Job ID = 6455275 SRX = SRX287655 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:44:56 prefetch.2.10.7: 1) Downloading 'SRR869842'... 2020-06-21T09:44:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:46:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:46:53 prefetch.2.10.7: 1) 'SRR869842' was downloaded successfully Read 16271348 spots for SRR869842/SRR869842.sra Written 16271348 spots for SRR869842/SRR869842.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: 00:06:03 16271348 reads; of these: 16271348 (100.00%) were unpaired; of these: 1158209 (7.12%) aligned 0 times 8418902 (51.74%) aligned exactly 1 time 6694237 (41.14%) aligned >1 times 92.88% overall alignment rate Time searching: 00:06:03 Overall time: 00:06:03 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] 2695576 / 15113139 = 0.1784 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 18:58:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.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 18:58:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:58:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:58:19: 1000000 INFO @ Sun, 21 Jun 2020 18:58:25: 2000000 INFO @ Sun, 21 Jun 2020 18:58:31: 3000000 INFO @ Sun, 21 Jun 2020 18:58:37: 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 18:58:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.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 18:58:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:58:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:58:43: 5000000 INFO @ Sun, 21 Jun 2020 18:58:50: 1000000 INFO @ Sun, 21 Jun 2020 18:58:51: 6000000 INFO @ Sun, 21 Jun 2020 18:58:58: 7000000 INFO @ Sun, 21 Jun 2020 18:58:59: 2000000 INFO @ Sun, 21 Jun 2020 18:59:05: 8000000 INFO @ Sun, 21 Jun 2020 18:59:07: 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 18:59:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.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 18:59:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:59:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:59:13: 9000000 INFO @ Sun, 21 Jun 2020 18:59:15: 4000000 INFO @ Sun, 21 Jun 2020 18:59:20: 1000000 INFO @ Sun, 21 Jun 2020 18:59:21: 10000000 INFO @ Sun, 21 Jun 2020 18:59:24: 5000000 INFO @ Sun, 21 Jun 2020 18:59:27: 2000000 INFO @ Sun, 21 Jun 2020 18:59:28: 11000000 INFO @ Sun, 21 Jun 2020 18:59:32: 6000000 INFO @ Sun, 21 Jun 2020 18:59:35: 3000000 INFO @ Sun, 21 Jun 2020 18:59:36: 12000000 INFO @ Sun, 21 Jun 2020 18:59:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:59:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:59:39: #1 total tags in treatment: 12417563 INFO @ Sun, 21 Jun 2020 18:59:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:59:39: #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 18:59:40: #1 tags after filtering in treatment: 12417563 INFO @ Sun, 21 Jun 2020 18:59:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:59:40: #1 finished! INFO @ Sun, 21 Jun 2020 18:59:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:59:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:59:41: #2 number of paired peaks: 804 WARNING @ Sun, 21 Jun 2020 18:59:41: Fewer paired peaks (804) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 804 pairs to build model! INFO @ Sun, 21 Jun 2020 18:59:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:59:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:59:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:59:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:59:41: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 18:59:41: #2 alternative fragment length(s) may be 3,52,573 bps INFO @ Sun, 21 Jun 2020 18:59:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.05_model.r WARNING @ Sun, 21 Jun 2020 18:59:41: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:59:41: #2 You may need to consider one of the other alternative d(s): 3,52,573 WARNING @ Sun, 21 Jun 2020 18:59:41: #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 18:59:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:59:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:59:41: 7000000 INFO @ Sun, 21 Jun 2020 18:59:42: 4000000 INFO @ Sun, 21 Jun 2020 18:59:49: 8000000 INFO @ Sun, 21 Jun 2020 18:59:50: 5000000 INFO @ Sun, 21 Jun 2020 18:59:57: 9000000 INFO @ Sun, 21 Jun 2020 18:59:58: 6000000 INFO @ Sun, 21 Jun 2020 19:00:05: 7000000 INFO @ Sun, 21 Jun 2020 19:00:06: 10000000 INFO @ Sun, 21 Jun 2020 19:00:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:00:13: 8000000 INFO @ Sun, 21 Jun 2020 19:00:14: 11000000 INFO @ Sun, 21 Jun 2020 19:00:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:00:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:00:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.05_summits.bed INFO @ Sun, 21 Jun 2020 19:00:19: Done! pass1 - making usageList (869 chroms): 1 millis pass2 - checking and writing primary data (3605 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:00:20: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:00:23: 12000000 INFO @ Sun, 21 Jun 2020 19:00:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:00:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:00:26: #1 total tags in treatment: 12417563 INFO @ Sun, 21 Jun 2020 19:00:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:00:26: #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 19:00:27: #1 tags after filtering in treatment: 12417563 INFO @ Sun, 21 Jun 2020 19:00:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:00:27: #1 finished! INFO @ Sun, 21 Jun 2020 19:00:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:00:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:00:28: 10000000 INFO @ Sun, 21 Jun 2020 19:00:28: #2 number of paired peaks: 804 WARNING @ Sun, 21 Jun 2020 19:00:28: Fewer paired peaks (804) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 804 pairs to build model! INFO @ Sun, 21 Jun 2020 19:00:28: start model_add_line... INFO @ Sun, 21 Jun 2020 19:00:28: start X-correlation... INFO @ Sun, 21 Jun 2020 19:00:28: end of X-cor INFO @ Sun, 21 Jun 2020 19:00:28: #2 finished! INFO @ Sun, 21 Jun 2020 19:00:28: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 19:00:28: #2 alternative fragment length(s) may be 3,52,573 bps INFO @ Sun, 21 Jun 2020 19:00:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.10_model.r WARNING @ Sun, 21 Jun 2020 19:00:28: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:00:28: #2 You may need to consider one of the other alternative d(s): 3,52,573 WARNING @ Sun, 21 Jun 2020 19:00:28: #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 19:00:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:00:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:00:34: 11000000 INFO @ Sun, 21 Jun 2020 19:00:40: 12000000 INFO @ Sun, 21 Jun 2020 19:00:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:00:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:00:43: #1 total tags in treatment: 12417563 INFO @ Sun, 21 Jun 2020 19:00:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:00:43: #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 19:00:43: #1 tags after filtering in treatment: 12417563 INFO @ Sun, 21 Jun 2020 19:00:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:00:43: #1 finished! INFO @ Sun, 21 Jun 2020 19:00:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:00:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:00:44: #2 number of paired peaks: 804 WARNING @ Sun, 21 Jun 2020 19:00:44: Fewer paired peaks (804) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 804 pairs to build model! INFO @ Sun, 21 Jun 2020 19:00:44: start model_add_line... INFO @ Sun, 21 Jun 2020 19:00:44: start X-correlation... INFO @ Sun, 21 Jun 2020 19:00:44: end of X-cor INFO @ Sun, 21 Jun 2020 19:00:44: #2 finished! INFO @ Sun, 21 Jun 2020 19:00:44: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 19:00:44: #2 alternative fragment length(s) may be 3,52,573 bps INFO @ Sun, 21 Jun 2020 19:00:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.20_model.r WARNING @ Sun, 21 Jun 2020 19:00:44: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:00:44: #2 You may need to consider one of the other alternative d(s): 3,52,573 WARNING @ Sun, 21 Jun 2020 19:00:44: #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 19:00:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:00:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:00:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:01:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:01:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:01:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.10_summits.bed INFO @ Sun, 21 Jun 2020 19:01:08: Done! pass1 - making usageList (663 chroms): 2 millis pass2 - checking and writing primary data (1922 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:01:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:01:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:01:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:01:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287655/SRX287655.20_summits.bed INFO @ Sun, 21 Jun 2020 19:01:23: Done! pass1 - making usageList (318 chroms): 1 millis pass2 - checking and writing primary data (634 records, 4 fields): 10 millis CompletedMACS2peakCalling