Job ID = 6454553 SRX = SRX231887 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:15:24 prefetch.2.10.7: 1) Downloading 'SRR696805'... 2020-06-21T09:15:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:15:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:15:42 prefetch.2.10.7: 'SRR696805' is valid 2020-06-21T09:15:42 prefetch.2.10.7: 1) 'SRR696805' was downloaded successfully Read 2713261 spots for SRR696805/SRR696805.sra Written 2713261 spots for SRR696805/SRR696805.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: 00:00:26 2713261 reads; of these: 2713261 (100.00%) were unpaired; of these: 1083016 (39.92%) aligned 0 times 1305296 (48.11%) aligned exactly 1 time 324949 (11.98%) aligned >1 times 60.08% overall alignment rate Time searching: 00:00:26 Overall time: 00:00:26 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] 87974 / 1630245 = 0.0540 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 18:17:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.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 18:17:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:10: 1000000 INFO @ Sun, 21 Jun 2020 18:17:12: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 18:17:12: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 18:17:12: #1 total tags in treatment: 1542271 INFO @ Sun, 21 Jun 2020 18:17:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:17:12: #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 18:17:13: #1 tags after filtering in treatment: 1541922 INFO @ Sun, 21 Jun 2020 18:17:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:17:13: #1 finished! INFO @ Sun, 21 Jun 2020 18:17:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:17:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:17:13: #2 number of paired peaks: 2122 INFO @ Sun, 21 Jun 2020 18:17:13: start model_add_line... INFO @ Sun, 21 Jun 2020 18:17:13: start X-correlation... INFO @ Sun, 21 Jun 2020 18:17:13: end of X-cor INFO @ Sun, 21 Jun 2020 18:17:13: #2 finished! INFO @ Sun, 21 Jun 2020 18:17:13: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 18:17:13: #2 alternative fragment length(s) may be 58,490,578 bps INFO @ Sun, 21 Jun 2020 18:17:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.05_model.r WARNING @ Sun, 21 Jun 2020 18:17:13: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:17:13: #2 You may need to consider one of the other alternative d(s): 58,490,578 WARNING @ Sun, 21 Jun 2020 18:17:13: #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 18:17:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:17:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:17:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:17:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:17:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:17:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.05_summits.bed INFO @ Sun, 21 Jun 2020 18:17:18: Done! pass1 - making usageList (151 chroms): 2 millis pass2 - checking and writing primary data (3408 records, 4 fields): 7 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 18:17:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.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 18:17:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:40: 1000000 INFO @ Sun, 21 Jun 2020 18:17:42: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 18:17:42: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 18:17:42: #1 total tags in treatment: 1542271 INFO @ Sun, 21 Jun 2020 18:17:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:17:42: #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 18:17:43: #1 tags after filtering in treatment: 1541922 INFO @ Sun, 21 Jun 2020 18:17:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:17:43: #1 finished! INFO @ Sun, 21 Jun 2020 18:17:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:17:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:17:43: #2 number of paired peaks: 2122 INFO @ Sun, 21 Jun 2020 18:17:43: start model_add_line... INFO @ Sun, 21 Jun 2020 18:17:43: start X-correlation... INFO @ Sun, 21 Jun 2020 18:17:43: end of X-cor INFO @ Sun, 21 Jun 2020 18:17:43: #2 finished! INFO @ Sun, 21 Jun 2020 18:17:43: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 18:17:43: #2 alternative fragment length(s) may be 58,490,578 bps INFO @ Sun, 21 Jun 2020 18:17:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.10_model.r WARNING @ Sun, 21 Jun 2020 18:17:43: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:17:43: #2 You may need to consider one of the other alternative d(s): 58,490,578 WARNING @ Sun, 21 Jun 2020 18:17:43: #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 18:17:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:17:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:17:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:17:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:17:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:17:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.10_summits.bed INFO @ Sun, 21 Jun 2020 18:17:48: Done! pass1 - making usageList (70 chroms): 1 millis pass2 - checking and writing primary data (1670 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 18:18:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.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 18:18:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:18:10: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:18:13: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 18:18:13: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 18:18:13: #1 total tags in treatment: 1542271 INFO @ Sun, 21 Jun 2020 18:18:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:18:13: #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 18:18:13: #1 tags after filtering in treatment: 1541922 INFO @ Sun, 21 Jun 2020 18:18:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:18:13: #1 finished! INFO @ Sun, 21 Jun 2020 18:18:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:18:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:18:13: #2 number of paired peaks: 2122 INFO @ Sun, 21 Jun 2020 18:18:13: start model_add_line... INFO @ Sun, 21 Jun 2020 18:18:13: start X-correlation... INFO @ Sun, 21 Jun 2020 18:18:13: end of X-cor INFO @ Sun, 21 Jun 2020 18:18:13: #2 finished! INFO @ Sun, 21 Jun 2020 18:18:13: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 18:18:13: #2 alternative fragment length(s) may be 58,490,578 bps INFO @ Sun, 21 Jun 2020 18:18:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.20_model.r WARNING @ Sun, 21 Jun 2020 18:18:13: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:18:13: #2 You may need to consider one of the other alternative d(s): 58,490,578 WARNING @ Sun, 21 Jun 2020 18:18:13: #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 18:18:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:18:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:18:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:18:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:18:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:18:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231887/SRX231887.20_summits.bed INFO @ Sun, 21 Jun 2020 18:18:19: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (563 records, 4 fields): 2 millis CompletedMACS2peakCalling