Job ID = 6456483 SRX = SRX348468 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:21:54 prefetch.2.10.7: 1) Downloading 'SRR976152'... 2020-06-21T11:21:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:33:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:33:34 prefetch.2.10.7: 1) 'SRR976152' was downloaded successfully Read 37626081 spots for SRR976152/SRR976152.sra Written 37626081 spots for SRR976152/SRR976152.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: 00:12:10 37626081 reads; of these: 37626081 (100.00%) were unpaired; of these: 29187698 (77.57%) aligned 0 times 6069000 (16.13%) aligned exactly 1 time 2369383 (6.30%) aligned >1 times 22.43% overall alignment rate Time searching: 00:12:10 Overall time: 00:12:10 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] 4193302 / 8438383 = 0.4969 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 20:52:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.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 20:52:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:52:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:52:36: 1000000 INFO @ Sun, 21 Jun 2020 20:52:47: 2000000 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 20:52:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.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 20:52:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:52:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:52:59: 3000000 INFO @ Sun, 21 Jun 2020 20:53:07: 1000000 INFO @ Sun, 21 Jun 2020 20:53:11: 4000000 INFO @ Sun, 21 Jun 2020 20:53:14: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:53:14: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:53:14: #1 total tags in treatment: 4245081 INFO @ Sun, 21 Jun 2020 20:53:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:53:14: #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 20:53:15: #1 tags after filtering in treatment: 4245041 INFO @ Sun, 21 Jun 2020 20:53:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:53:15: #1 finished! INFO @ Sun, 21 Jun 2020 20:53:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:53:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:53:15: #2 number of paired peaks: 1061 INFO @ Sun, 21 Jun 2020 20:53:15: start model_add_line... INFO @ Sun, 21 Jun 2020 20:53:15: start X-correlation... INFO @ Sun, 21 Jun 2020 20:53:15: end of X-cor INFO @ Sun, 21 Jun 2020 20:53:15: #2 finished! INFO @ Sun, 21 Jun 2020 20:53:15: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 20:53:15: #2 alternative fragment length(s) may be 95,545 bps INFO @ Sun, 21 Jun 2020 20:53:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.05_model.r WARNING @ Sun, 21 Jun 2020 20:53:15: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:53:15: #2 You may need to consider one of the other alternative d(s): 95,545 WARNING @ Sun, 21 Jun 2020 20:53:15: #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 20:53:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:53:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:53:19: 2000000 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 20:53:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:53:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.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 20:53:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:53:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:53:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:53:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:53:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.05_summits.bed INFO @ Sun, 21 Jun 2020 20:53:30: Done! pass1 - making usageList (656 chroms): 1 millis pass2 - checking and writing primary data (1830 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:53:31: 3000000 INFO @ Sun, 21 Jun 2020 20:53:36: 1000000 INFO @ Sun, 21 Jun 2020 20:53:44: 4000000 INFO @ Sun, 21 Jun 2020 20:53:46: 2000000 INFO @ Sun, 21 Jun 2020 20:53:47: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:53:47: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:53:47: #1 total tags in treatment: 4245081 INFO @ Sun, 21 Jun 2020 20:53:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:53:47: #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 20:53:48: #1 tags after filtering in treatment: 4245041 INFO @ Sun, 21 Jun 2020 20:53:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:53:48: #1 finished! INFO @ Sun, 21 Jun 2020 20:53:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:53:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:53:48: #2 number of paired peaks: 1061 INFO @ Sun, 21 Jun 2020 20:53:48: start model_add_line... INFO @ Sun, 21 Jun 2020 20:53:48: start X-correlation... INFO @ Sun, 21 Jun 2020 20:53:48: end of X-cor INFO @ Sun, 21 Jun 2020 20:53:48: #2 finished! INFO @ Sun, 21 Jun 2020 20:53:48: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 20:53:48: #2 alternative fragment length(s) may be 95,545 bps INFO @ Sun, 21 Jun 2020 20:53:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.10_model.r WARNING @ Sun, 21 Jun 2020 20:53:48: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:53:48: #2 You may need to consider one of the other alternative d(s): 95,545 WARNING @ Sun, 21 Jun 2020 20:53:48: #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 20:53:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:53:48: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:53:56: 3000000 INFO @ Sun, 21 Jun 2020 20:53:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:54:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:54:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:54:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.10_summits.bed INFO @ Sun, 21 Jun 2020 20:54:02: Done! pass1 - making usageList (501 chroms): 1 millis pass2 - checking and writing primary data (1108 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:54:07: 4000000 INFO @ Sun, 21 Jun 2020 20:54:10: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:54:10: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:54:10: #1 total tags in treatment: 4245081 INFO @ Sun, 21 Jun 2020 20:54:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:54:10: #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 20:54:10: #1 tags after filtering in treatment: 4245041 INFO @ Sun, 21 Jun 2020 20:54:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:54:10: #1 finished! INFO @ Sun, 21 Jun 2020 20:54:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:54:10: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:54:11: #2 number of paired peaks: 1061 INFO @ Sun, 21 Jun 2020 20:54:11: start model_add_line... INFO @ Sun, 21 Jun 2020 20:54:11: start X-correlation... INFO @ Sun, 21 Jun 2020 20:54:11: end of X-cor INFO @ Sun, 21 Jun 2020 20:54:11: #2 finished! INFO @ Sun, 21 Jun 2020 20:54:11: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 20:54:11: #2 alternative fragment length(s) may be 95,545 bps INFO @ Sun, 21 Jun 2020 20:54:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.20_model.r WARNING @ Sun, 21 Jun 2020 20:54:11: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:54:11: #2 You may need to consider one of the other alternative d(s): 95,545 WARNING @ Sun, 21 Jun 2020 20:54:11: #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 20:54:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:54:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:54:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:54:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:54:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:54:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX348468/SRX348468.20_summits.bed INFO @ Sun, 21 Jun 2020 20:54:25: Done! pass1 - making usageList (330 chroms): 1 millis pass2 - checking and writing primary data (546 records, 4 fields): 19 millis CompletedMACS2peakCalling