Job ID = 6458234 SRX = SRX495787 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:18:34 prefetch.2.10.7: 1) Downloading 'SRR1199485'... 2020-06-21T12:18:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:20:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:20:19 prefetch.2.10.7: 1) 'SRR1199485' was downloaded successfully Read 16173126 spots for SRR1199485/SRR1199485.sra Written 16173126 spots for SRR1199485/SRR1199485.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: 00:04:47 16173126 reads; of these: 16173126 (100.00%) were unpaired; of these: 7357817 (45.49%) aligned 0 times 4436449 (27.43%) aligned exactly 1 time 4378860 (27.07%) aligned >1 times 54.51% overall alignment rate Time searching: 00:04:47 Overall time: 00:04:47 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] 4628387 / 8815309 = 0.5250 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 21:28:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.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 21:28:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:28:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:28:17: 1000000 INFO @ Sun, 21 Jun 2020 21:28:23: 2000000 INFO @ Sun, 21 Jun 2020 21:28:28: 3000000 INFO @ Sun, 21 Jun 2020 21:28:34: 4000000 INFO @ Sun, 21 Jun 2020 21:28:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:28:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:28:35: #1 total tags in treatment: 4186922 INFO @ Sun, 21 Jun 2020 21:28:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:28:35: #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 21:28:36: #1 tags after filtering in treatment: 4186759 INFO @ Sun, 21 Jun 2020 21:28:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:28:36: #1 finished! INFO @ Sun, 21 Jun 2020 21:28:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:28:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:28:36: #2 number of paired peaks: 2925 INFO @ Sun, 21 Jun 2020 21:28:36: start model_add_line... INFO @ Sun, 21 Jun 2020 21:28:36: start X-correlation... INFO @ Sun, 21 Jun 2020 21:28:36: end of X-cor INFO @ Sun, 21 Jun 2020 21:28:36: #2 finished! INFO @ Sun, 21 Jun 2020 21:28:36: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 21:28:36: #2 alternative fragment length(s) may be 3,50,581 bps INFO @ Sun, 21 Jun 2020 21:28:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.05_model.r WARNING @ Sun, 21 Jun 2020 21:28:36: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:28:36: #2 You may need to consider one of the other alternative d(s): 3,50,581 WARNING @ Sun, 21 Jun 2020 21:28:36: #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 21:28:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:28:36: #3 Pre-compute pvalue-qvalue table... 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 21:28:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.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 21:28:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:28:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:28:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:28:47: 1000000 INFO @ Sun, 21 Jun 2020 21:28:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:28:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:28:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.05_summits.bed INFO @ Sun, 21 Jun 2020 21:28:50: Done! pass1 - making usageList (702 chroms): 1 millis pass2 - checking and writing primary data (2605 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:28:53: 2000000 INFO @ Sun, 21 Jun 2020 21:28:59: 3000000 INFO @ Sun, 21 Jun 2020 21:29:05: 4000000 INFO @ Sun, 21 Jun 2020 21:29:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:29:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:29:06: #1 total tags in treatment: 4186922 INFO @ Sun, 21 Jun 2020 21:29:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:29:06: #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 21:29:06: #1 tags after filtering in treatment: 4186759 INFO @ Sun, 21 Jun 2020 21:29:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:29:06: #1 finished! INFO @ Sun, 21 Jun 2020 21:29:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:29:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:29:06: #2 number of paired peaks: 2925 INFO @ Sun, 21 Jun 2020 21:29:06: start model_add_line... INFO @ Sun, 21 Jun 2020 21:29:07: start X-correlation... INFO @ Sun, 21 Jun 2020 21:29:07: end of X-cor INFO @ Sun, 21 Jun 2020 21:29:07: #2 finished! INFO @ Sun, 21 Jun 2020 21:29:07: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 21:29:07: #2 alternative fragment length(s) may be 3,50,581 bps INFO @ Sun, 21 Jun 2020 21:29:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.10_model.r WARNING @ Sun, 21 Jun 2020 21:29:07: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:29:07: #2 You may need to consider one of the other alternative d(s): 3,50,581 WARNING @ Sun, 21 Jun 2020 21:29:07: #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 21:29:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:29:07: #3 Pre-compute pvalue-qvalue table... 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 21:29:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.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 21:29:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:29:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:29:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:29:17: 1000000 INFO @ Sun, 21 Jun 2020 21:29:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:29:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:29:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.10_summits.bed INFO @ Sun, 21 Jun 2020 21:29:20: Done! pass1 - making usageList (545 chroms): 1 millis pass2 - checking and writing primary data (1911 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:29:23: 2000000 INFO @ Sun, 21 Jun 2020 21:29:29: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:29:34: 4000000 INFO @ Sun, 21 Jun 2020 21:29:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:29:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:29:36: #1 total tags in treatment: 4186922 INFO @ Sun, 21 Jun 2020 21:29:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:29:36: #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 21:29:36: #1 tags after filtering in treatment: 4186759 INFO @ Sun, 21 Jun 2020 21:29:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:29:36: #1 finished! INFO @ Sun, 21 Jun 2020 21:29:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:29:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:29:36: #2 number of paired peaks: 2925 INFO @ Sun, 21 Jun 2020 21:29:36: start model_add_line... INFO @ Sun, 21 Jun 2020 21:29:36: start X-correlation... INFO @ Sun, 21 Jun 2020 21:29:36: end of X-cor INFO @ Sun, 21 Jun 2020 21:29:36: #2 finished! INFO @ Sun, 21 Jun 2020 21:29:36: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 21:29:36: #2 alternative fragment length(s) may be 3,50,581 bps INFO @ Sun, 21 Jun 2020 21:29:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.20_model.r WARNING @ Sun, 21 Jun 2020 21:29:36: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:29:36: #2 You may need to consider one of the other alternative d(s): 3,50,581 WARNING @ Sun, 21 Jun 2020 21:29:36: #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 21:29:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:29:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:29:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:29:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:29:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:29:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495787/SRX495787.20_summits.bed INFO @ Sun, 21 Jun 2020 21:29:50: Done! pass1 - making usageList (346 chroms): 1 millis pass2 - checking and writing primary data (797 records, 4 fields): 10 millis CompletedMACS2peakCalling