Job ID = 6455181 SRX = SRX2829098 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:53:10 prefetch.2.10.7: 1) Downloading 'SRR5569908'... 2020-06-21T09:53:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:57:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:57:02 prefetch.2.10.7: 1) 'SRR5569908' was downloaded successfully Read 19779275 spots for SRR5569908/SRR5569908.sra Written 19779275 spots for SRR5569908/SRR5569908.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: 00:05:14 19779275 reads; of these: 19779275 (100.00%) were unpaired; of these: 3807580 (19.25%) aligned 0 times 11334723 (57.31%) aligned exactly 1 time 4636972 (23.44%) aligned >1 times 80.75% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 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_sort_core] merging from 8 files... [bam_rmdupse_core] 9070059 / 15971695 = 0.5679 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 19:07:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.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 19:07:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:07:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:07:51: 1000000 INFO @ Sun, 21 Jun 2020 19:07:57: 2000000 INFO @ Sun, 21 Jun 2020 19:08:03: 3000000 INFO @ Sun, 21 Jun 2020 19:08:10: 4000000 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 19:08:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.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 19:08:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:16: 5000000 INFO @ Sun, 21 Jun 2020 19:08:22: 1000000 INFO @ Sun, 21 Jun 2020 19:08:24: 6000000 INFO @ Sun, 21 Jun 2020 19:08:28: 2000000 INFO @ Sun, 21 Jun 2020 19:08:31: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:08:31: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:08:31: #1 total tags in treatment: 6901636 INFO @ Sun, 21 Jun 2020 19:08:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:08:31: #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 19:08:32: #1 tags after filtering in treatment: 6901636 INFO @ Sun, 21 Jun 2020 19:08:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:08:32: #1 finished! INFO @ Sun, 21 Jun 2020 19:08:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:08:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:08:32: #2 number of paired peaks: 1044 INFO @ Sun, 21 Jun 2020 19:08:32: start model_add_line... INFO @ Sun, 21 Jun 2020 19:08:32: start X-correlation... INFO @ Sun, 21 Jun 2020 19:08:32: end of X-cor INFO @ Sun, 21 Jun 2020 19:08:32: #2 finished! INFO @ Sun, 21 Jun 2020 19:08:32: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 19:08:32: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sun, 21 Jun 2020 19:08:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.05_model.r WARNING @ Sun, 21 Jun 2020 19:08:32: #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 19:08:32: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sun, 21 Jun 2020 19:08:32: #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 19:08:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:08:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:08:35: 3000000 INFO @ Sun, 21 Jun 2020 19:08:41: 4000000 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 19:08:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.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 19:08:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:08:48: 5000000 INFO @ Sun, 21 Jun 2020 19:08:53: 1000000 INFO @ Sun, 21 Jun 2020 19:08:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:08:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:08:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.05_summits.bed INFO @ Sun, 21 Jun 2020 19:08:54: Done! pass1 - making usageList (669 chroms): 2 millis pass2 - checking and writing primary data (2524 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:08:56: 6000000 INFO @ Sun, 21 Jun 2020 19:09:00: 2000000 INFO @ Sun, 21 Jun 2020 19:09:03: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:09:03: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:09:03: #1 total tags in treatment: 6901636 INFO @ Sun, 21 Jun 2020 19:09:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:03: #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 19:09:03: #1 tags after filtering in treatment: 6901636 INFO @ Sun, 21 Jun 2020 19:09:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:03: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:09:04: #2 number of paired peaks: 1044 INFO @ Sun, 21 Jun 2020 19:09:04: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:04: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:04: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:04: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:04: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 19:09:04: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sun, 21 Jun 2020 19:09:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.10_model.r WARNING @ Sun, 21 Jun 2020 19:09:04: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:09:04: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sun, 21 Jun 2020 19:09:04: #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 19:09:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:09:07: 3000000 INFO @ Sun, 21 Jun 2020 19:09:14: 4000000 INFO @ Sun, 21 Jun 2020 19:09:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:09:21: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:09:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:09:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:09:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.10_summits.bed INFO @ Sun, 21 Jun 2020 19:09:26: Done! pass1 - making usageList (527 chroms): 2 millis pass2 - checking and writing primary data (1711 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:09:30: 6000000 INFO @ Sun, 21 Jun 2020 19:09:37: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:09:37: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:09:37: #1 total tags in treatment: 6901636 INFO @ Sun, 21 Jun 2020 19:09:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:37: #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 19:09:38: #1 tags after filtering in treatment: 6901636 INFO @ Sun, 21 Jun 2020 19:09:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:38: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:09:38: #2 number of paired peaks: 1044 INFO @ Sun, 21 Jun 2020 19:09:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:38: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:38: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:38: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 19:09:38: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sun, 21 Jun 2020 19:09:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.20_model.r WARNING @ Sun, 21 Jun 2020 19:09:38: #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 19:09:38: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sun, 21 Jun 2020 19:09:38: #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 19:09:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:09:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:10:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:10:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:10:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2829098/SRX2829098.20_summits.bed INFO @ Sun, 21 Jun 2020 19:10:00: Done! pass1 - making usageList (269 chroms): 1 millis pass2 - checking and writing primary data (516 records, 4 fields): 16 millis CompletedMACS2peakCalling