Job ID = 6454560 SRX = SRX2321783 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:18:24 prefetch.2.10.7: 1) Downloading 'SRR4841809'... 2020-06-21T09:18:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:22:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:22:29 prefetch.2.10.7: 1) 'SRR4841809' was downloaded successfully Read 47268691 spots for SRR4841809/SRR4841809.sra Written 47268691 spots for SRR4841809/SRR4841809.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: 00:08:25 47268691 reads; of these: 47268691 (100.00%) were unpaired; of these: 3096671 (6.55%) aligned 0 times 32192013 (68.10%) aligned exactly 1 time 11980007 (25.34%) aligned >1 times 93.45% overall alignment rate Time searching: 00:08:25 Overall time: 00:08:25 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 12 files... [bam_rmdupse_core] 31276347 / 44172020 = 0.7081 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 18:40:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.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 18:40:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:40:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:40:20: 1000000 INFO @ Sun, 21 Jun 2020 18:40:26: 2000000 INFO @ Sun, 21 Jun 2020 18:40:31: 3000000 INFO @ Sun, 21 Jun 2020 18:40:37: 4000000 INFO @ Sun, 21 Jun 2020 18:40:43: 5000000 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 18:40:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.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 18:40:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:40:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:40:48: 6000000 INFO @ Sun, 21 Jun 2020 18:40:50: 1000000 INFO @ Sun, 21 Jun 2020 18:40:54: 7000000 INFO @ Sun, 21 Jun 2020 18:40:56: 2000000 INFO @ Sun, 21 Jun 2020 18:41:01: 8000000 INFO @ Sun, 21 Jun 2020 18:41:02: 3000000 INFO @ Sun, 21 Jun 2020 18:41:07: 9000000 INFO @ Sun, 21 Jun 2020 18:41:08: 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 18:41:13: 10000000 INFO @ Sun, 21 Jun 2020 18:41:14: 5000000 INFO @ Sun, 21 Jun 2020 18:41:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.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 18:41:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:41:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:41:19: 11000000 INFO @ Sun, 21 Jun 2020 18:41:19: 6000000 INFO @ Sun, 21 Jun 2020 18:41:20: 1000000 INFO @ Sun, 21 Jun 2020 18:41:25: 7000000 INFO @ Sun, 21 Jun 2020 18:41:26: 12000000 INFO @ Sun, 21 Jun 2020 18:41:27: 2000000 INFO @ Sun, 21 Jun 2020 18:41:31: 8000000 INFO @ Sun, 21 Jun 2020 18:41:31: #1 tag size is determined as 42 bps INFO @ Sun, 21 Jun 2020 18:41:31: #1 tag size = 42 INFO @ Sun, 21 Jun 2020 18:41:31: #1 total tags in treatment: 12895673 INFO @ Sun, 21 Jun 2020 18:41:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:41:31: #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 18:41:32: #1 tags after filtering in treatment: 12895673 INFO @ Sun, 21 Jun 2020 18:41:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:41:32: #1 finished! INFO @ Sun, 21 Jun 2020 18:41:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:41:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:41:33: #2 number of paired peaks: 1422 INFO @ Sun, 21 Jun 2020 18:41:33: start model_add_line... INFO @ Sun, 21 Jun 2020 18:41:33: 3000000 INFO @ Sun, 21 Jun 2020 18:41:33: start X-correlation... INFO @ Sun, 21 Jun 2020 18:41:33: end of X-cor INFO @ Sun, 21 Jun 2020 18:41:33: #2 finished! INFO @ Sun, 21 Jun 2020 18:41:33: #2 predicted fragment length is 36 bps INFO @ Sun, 21 Jun 2020 18:41:33: #2 alternative fragment length(s) may be 2,36 bps INFO @ Sun, 21 Jun 2020 18:41:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.05_model.r WARNING @ Sun, 21 Jun 2020 18:41:33: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:41:33: #2 You may need to consider one of the other alternative d(s): 2,36 WARNING @ Sun, 21 Jun 2020 18:41:33: #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 18:41:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:41:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:41:36: 9000000 INFO @ Sun, 21 Jun 2020 18:41:39: 4000000 INFO @ Sun, 21 Jun 2020 18:41:42: 10000000 INFO @ Sun, 21 Jun 2020 18:41:45: 5000000 INFO @ Sun, 21 Jun 2020 18:41:48: 11000000 INFO @ Sun, 21 Jun 2020 18:41:51: 6000000 INFO @ Sun, 21 Jun 2020 18:41:54: 12000000 INFO @ Sun, 21 Jun 2020 18:41:57: 7000000 INFO @ Sun, 21 Jun 2020 18:41:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:41:59: #1 tag size is determined as 42 bps INFO @ Sun, 21 Jun 2020 18:41:59: #1 tag size = 42 INFO @ Sun, 21 Jun 2020 18:41:59: #1 total tags in treatment: 12895673 INFO @ Sun, 21 Jun 2020 18:41:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:41:59: #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 18:42:00: #1 tags after filtering in treatment: 12895673 INFO @ Sun, 21 Jun 2020 18:42:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:42:00: #1 finished! INFO @ Sun, 21 Jun 2020 18:42:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:42:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:42:01: #2 number of paired peaks: 1422 INFO @ Sun, 21 Jun 2020 18:42:01: start model_add_line... INFO @ Sun, 21 Jun 2020 18:42:01: start X-correlation... INFO @ Sun, 21 Jun 2020 18:42:01: end of X-cor INFO @ Sun, 21 Jun 2020 18:42:01: #2 finished! INFO @ Sun, 21 Jun 2020 18:42:01: #2 predicted fragment length is 36 bps INFO @ Sun, 21 Jun 2020 18:42:01: #2 alternative fragment length(s) may be 2,36 bps INFO @ Sun, 21 Jun 2020 18:42:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.10_model.r WARNING @ Sun, 21 Jun 2020 18:42:01: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:42:01: #2 You may need to consider one of the other alternative d(s): 2,36 WARNING @ Sun, 21 Jun 2020 18:42:01: #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 18:42:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:42:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:42:03: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:42:09: 9000000 INFO @ Sun, 21 Jun 2020 18:42:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:42:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:42:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.05_summits.bed INFO @ Sun, 21 Jun 2020 18:42:11: Done! pass1 - making usageList (975 chroms): 2 millis pass2 - checking and writing primary data (4663 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:42:15: 10000000 INFO @ Sun, 21 Jun 2020 18:42:21: 11000000 INFO @ Sun, 21 Jun 2020 18:42:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:42:27: 12000000 INFO @ Sun, 21 Jun 2020 18:42:32: #1 tag size is determined as 42 bps INFO @ Sun, 21 Jun 2020 18:42:32: #1 tag size = 42 INFO @ Sun, 21 Jun 2020 18:42:32: #1 total tags in treatment: 12895673 INFO @ Sun, 21 Jun 2020 18:42:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:42:32: #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 18:42:33: #1 tags after filtering in treatment: 12895673 INFO @ Sun, 21 Jun 2020 18:42:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:42:33: #1 finished! INFO @ Sun, 21 Jun 2020 18:42:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:42:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:42:34: #2 number of paired peaks: 1422 INFO @ Sun, 21 Jun 2020 18:42:34: start model_add_line... INFO @ Sun, 21 Jun 2020 18:42:34: start X-correlation... INFO @ Sun, 21 Jun 2020 18:42:34: end of X-cor INFO @ Sun, 21 Jun 2020 18:42:34: #2 finished! INFO @ Sun, 21 Jun 2020 18:42:34: #2 predicted fragment length is 36 bps INFO @ Sun, 21 Jun 2020 18:42:34: #2 alternative fragment length(s) may be 2,36 bps INFO @ Sun, 21 Jun 2020 18:42:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.20_model.r WARNING @ Sun, 21 Jun 2020 18:42:34: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:42:34: #2 You may need to consider one of the other alternative d(s): 2,36 WARNING @ Sun, 21 Jun 2020 18:42:34: #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 18:42:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:42:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:42:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:42:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:42:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.10_summits.bed INFO @ Sun, 21 Jun 2020 18:42:38: Done! pass1 - making usageList (740 chroms): 2 millis pass2 - checking and writing primary data (3115 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:42:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:43:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:43:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:43:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2321783/SRX2321783.20_summits.bed INFO @ Sun, 21 Jun 2020 18:43:10: Done! pass1 - making usageList (500 chroms): 1 millis pass2 - checking and writing primary data (1959 records, 4 fields): 15 millis CompletedMACS2peakCalling