Job ID = 6508883 SRX = SRX495278 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:10:43 prefetch.2.10.7: 1) Downloading 'SRR1198783'... 2020-06-26T15:10:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:12:49 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:12:49 prefetch.2.10.7: 1) 'SRR1198783' was downloaded successfully Read 24529628 spots for SRR1198783/SRR1198783.sra Written 24529628 spots for SRR1198783/SRR1198783.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: 00:08:50 24529628 reads; of these: 24529628 (100.00%) were unpaired; of these: 4158581 (16.95%) aligned 0 times 10553245 (43.02%) aligned exactly 1 time 9817802 (40.02%) aligned >1 times 83.05% overall alignment rate Time searching: 00:08:50 Overall time: 00:08:50 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 12 files... [bam_rmdupse_core] 8939213 / 20371047 = 0.4388 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 @ Sat, 27 Jun 2020 00:27:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.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 @ Sat, 27 Jun 2020 00:27:48: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:27:48: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:27:54: 1000000 INFO @ Sat, 27 Jun 2020 00:28:01: 2000000 INFO @ Sat, 27 Jun 2020 00:28:07: 3000000 INFO @ Sat, 27 Jun 2020 00:28:14: 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 @ Sat, 27 Jun 2020 00:28:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.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 @ Sat, 27 Jun 2020 00:28:18: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:28:18: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:28:20: 5000000 INFO @ Sat, 27 Jun 2020 00:28:25: 1000000 INFO @ Sat, 27 Jun 2020 00:28:27: 6000000 INFO @ Sat, 27 Jun 2020 00:28:32: 2000000 INFO @ Sat, 27 Jun 2020 00:28:34: 7000000 INFO @ Sat, 27 Jun 2020 00:28:39: 3000000 INFO @ Sat, 27 Jun 2020 00:28:41: 8000000 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 @ Sat, 27 Jun 2020 00:28:46: 4000000 INFO @ Sat, 27 Jun 2020 00:28:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.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 @ Sat, 27 Jun 2020 00:28:48: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:28:48: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:28:48: 9000000 INFO @ Sat, 27 Jun 2020 00:28:54: 5000000 INFO @ Sat, 27 Jun 2020 00:28:55: 1000000 INFO @ Sat, 27 Jun 2020 00:28:56: 10000000 INFO @ Sat, 27 Jun 2020 00:29:01: 6000000 INFO @ Sat, 27 Jun 2020 00:29:02: 2000000 INFO @ Sat, 27 Jun 2020 00:29:04: 11000000 INFO @ Sat, 27 Jun 2020 00:29:07: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:29:07: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:29:07: #1 total tags in treatment: 11431834 INFO @ Sat, 27 Jun 2020 00:29:07: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:29:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:29:07: #1 tags after filtering in treatment: 11431700 INFO @ Sat, 27 Jun 2020 00:29:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:29:07: #1 finished! INFO @ Sat, 27 Jun 2020 00:29:07: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:29:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:29:08: 7000000 INFO @ Sat, 27 Jun 2020 00:29:09: #2 number of paired peaks: 2398 INFO @ Sat, 27 Jun 2020 00:29:09: start model_add_line... INFO @ Sat, 27 Jun 2020 00:29:09: start X-correlation... INFO @ Sat, 27 Jun 2020 00:29:09: end of X-cor INFO @ Sat, 27 Jun 2020 00:29:09: #2 finished! INFO @ Sat, 27 Jun 2020 00:29:09: #2 predicted fragment length is 2 bps INFO @ Sat, 27 Jun 2020 00:29:09: #2 alternative fragment length(s) may be 2,43,584 bps INFO @ Sat, 27 Jun 2020 00:29:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.05_model.r WARNING @ Sat, 27 Jun 2020 00:29:09: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:29:09: #2 You may need to consider one of the other alternative d(s): 2,43,584 WARNING @ Sat, 27 Jun 2020 00:29:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:29:09: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:29:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:29:10: 3000000 INFO @ Sat, 27 Jun 2020 00:29:15: 8000000 INFO @ Sat, 27 Jun 2020 00:29:17: 4000000 INFO @ Sat, 27 Jun 2020 00:29:23: 9000000 INFO @ Sat, 27 Jun 2020 00:29:24: 5000000 INFO @ Sat, 27 Jun 2020 00:29:30: 