Job ID = 6456362 SRX = SRX3380806 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:52:16 prefetch.2.10.7: 1) Downloading 'SRR6278169'... 2020-06-21T10:52:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:56:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:56:18 prefetch.2.10.7: 1) 'SRR6278169' was downloaded successfully Read 20822653 spots for SRR6278169/SRR6278169.sra Written 20822653 spots for SRR6278169/SRR6278169.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: 00:05:09 20822653 reads; of these: 20822653 (100.00%) were unpaired; of these: 2811408 (13.50%) aligned 0 times 13271195 (63.73%) aligned exactly 1 time 4740050 (22.76%) aligned >1 times 86.50% overall alignment rate Time searching: 00:05:09 Overall time: 00:05:09 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_sort_core] merging from 8 files... [bam_rmdupse_core] 15254758 / 18011245 = 0.8470 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 20:05:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.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 20:05:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:05:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:05:27: 1000000 INFO @ Sun, 21 Jun 2020 20:05:33: 2000000 INFO @ Sun, 21 Jun 2020 20:05:38: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:05:38: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:05:38: #1 total tags in treatment: 2756487 INFO @ Sun, 21 Jun 2020 20:05:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:05:38: #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 20:05:38: #1 tags after filtering in treatment: 2756437 INFO @ Sun, 21 Jun 2020 20:05:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:05:38: #1 finished! INFO @ Sun, 21 Jun 2020 20:05:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:05:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:05:38: #2 number of paired peaks: 4206 INFO @ Sun, 21 Jun 2020 20:05:38: start model_add_line... INFO @ Sun, 21 Jun 2020 20:05:39: start X-correlation... INFO @ Sun, 21 Jun 2020 20:05:39: end of X-cor INFO @ Sun, 21 Jun 2020 20:05:39: #2 finished! INFO @ Sun, 21 Jun 2020 20:05:39: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 20:05:39: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sun, 21 Jun 2020 20:05:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.05_model.r WARNING @ Sun, 21 Jun 2020 20:05:39: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:05:39: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sun, 21 Jun 2020 20:05:39: #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 20:05:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:05:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:05:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:05:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:05:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:05:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.05_summits.bed INFO @ Sun, 21 Jun 2020 20:05:48: Done! pass1 - making usageList (690 chroms): 1 millis pass2 - checking and writing primary data (2553 records, 4 fields): 20 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 20:05:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.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 20:05:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:05:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:05:57: 1000000 INFO @ Sun, 21 Jun 2020 20:06:03: 2000000 INFO @ Sun, 21 Jun 2020 20:06:08: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:06:08: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:06:08: #1 total tags in treatment: 2756487 INFO @ Sun, 21 Jun 2020 20:06:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:06:08: #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 20:06:08: #1 tags after filtering in treatment: 2756437 INFO @ Sun, 21 Jun 2020 20:06:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:06:08: #1 finished! INFO @ Sun, 21 Jun 2020 20:06:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:06:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:06:08: #2 number of paired peaks: 4206 INFO @ Sun, 21 Jun 2020 20:06:08: start model_add_line... INFO @ Sun, 21 Jun 2020 20:06:08: start X-correlation... INFO @ Sun, 21 Jun 2020 20:06:08: end of X-cor INFO @ Sun, 21 Jun 2020 20:06:08: #2 finished! INFO @ Sun, 21 Jun 2020 20:06:08: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 20:06:08: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sun, 21 Jun 2020 20:06:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.10_model.r WARNING @ Sun, 21 Jun 2020 20:06:08: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:06:08: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sun, 21 Jun 2020 20:06:08: #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 20:06:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:06:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:06:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:06:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:06:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:06:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.10_summits.bed INFO @ Sun, 21 Jun 2020 20:06:17: Done! pass1 - making usageList (524 chroms): 1 millis pass2 - checking and writing primary data (1875 records, 4 fields): 15 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 20:06:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.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 20:06:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:06:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:06:27: 1000000 INFO @ Sun, 21 Jun 2020 20:06:33: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:06:37: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:06:37: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:06:37: #1 total tags in treatment: 2756487 INFO @ Sun, 21 Jun 2020 20:06:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:06:37: #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 20:06:38: #1 tags after filtering in treatment: 2756437 INFO @ Sun, 21 Jun 2020 20:06:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:06:38: #1 finished! INFO @ Sun, 21 Jun 2020 20:06:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:06:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:06:38: #2 number of paired peaks: 4206 INFO @ Sun, 21 Jun 2020 20:06:38: start model_add_line... INFO @ Sun, 21 Jun 2020 20:06:38: start X-correlation... INFO @ Sun, 21 Jun 2020 20:06:38: end of X-cor INFO @ Sun, 21 Jun 2020 20:06:38: #2 finished! INFO @ Sun, 21 Jun 2020 20:06:38: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 20:06:38: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sun, 21 Jun 2020 20:06:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.20_model.r WARNING @ Sun, 21 Jun 2020 20:06:38: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:06:38: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sun, 21 Jun 2020 20:06:38: #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 20:06:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:06:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:06:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:06:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:06:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:06:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380806/SRX3380806.20_summits.bed INFO @ Sun, 21 Jun 2020 20:06:47: Done! pass1 - making usageList (417 chroms): 1 millis pass2 - checking and writing primary data (1073 records, 4 fields): 13 millis CompletedMACS2peakCalling