Job ID = 6455356 SRX = SRX287721 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:10:21 prefetch.2.10.7: 1) Downloading 'SRR869910'... 2020-06-21T10:10:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:15:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:15:37 prefetch.2.10.7: 1) 'SRR869910' was downloaded successfully Read 24101770 spots for SRR869910/SRR869910.sra Written 24101770 spots for SRR869910/SRR869910.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: 00:07:09 24101770 reads; of these: 24101770 (100.00%) were unpaired; of these: 1663143 (6.90%) aligned 0 times 17058916 (70.78%) aligned exactly 1 time 5379711 (22.32%) aligned >1 times 93.10% overall alignment rate Time searching: 00:07:09 Overall time: 00:07:09 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] 3879886 / 22438627 = 0.1729 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 19:31:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.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 19:31:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:31:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:31:28: 1000000 INFO @ Sun, 21 Jun 2020 19:31:36: 2000000 INFO @ Sun, 21 Jun 2020 19:31:43: 3000000 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 19:31:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.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 19:31:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:31:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:31:51: 4000000 INFO @ Sun, 21 Jun 2020 19:31:57: 5000000 INFO @ Sun, 21 Jun 2020 19:31:58: 1000000 INFO @ Sun, 21 Jun 2020 19:32:04: 6000000 INFO @ Sun, 21 Jun 2020 19:32:06: 2000000 INFO @ Sun, 21 Jun 2020 19:32:10: 7000000 INFO @ Sun, 21 Jun 2020 19:32:13: 3000000 INFO @ Sun, 21 Jun 2020 19:32:16: 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 @ Sun, 21 Jun 2020 19:32:20: 4000000 INFO @ Sun, 21 Jun 2020 19:32:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.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 19:32:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:32:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:32:22: 9000000 INFO @ Sun, 21 Jun 2020 19:32:27: 5000000 INFO @ Sun, 21 Jun 2020 19:32:28: 1000000 INFO @ Sun, 21 Jun 2020 19:32:28: 10000000 INFO @ Sun, 21 Jun 2020 19:32:35: 6000000 INFO @ Sun, 21 Jun 2020 19:32:35: 11000000 INFO @ Sun, 21 Jun 2020 19:32:36: 2000000 INFO @ Sun, 21 Jun 2020 19:32:41: 12000000 INFO @ Sun, 21 Jun 2020 19:32:42: 7000000 INFO @ Sun, 21 Jun 2020 19:32:43: 3000000 INFO @ Sun, 21 Jun 2020 19:32:48: 13000000 INFO @ Sun, 21 Jun 2020 19:32:49: 8000000 INFO @ Sun, 21 Jun 2020 19:32:50: 4000000 INFO @ Sun, 21 Jun 2020 19:32:54: 14000000 INFO @ Sun, 21 Jun 2020 19:32:57: 9000000 INFO @ Sun, 21 Jun 2020 19:32:57: 5000000 INFO @ Sun, 21 Jun 2020 19:33:01: 15000000 INFO @ Sun, 21 Jun 2020 19:33:04: 10000000 INFO @ Sun, 21 Jun 2020 19:33:04: 6000000 INFO @ Sun, 21 Jun 2020 19:33:08: 16000000 INFO @ Sun, 21 Jun 2020 19:33:11: 11000000 INFO @ Sun, 21 Jun 2020 19:33:12: 7000000 INFO @ Sun, 21 Jun 2020 19:33:15: 17000000 INFO @ Sun, 21 Jun 2020 19:33:18: 12000000 INFO @ Sun, 21 Jun 2020 19:33:19: 8000000 INFO @ Sun, 21 Jun 2020 19:33:21: 18000000 INFO @ Sun, 21 Jun 2020 19:33:25: 13000000 INFO @ Sun, 21 Jun 2020 19:33:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:33:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:33:26: #1 total tags in treatment: 18558741 INFO @ Sun, 21 Jun 2020 19:33:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:33:26: #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 19:33:26: 9000000 INFO @ Sun, 21 Jun 2020 19:33:27: #1 tags after filtering in treatment: 18558732 INFO @ Sun, 21 Jun 2020 19:33:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:33:27: #1 finished! INFO @ Sun, 21 Jun 2020 19:33:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:33:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:33:28: #2 number of paired peaks: 477 WARNING @ Sun, 21 Jun 2020 19:33:28: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Sun, 21 Jun 2020 19:33:28: start model_add_line... INFO @ Sun, 21 Jun 2020 19:33:28: start X-correlation... INFO @ Sun, 21 Jun 2020 19:33:28: end of X-cor INFO @ Sun, 21 Jun 2020 19:33:28: #2 finished! INFO @ Sun, 21 Jun 2020 19:33:28: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:33:28: #2 alternative fragment length(s) may be 3,42 bps INFO @ Sun, 21 Jun 2020 19:33:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.05_model.r WARNING @ Sun, 21 Jun 2020 19:33:28: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:33:28: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Sun, 21 Jun 2020 19:33:28: #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 19:33:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:33:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:33:33: 14000000 INFO @ Sun, 21 Jun 2020 19:33:33: 10000000 INFO @ Sun, 21 Jun 2020 19:33:40: 15000000 INFO @ Sun, 21 Jun 2020 19:33:41: 11000000 INFO @ Sun, 21 Jun 2020 19:33:48: 12000000 INFO @ Sun, 21 Jun 2020 19:33:48: 16000000 INFO @ Sun, 21 Jun 2020 19:33:55: 13000000 INFO @ Sun, 21 Jun 2020 19:33:55: 17000000 INFO @ Sun, 21 Jun 2020 19:34:00: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:34:02: 14000000 INFO @ Sun, 21 Jun 2020 19:34:03: 18000000 INFO @ Sun, 21 Jun 2020 19:34:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:34:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:34:07: #1 total tags in treatment: 18558741 INFO @ Sun, 21 Jun 2020 19:34:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:34:07: #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 19:34:08: #1 tags after filtering in treatment: 18558732 INFO @ Sun, 21 Jun 2020 19:34:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:34:08: #1 finished! INFO @ Sun, 21 Jun 2020 19:34:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:34:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:34:09: #2 number of paired peaks: 477 WARNING @ Sun, 21 Jun 2020 19:34:09: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Sun, 21 Jun 2020 19:34:09: start model_add_line... INFO @ Sun, 21 Jun 2020 19:34:10: start X-correlation... INFO @ Sun, 21 Jun 2020 19:34:10: end of X-cor INFO @ Sun, 21 Jun 2020 19:34:10: #2 finished! INFO @ Sun, 21 Jun 2020 19:34:10: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:34:10: #2 alternative fragment length(s) may be 3,42 bps INFO @ Sun, 21 Jun 2020 19:34:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.10_model.r WARNING @ Sun, 21 Jun 2020 19:34:10: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:34:10: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Sun, 21 Jun 2020 19:34:10: #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 19:34:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:34:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:34:10: 15000000 INFO @ Sun, 21 Jun 2020 19:34:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:34:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:34:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.05_summits.bed INFO @ Sun, 21 Jun 2020 19:34:18: 16000000 INFO @ Sun, 21 Jun 2020 19:34:18: Done! pass1 - making usageList (642 chroms): 2 millis pass2 - checking and writing primary data (2681 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:34:25: 17000000 INFO @ Sun, 21 Jun 2020 19:34:32: 18000000 INFO @ Sun, 21 Jun 2020 19:34:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:34:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:34:37: #1 total tags in treatment: 18558741 INFO @ Sun, 21 Jun 2020 19:34:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:34:37: #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 19:34:38: #1 tags after filtering in treatment: 18558732 INFO @ Sun, 21 Jun 2020 19:34:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:34:38: #1 finished! INFO @ Sun, 21 Jun 2020 19:34:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:34:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:34:39: #2 number of paired peaks: 477 WARNING @ Sun, 21 Jun 2020 19:34:39: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Sun, 21 Jun 2020 19:34:39: start model_add_line... INFO @ Sun, 21 Jun 2020 19:34:39: start X-correlation... INFO @ Sun, 21 Jun 2020 19:34:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:34:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:34:39: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:34:39: #2 alternative fragment length(s) may be 3,42 bps INFO @ Sun, 21 Jun 2020 19:34:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.20_model.r WARNING @ Sun, 21 Jun 2020 19:34:39: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:34:39: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Sun, 21 Jun 2020 19:34:39: #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 19:34:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:34:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:34:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:34:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:34:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:34:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.10_summits.bed INFO @ Sun, 21 Jun 2020 19:34:59: Done! pass1 - making usageList (536 chroms): 1 millis pass2 - checking and writing primary data (1972 records, 4 fields): 34 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:35:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:35:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287721/SRX287721.20_summits.bed INFO @ Sun, 21 Jun 2020 19:35:28: Done! pass1 - making usageList (397 chroms): 1 millis pass2 - checking and writing primary data (1072 records, 4 fields): 24 millis CompletedMACS2peakCalling