10000000 INFO @ Sat, 27 Jun 2020 00:29:31: 6000000 INFO @ Sat, 27 Jun 2020 00:29:33: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:29:37: 11000000 INFO @ Sat, 27 Jun 2020 00:29:38: 7000000 INFO @ Sat, 27 Jun 2020 00:29:41: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:29:41: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:29:41: #1 total tags in treatment: 11431834 INFO @ Sat, 27 Jun 2020 00:29:41: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:29:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:29:41: #1 tags after filtering in treatment: 11431700 INFO @ Sat, 27 Jun 2020 00:29:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:29:41: #1 finished! INFO @ Sat, 27 Jun 2020 00:29:41: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:29:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:29:42: #2 number of paired peaks: 2398 INFO @ Sat, 27 Jun 2020 00:29:42: start model_add_line... INFO @ Sat, 27 Jun 2020 00:29:42: start X-correlation... INFO @ Sat, 27 Jun 2020 00:29:42: end of X-cor INFO @ Sat, 27 Jun 2020 00:29:42: #2 finished! INFO @ Sat, 27 Jun 2020 00:29:42: #2 predicted fragment length is 2 bps INFO @ Sat, 27 Jun 2020 00:29:42: #2 alternative fragment length(s) may be 2,43,584 bps INFO @ Sat, 27 Jun 2020 00:29:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.10_model.r WARNING @ Sat, 27 Jun 2020 00:29:42: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:29:42: #2 You may need to consider one of the other alternative d(s): 2,43,584 WARNING @ Sat, 27 Jun 2020 00:29:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:29:42: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:29:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:29:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:29:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:29:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.05_summits.bed INFO @ Sat, 27 Jun 2020 00:29:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:29:45: 8000000 INFO @ Sat, 27 Jun 2020 00:29:51: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:29:58: 10000000 INFO @ Sat, 27 Jun 2020 00:30:05: 11000000 INFO @ Sat, 27 Jun 2020 00:30:07: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:30:08: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:30:08: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:30:08: #1 total tags in treatment: 11431834 INFO @ Sat, 27 Jun 2020 00:30:08: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:30:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:30:08: #1 tags after filtering in treatment: 11431700 INFO @ Sat, 27 Jun 2020 00:30:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:30:08: #1 finished! INFO @ Sat, 27 Jun 2020 00:30:08: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:30:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:30:09: #2 number of paired peaks: 2398 INFO @ Sat, 27 Jun 2020 00:30:09: start model_add_line... INFO @ Sat, 27 Jun 2020 00:30:09: start X-correlation... INFO @ Sat, 27 Jun 2020 00:30:09: end of X-cor INFO @ Sat, 27 Jun 2020 00:30:09: #2 finished! INFO @ Sat, 27 Jun 2020 00:30:09: #2 predicted fragment length is 2 bps INFO @ Sat, 27 Jun 2020 00:30:09: #2 alternative fragment length(s) may be 2,43,584 bps INFO @ Sat, 27 Jun 2020 00:30:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.20_model.r WARNING @ Sat, 27 Jun 2020 00:30:09: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:30:09: #2 You may need to consider one of the other alternative d(s): 2,43,584 WARNING @ Sat, 27 Jun 2020 00:30:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:30:09: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:30:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:30:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:30:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:30:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.10_summits.bed INFO @ Sat, 27 Jun 2020 00:30:18: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:30:32: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:30:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:30:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:30:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495278/SRX495278.20_summits.bed INFO @ Sat, 27 Jun 2020 00:30:44: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling