Job ID = 6455086 SRX = SRX2663650 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:02:25 prefetch.2.10.7: 1) Downloading 'SRR5368386'... 2020-06-21T10:02:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:04:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:04:58 prefetch.2.10.7: 1) 'SRR5368386' was downloaded successfully 2020-06-21T10:04:58 prefetch.2.10.7: 'SRR5368386' has 0 unresolved dependencies Read 22425200 spots for SRR5368386/SRR5368386.sra Written 22425200 spots for SRR5368386/SRR5368386.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: 00:05:25 22425200 reads; of these: 22425200 (100.00%) were unpaired; of these: 3638315 (16.22%) aligned 0 times 14446327 (64.42%) aligned exactly 1 time 4340558 (19.36%) aligned >1 times 83.78% overall alignment rate Time searching: 00:05:25 Overall time: 00:05:25 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] 6944308 / 18786885 = 0.3696 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 19:16:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.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 19:16:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:16:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:16:22: 1000000 INFO @ Sun, 21 Jun 2020 19:16:28: 2000000 INFO @ Sun, 21 Jun 2020 19:16:34: 3000000 INFO @ Sun, 21 Jun 2020 19:16:40: 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 19:16:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.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 19:16:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:16:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:16:46: 5000000 INFO @ Sun, 21 Jun 2020 19:16:53: 6000000 INFO @ Sun, 21 Jun 2020 19:16:54: 1000000 INFO @ Sun, 21 Jun 2020 19:17:01: 7000000 INFO @ Sun, 21 Jun 2020 19:17:01: 2000000 INFO @ Sun, 21 Jun 2020 19:17:08: 8000000 INFO @ Sun, 21 Jun 2020 19:17:09: 3000000 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 19:17:15: 9000000 INFO @ Sun, 21 Jun 2020 19:17:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.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 19:17:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:17:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:17:16: 4000000 INFO @ Sun, 21 Jun 2020 19:17:22: 10000000 INFO @ Sun, 21 Jun 2020 19:17:24: 1000000 INFO @ Sun, 21 Jun 2020 19:17:24: 5000000 INFO @ Sun, 21 Jun 2020 19:17:30: 11000000 INFO @ Sun, 21 Jun 2020 19:17:31: 2000000 INFO @ Sun, 21 Jun 2020 19:17:32: 6000000 INFO @ Sun, 21 Jun 2020 19:17:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:17:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:17:36: #1 total tags in treatment: 11842577 INFO @ Sun, 21 Jun 2020 19:17:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:17:36: #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 19:17:37: #1 tags after filtering in treatment: 11842573 INFO @ Sun, 21 Jun 2020 19:17:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:17:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:17:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:17:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:17:38: #2 number of paired peaks: 348 WARNING @ Sun, 21 Jun 2020 19:17:38: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Sun, 21 Jun 2020 19:17:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:17:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:17:38: end of X-cor INFO @ Sun, 21 Jun 2020 19:17:38: #2 finished! INFO @ Sun, 21 Jun 2020 19:17:38: #2 predicted fragment length is 61 bps INFO @ Sun, 21 Jun 2020 19:17:38: #2 alternative fragment length(s) may be 4,61 bps INFO @ Sun, 21 Jun 2020 19:17:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.05_model.r WARNING @ Sun, 21 Jun 2020 19:17:38: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:17:38: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Sun, 21 Jun 2020 19:17:38: #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 19:17:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:17:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:17:39: 3000000 INFO @ Sun, 21 Jun 2020 19:17:39: 7000000 INFO @ Sun, 21 Jun 2020 19:17:46: 4000000 INFO @ Sun, 21 Jun 2020 19:17:47: 8000000 INFO @ Sun, 21 Jun 2020 19:17:54: 5000000 INFO @ Sun, 21 Jun 2020 19:17:54: 9000000 INFO @ Sun, 21 Jun 2020 19:18:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:18:02: 6000000 INFO @ Sun, 21 Jun 2020 19:18:02: 10000000 INFO @ Sun, 21 Jun 2020 19:18:09: 7000000 INFO @ Sun, 21 Jun 2020 19:18:10: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:18:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:18:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:18:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.05_summits.bed INFO @ Sun, 21 Jun 2020 19:18:13: Done! pass1 - making usageList (508 chroms): 1 millis pass2 - checking and writing primary data (1518 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:18:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:18:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:18:16: #1 total tags in treatment: 11842577 INFO @ Sun, 21 Jun 2020 19:18:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:18:16: #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 19:18:17: #1 tags after filtering in treatment: 11842573 INFO @ Sun, 21 Jun 2020 19:18:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:18:17: #1 finished! INFO @ Sun, 21 Jun 2020 19:18:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:18:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:18:17: 8000000 INFO @ Sun, 21 Jun 2020 19:18:18: #2 number of paired peaks: 348 WARNING @ Sun, 21 Jun 2020 19:18:18: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Sun, 21 Jun 2020 19:18:18: start model_add_line... INFO @ Sun, 21 Jun 2020 19:18:18: start X-correlation... INFO @ Sun, 21 Jun 2020 19:18:18: end of X-cor INFO @ Sun, 21 Jun 2020 19:18:18: #2 finished! INFO @ Sun, 21 Jun 2020 19:18:18: #2 predicted fragment length is 61 bps INFO @ Sun, 21 Jun 2020 19:18:18: #2 alternative fragment length(s) may be 4,61 bps INFO @ Sun, 21 Jun 2020 19:18:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.10_model.r WARNING @ Sun, 21 Jun 2020 19:18:18: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:18:18: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Sun, 21 Jun 2020 19:18:18: #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 19:18:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:18:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:18:25: 9000000 INFO @ Sun, 21 Jun 2020 19:18:33: 10000000 INFO @ Sun, 21 Jun 2020 19:18:40: 11000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:18:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:18:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:18:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:18:46: #1 total tags in treatment: 11842577 INFO @ Sun, 21 Jun 2020 19:18:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:18:46: #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 19:18:47: #1 tags after filtering in treatment: 11842573 INFO @ Sun, 21 Jun 2020 19:18:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:18:47: #1 finished! INFO @ Sun, 21 Jun 2020 19:18:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:18:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:18:48: #2 number of paired peaks: 348 WARNING @ Sun, 21 Jun 2020 19:18:48: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Sun, 21 Jun 2020 19:18:48: start model_add_line... INFO @ Sun, 21 Jun 2020 19:18:48: start X-correlation... INFO @ Sun, 21 Jun 2020 19:18:48: end of X-cor INFO @ Sun, 21 Jun 2020 19:18:48: #2 finished! INFO @ Sun, 21 Jun 2020 19:18:48: #2 predicted fragment length is 61 bps INFO @ Sun, 21 Jun 2020 19:18:48: #2 alternative fragment length(s) may be 4,61 bps INFO @ Sun, 21 Jun 2020 19:18:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.20_model.r WARNING @ Sun, 21 Jun 2020 19:18:48: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:18:48: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Sun, 21 Jun 2020 19:18:48: #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 19:18:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:18:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:18:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:18:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:18:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.10_summits.bed INFO @ Sun, 21 Jun 2020 19:18:55: Done! pass1 - making usageList (319 chroms): 1 millis pass2 - checking and writing primary data (711 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:19:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:19:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:19:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:19:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2663650/SRX2663650.20_summits.bed INFO @ Sun, 21 Jun 2020 19:19:25: Done! pass1 - making usageList (154 chroms): 1 millis pass2 - checking and writing primary data (360 records, 4 fields): 6 millis CompletedMACS2peakCalling