Job ID = 6458567 SRX = SRX5343101 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:31:19 prefetch.2.10.7: 1) Downloading 'SRR8540878'... 2020-06-21T12:31:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:33:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:33:35 prefetch.2.10.7: 'SRR8540878' is valid 2020-06-21T12:33:35 prefetch.2.10.7: 1) 'SRR8540878' was downloaded successfully 2020-06-21T12:33:35 prefetch.2.10.7: 'SRR8540878' has 0 unresolved dependencies Read 16167549 spots for SRR8540878/SRR8540878.sra Written 16167549 spots for SRR8540878/SRR8540878.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: 00:07:36 16167549 reads; of these: 16167549 (100.00%) were unpaired; of these: 1340476 (8.29%) aligned 0 times 5605001 (34.67%) aligned exactly 1 time 9222072 (57.04%) aligned >1 times 91.71% overall alignment rate Time searching: 00:07:36 Overall time: 00:07:36 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] 5325732 / 14827073 = 0.3592 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 21:45:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.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 21:45:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:45:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:45:57: 1000000 INFO @ Sun, 21 Jun 2020 21:46:03: 2000000 INFO @ Sun, 21 Jun 2020 21:46:09: 3000000 INFO @ Sun, 21 Jun 2020 21:46:16: 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 21:46:22: 5000000 INFO @ Sun, 21 Jun 2020 21:46:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.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 21:46:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:46:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:46:29: 6000000 INFO @ Sun, 21 Jun 2020 21:46:29: 1000000 INFO @ Sun, 21 Jun 2020 21:46:35: 2000000 INFO @ Sun, 21 Jun 2020 21:46:36: 7000000 INFO @ Sun, 21 Jun 2020 21:46:41: 3000000 INFO @ Sun, 21 Jun 2020 21:46:43: 8000000 INFO @ Sun, 21 Jun 2020 21:46:48: 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 21:46:50: 9000000 INFO @ Sun, 21 Jun 2020 21:46:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.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 21:46:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:46:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:46:54: 5000000 INFO @ Sun, 21 Jun 2020 21:46:54: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:46:54: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:46:54: #1 total tags in treatment: 9501341 INFO @ Sun, 21 Jun 2020 21:46:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:46:54: #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 21:46:54: #1 tags after filtering in treatment: 9501341 INFO @ Sun, 21 Jun 2020 21:46:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:46:54: #1 finished! INFO @ Sun, 21 Jun 2020 21:46:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:46:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:46:55: #2 number of paired peaks: 4452 INFO @ Sun, 21 Jun 2020 21:46:55: start model_add_line... INFO @ Sun, 21 Jun 2020 21:46:55: start X-correlation... INFO @ Sun, 21 Jun 2020 21:46:55: end of X-cor INFO @ Sun, 21 Jun 2020 21:46:55: #2 finished! INFO @ Sun, 21 Jun 2020 21:46:55: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 21:46:55: #2 alternative fragment length(s) may be 4,77 bps INFO @ Sun, 21 Jun 2020 21:46:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.05_model.r WARNING @ Sun, 21 Jun 2020 21:46:55: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:46:55: #2 You may need to consider one of the other alternative d(s): 4,77 WARNING @ Sun, 21 Jun 2020 21:46:55: #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 21:46:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:46:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:46:58: 1000000 INFO @ Sun, 21 Jun 2020 21:47:00: 6000000 INFO @ Sun, 21 Jun 2020 21:47:05: 2000000 INFO @ Sun, 21 Jun 2020 21:47:06: 7000000 INFO @ Sun, 21 Jun 2020 21:47:11: 3000000 INFO @ Sun, 21 Jun 2020 21:47:12: 8000000 INFO @ Sun, 21 Jun 2020 21:47:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:47:18: 4000000 INFO @ Sun, 21 Jun 2020 21:47:19: 9000000 INFO @ Sun, 21 Jun 2020 21:47:22: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:47:22: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:47:22: #1 total tags in treatment: 9501341 INFO @ Sun, 21 Jun 2020 21:47:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:47:22: #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 21:47:22: #1 tags after filtering in treatment: 9501341 INFO @ Sun, 21 Jun 2020 21:47:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:47:22: #1 finished! INFO @ Sun, 21 Jun 2020 21:47:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:47:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:47:23: #2 number of paired peaks: 4452 INFO @ Sun, 21 Jun 2020 21:47:23: start model_add_line... INFO @ Sun, 21 Jun 2020 21:47:23: start X-correlation... INFO @ Sun, 21 Jun 2020 21:47:23: end of X-cor INFO @ Sun, 21 Jun 2020 21:47:23: #2 finished! INFO @ Sun, 21 Jun 2020 21:47:23: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 21:47:23: #2 alternative fragment length(s) may be 4,77 bps INFO @ Sun, 21 Jun 2020 21:47:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.10_model.r WARNING @ Sun, 21 Jun 2020 21:47:23: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:47:23: #2 You may need to consider one of the other alternative d(s): 4,77 WARNING @ Sun, 21 Jun 2020 21:47:23: #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 21:47:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:47:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:47:25: 5000000 INFO @ Sun, 21 Jun 2020 21:47:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:47:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:47:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.05_summits.bed INFO @ Sun, 21 Jun 2020 21:47:28: Done! pass1 - making usageList (1059 chroms): 2 millis pass2 - checking and writing primary data (5248 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:47:31: 6000000 INFO @ Sun, 21 Jun 2020 21:47:37: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:47:43: 8000000 INFO @ Sun, 21 Jun 2020 21:47:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:47:50: 9000000 INFO @ Sun, 21 Jun 2020 21:47:53: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:47:53: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:47:53: #1 total tags in treatment: 9501341 INFO @ Sun, 21 Jun 2020 21:47:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:47:53: #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 21:47:54: #1 tags after filtering in treatment: 9501341 INFO @ Sun, 21 Jun 2020 21:47:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:47:54: #1 finished! INFO @ Sun, 21 Jun 2020 21:47:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:47:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:47:55: #2 number of paired peaks: 4452 INFO @ Sun, 21 Jun 2020 21:47:55: start model_add_line... INFO @ Sun, 21 Jun 2020 21:47:55: start X-correlation... INFO @ Sun, 21 Jun 2020 21:47:55: end of X-cor INFO @ Sun, 21 Jun 2020 21:47:55: #2 finished! INFO @ Sun, 21 Jun 2020 21:47:55: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 21:47:55: #2 alternative fragment length(s) may be 4,77 bps INFO @ Sun, 21 Jun 2020 21:47:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.20_model.r WARNING @ Sun, 21 Jun 2020 21:47:55: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:47:55: #2 You may need to consider one of the other alternative d(s): 4,77 WARNING @ Sun, 21 Jun 2020 21:47:55: #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 21:47:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:47:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:47:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:47:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:47:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.10_summits.bed INFO @ Sun, 21 Jun 2020 21:47:56: Done! pass1 - making usageList (808 chroms): 1 millis pass2 - checking and writing primary data (2574 records, 4 fields): 24 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:48:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:48:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:48:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:48:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343101/SRX5343101.20_summits.bed INFO @ Sun, 21 Jun 2020 21:48:25: Done! pass1 - making usageList (509 chroms): 1 millis pass2 - checking and writing primary data (1183 records, 4 fields): 37 millis CompletedMACS2peakCalling