Job ID = 6455420 SRX = SRX287774 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:04:25 prefetch.2.10.7: 1) Downloading 'SRR869963'... 2020-06-21T10:04:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:05:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:05:49 prefetch.2.10.7: 'SRR869963' is valid 2020-06-21T10:05:49 prefetch.2.10.7: 1) 'SRR869963' was downloaded successfully Read 11258758 spots for SRR869963/SRR869963.sra Written 11258758 spots for SRR869963/SRR869963.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:43 11258758 reads; of these: 11258758 (100.00%) were unpaired; of these: 690822 (6.14%) aligned 0 times 7184217 (63.81%) aligned exactly 1 time 3383719 (30.05%) aligned >1 times 93.86% overall alignment rate Time searching: 00:03:44 Overall time: 00:03:44 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] 1456407 / 10567936 = 0.1378 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 19:13:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.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 19:13:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:32: 1000000 INFO @ Sun, 21 Jun 2020 19:13:37: 2000000 INFO @ Sun, 21 Jun 2020 19:13:43: 3000000 INFO @ Sun, 21 Jun 2020 19:13:48: 4000000 INFO @ Sun, 21 Jun 2020 19:13:53: 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 19:13:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.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 19:13:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:59: 6000000 INFO @ Sun, 21 Jun 2020 19:14:03: 1000000 INFO @ Sun, 21 Jun 2020 19:14:05: 7000000 INFO @ Sun, 21 Jun 2020 19:14:09: 2000000 INFO @ Sun, 21 Jun 2020 19:14:11: 8000000 INFO @ Sun, 21 Jun 2020 19:14:15: 3000000 INFO @ Sun, 21 Jun 2020 19:14:17: 9000000 INFO @ Sun, 21 Jun 2020 19:14:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:14:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:14:18: #1 total tags in treatment: 9111529 INFO @ Sun, 21 Jun 2020 19:14:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:14:18: #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 19:14:19: #1 tags after filtering in treatment: 9111529 INFO @ Sun, 21 Jun 2020 19:14:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:14:19: #1 finished! INFO @ Sun, 21 Jun 2020 19:14:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:14:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:14:19: #2 number of paired peaks: 837 WARNING @ Sun, 21 Jun 2020 19:14:19: Fewer paired peaks (837) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 837 pairs to build model! INFO @ Sun, 21 Jun 2020 19:14:19: start model_add_line... INFO @ Sun, 21 Jun 2020 19:14:19: start X-correlation... INFO @ Sun, 21 Jun 2020 19:14:19: end of X-cor INFO @ Sun, 21 Jun 2020 19:14:19: #2 finished! INFO @ Sun, 21 Jun 2020 19:14:19: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:14:19: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 19:14:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.05_model.r WARNING @ Sun, 21 Jun 2020 19:14:19: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:14:19: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 19:14:19: #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 19:14:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:14:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:14:21: 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 19:14:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.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 19:14:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:27: 5000000 INFO @ Sun, 21 Jun 2020 19:14:33: 1000000 INFO @ Sun, 21 Jun 2020 19:14:34: 6000000 INFO @ Sun, 21 Jun 2020 19:14:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:14:39: 2000000 INFO @ Sun, 21 Jun 2020 19:14:40: 7000000 INFO @ Sun, 21 Jun 2020 19:14:45: 3000000 INFO @ Sun, 21 Jun 2020 19:14:47: 8000000 INFO @ Sun, 21 Jun 2020 19:14:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:14:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:14:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.05_summits.bed INFO @ Sun, 21 Jun 2020 19:14:47: Done! pass1 - making usageList (596 chroms): 2 millis pass2 - checking and writing primary data (2203 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:14:51: 4000000 INFO @ Sun, 21 Jun 2020 19:14:53: 9000000 INFO @ Sun, 21 Jun 2020 19:14:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:14:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:14:54: #1 total tags in treatment: 9111529 INFO @ Sun, 21 Jun 2020 19:14:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:14:54: #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 19:14:54: #1 tags after filtering in treatment: 9111529 INFO @ Sun, 21 Jun 2020 19:14:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:14:54: #1 finished! INFO @ Sun, 21 Jun 2020 19:14:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:14:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:14:55: #2 number of paired peaks: 837 WARNING @ Sun, 21 Jun 2020 19:14:55: Fewer paired peaks (837) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 837 pairs to build model! INFO @ Sun, 21 Jun 2020 19:14:55: start model_add_line... INFO @ Sun, 21 Jun 2020 19:14:55: start X-correlation... INFO @ Sun, 21 Jun 2020 19:14:55: end of X-cor INFO @ Sun, 21 Jun 2020 19:14:55: #2 finished! INFO @ Sun, 21 Jun 2020 19:14:55: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:14:55: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 19:14:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.10_model.r WARNING @ Sun, 21 Jun 2020 19:14:55: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:14:55: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 19:14:55: #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 19:14:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:14:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:14:57: 5000000 INFO @ Sun, 21 Jun 2020 19:15:03: 6000000 INFO @ Sun, 21 Jun 2020 19:15:09: 7000000 INFO @ Sun, 21 Jun 2020 19:15:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:16: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:15:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.10_summits.bed INFO @ Sun, 21 Jun 2020 19:15:22: Done! INFO @ Sun, 21 Jun 2020 19:15:22: 9000000 pass1 - making usageList (487 chroms): 2 millis pass2 - checking and writing primary data (1762 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:15:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:22: #1 total tags in treatment: 9111529 INFO @ Sun, 21 Jun 2020 19:15:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:22: #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 19:15:23: #1 tags after filtering in treatment: 9111529 INFO @ Sun, 21 Jun 2020 19:15:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:23: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:24: #2 number of paired peaks: 837 WARNING @ Sun, 21 Jun 2020 19:15:24: Fewer paired peaks (837) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 837 pairs to build model! INFO @ Sun, 21 Jun 2020 19:15:24: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:24: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:24: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:24: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:24: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:15:24: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 19:15:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.20_model.r WARNING @ Sun, 21 Jun 2020 19:15:24: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:15:24: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 19:15:24: #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 19:15:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:15:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287774/SRX287774.20_summits.bed INFO @ Sun, 21 Jun 2020 19:15:51: Done! pass1 - making usageList (343 chroms): 1 millis pass2 - checking and writing primary data (715 records, 4 fields): 11 millis CompletedMACS2peakCalling