:01:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:01:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:01:17: #1 tags after filtering in treatment: 896302 INFO @ Sun, 21 Jun 2020 18:01:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:01:17: #1 finished! INFO @ Sun, 21 Jun 2020 18:01:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:01:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:01:17: #2 number of paired peaks: 811 WARNING @ Sun, 21 Jun 2020 18:01:17: Fewer paired peaks (811) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 811 pairs to build model! INFO @ Sun, 21 Jun 2020 18:01:17: start model_add_line... INFO @ Sun, 21 Jun 2020 18:01:17: start X-correlation... INFO @ Sun, 21 Jun 2020 18:01:17: end of X-cor INFO @ Sun, 21 Jun 2020 18:01:17: #2 finished! INFO @ Sun, 21 Jun 2020 18:01:17: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 18:01:17: #2 alternative fragment length(s) may be 53,227,524 bps INFO @ Sun, 21 Jun 2020 18:01:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.05_model.r WARNING @ Sun, 21 Jun 2020 18:01:17: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:01:17: #2 You may need to consider one of the other alternative d(s): 53,227,524 WARNING @ Sun, 21 Jun 2020 18:01:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:01:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:01:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:01:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:01:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:01:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:01:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.05_summits.bed INFO @ Sun, 21 Jun 2020 18:01:21: Done! pass1 - making usageList (82 chroms): 1 millis pass2 - checking and writing primary data (174 records, 4 fields): 4 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 @ Sun, 21 Jun 2020 18:01:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.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 @ Sun, 21 Jun 2020 18:01:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:01:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:01:46: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:01:46: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:01:46: #1 total tags in treatment: 896738 INFO @ Sun, 21 Jun 2020 18:01:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:01:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:01:47: #1 tags after filtering in treatment: 896302 INFO @ Sun, 21 Jun 2020 18:01:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:01:47: #1 finished! INFO @ Sun, 21 Jun 2020 18:01:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:01:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:01:47: #2 number of paired peaks: 811 WARNING @ Sun, 21 Jun 2020 18:01:47: Fewer paired peaks (811) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 811 pairs to build model! INFO @ Sun, 21 Jun 2020 18:01:47: start model_add_line... INFO @ Sun, 21 Jun 2020 18:01:47: start X-correlation... INFO @ Sun, 21 Jun 2020 18:01:47: end of X-cor INFO @ Sun, 21 Jun 2020 18:01:47: #2 finished! INFO @ Sun, 21 Jun 2020 18:01:47: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 18:01:47: #2 alternative fragment length(s) may be 53,227,524 bps INFO @ Sun, 21 Jun 2020 18:01:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.10_model.r WARNING @ Sun, 21 Jun 2020 18:01:47: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:01:47: #2 You may need to consider one of the other alternative d(s): 53,227,524 WARNING @ Sun, 21 Jun 2020 18:01:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:01:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:01:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:01:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:01:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:01:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:01:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.10_summits.bed INFO @ Sun, 21 Jun 2020 18:01:51: Done! pass1 - making usageList (52 chroms): 1 millis pass2 - checking and writing primary data (91 records, 4 fields): 4 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 @ Sun, 21 Jun 2020 18:02:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.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 @ Sun, 21 Jun 2020 18:02:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:02:11: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:02:16: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:02:16: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:02:16: #1 total tags in treatment: 896738 INFO @ Sun, 21 Jun 2020 18:02:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:02:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:02:17: #1 tags after filtering in treatment: 896302 INFO @ Sun, 21 Jun 2020 18:02:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:02:17: #1 finished! INFO @ Sun, 21 Jun 2020 18:02:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:02:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:02:17: #2 number of paired peaks: 811 WARNING @ Sun, 21 Jun 2020 18:02:17: Fewer paired peaks (811) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 811 pairs to build model! INFO @ Sun, 21 Jun 2020 18:02:17: start model_add_line... INFO @ Sun, 21 Jun 2020 18:02:17: start X-correlation... INFO @ Sun, 21 Jun 2020 18:02:17: end of X-cor INFO @ Sun, 21 Jun 2020 18:02:17: #2 finished! INFO @ Sun, 21 Jun 2020 18:02:17: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 18:02:17: #2 alternative fragment length(s) may be 53,227,524 bps INFO @ Sun, 21 Jun 2020 18:02:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.20_model.r WARNING @ Sun, 21 Jun 2020 18:02:17: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:02:17: #2 You may need to consider one of the other alternative d(s): 53,227,524 WARNING @ Sun, 21 Jun 2020 18:02:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:02:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:02:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:02:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:02:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:02:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:02:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181441/SRX181441.20_summits.bed INFO @ Sun, 21 Jun 2020 18:02:21: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (49 records, 4 fields): 2 millis CompletedMACS2peakCalling