Job ID = 6456587 SRX = SRX365704 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:54:31 prefetch.2.10.7: 1) Downloading 'SRR1013782'... 2020-06-21T10:54:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:56:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:56:24 prefetch.2.10.7: 'SRR1013782' is valid 2020-06-21T10:56:24 prefetch.2.10.7: 1) 'SRR1013782' was downloaded successfully Read 17312277 spots for SRR1013782/SRR1013782.sra Written 17312277 spots for SRR1013782/SRR1013782.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: 00:03:53 17312277 reads; of these: 17312277 (100.00%) were unpaired; of these: 736708 (4.26%) aligned 0 times 12212731 (70.54%) aligned exactly 1 time 4362838 (25.20%) aligned >1 times 95.74% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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] 2319771 / 16575569 = 0.1400 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 20:05:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.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 20:05:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:05:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:05:59: 1000000 INFO @ Sun, 21 Jun 2020 20:06:05: 2000000 INFO @ Sun, 21 Jun 2020 20:06:10: 3000000 INFO @ Sun, 21 Jun 2020 20:06:16: 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 20:06:22: 5000000 INFO @ Sun, 21 Jun 2020 20:06:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.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 20:06:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:06:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:06:27: 6000000 INFO @ Sun, 21 Jun 2020 20:06:30: 1000000 INFO @ Sun, 21 Jun 2020 20:06:33: 7000000 INFO @ Sun, 21 Jun 2020 20:06:38: 2000000 INFO @ Sun, 21 Jun 2020 20:06:39: 8000000 INFO @ Sun, 21 Jun 2020 20:06:44: 9000000 INFO @ Sun, 21 Jun 2020 20:06:45: 3000000 INFO @ Sun, 21 Jun 2020 20:06:50: 10000000 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 20:06:53: 4000000 INFO @ Sun, 21 Jun 2020 20:06:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.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 20:06:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:06:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:06:56: 11000000 INFO @ Sun, 21 Jun 2020 20:06:59: 1000000 INFO @ Sun, 21 Jun 2020 20:07:00: 5000000 INFO @ Sun, 21 Jun 2020 20:07:03: 12000000 INFO @ Sun, 21 Jun 2020 20:07:06: 2000000 INFO @ Sun, 21 Jun 2020 20:07:07: 6000000 INFO @ Sun, 21 Jun 2020 20:07:09: 13000000 INFO @ Sun, 21 Jun 2020 20:07:12: 3000000 INFO @ Sun, 21 Jun 2020 20:07:15: 7000000 INFO @ Sun, 21 Jun 2020 20:07:16: 14000000 INFO @ Sun, 21 Jun 2020 20:07:18: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:07:18: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:07:18: #1 total tags in treatment: 14255798 INFO @ Sun, 21 Jun 2020 20:07:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:07:18: #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 20:07:18: 4000000 INFO @ Sun, 21 Jun 2020 20:07:18: #1 tags after filtering in treatment: 14255729 INFO @ Sun, 21 Jun 2020 20:07:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:07:18: #1 finished! INFO @ Sun, 21 Jun 2020 20:07:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:07:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:07:19: #2 number of paired peaks: 530 WARNING @ Sun, 21 Jun 2020 20:07:19: Fewer paired peaks (530) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 530 pairs to build model! INFO @ Sun, 21 Jun 2020 20:07:19: start model_add_line... INFO @ Sun, 21 Jun 2020 20:07:20: start X-correlation... INFO @ Sun, 21 Jun 2020 20:07:20: end of X-cor INFO @ Sun, 21 Jun 2020 20:07:20: #2 finished! INFO @ Sun, 21 Jun 2020 20:07:20: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 20:07:20: #2 alternative fragment length(s) may be 56 bps INFO @ Sun, 21 Jun 2020 20:07:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.05_model.r WARNING @ Sun, 21 Jun 2020 20:07:20: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:07:20: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sun, 21 Jun 2020 20:07:20: #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 20:07:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:07:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:07:22: 8000000 INFO @ Sun, 21 Jun 2020 20:07:24: 5000000 INFO @ Sun, 21 Jun 2020 20:07:29: 9000000 INFO @ Sun, 21 Jun 2020 20:07:30: 6000000 INFO @ Sun, 21 Jun 2020 20:07:35: 7000000 INFO @ Sun, 21 Jun 2020 20:07:36: 10000000 INFO @ Sun, 21 Jun 2020 20:07:41: 8000000 INFO @ Sun, 21 Jun 2020 20:07:43: 11000000 INFO @ Sun, 21 Jun 2020 20:07:47: 9000000 INFO @ Sun, 21 Jun 2020 20:07:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:07:51: 12000000 INFO @ Sun, 21 Jun 2020 20:07:52: 10000000 INFO @ Sun, 21 Jun 2020 20:07:58: 11000000 INFO @ Sun, 21 Jun 2020 20:07:59: 13000000 INFO @ Sun, 21 Jun 2020 20:08:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:08:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:08:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.05_summits.bed INFO @ Sun, 21 Jun 2020 20:08:03: Done! pass1 - making usageList (587 chroms): 2 millis pass2 - checking and writing primary data (7060 records, 4 fields): 83 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:08:04: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:08:06: 14000000 INFO @ Sun, 21 Jun 2020 20:08:08: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:08:08: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:08:08: #1 total tags in treatment: 14255798 INFO @ Sun, 21 Jun 2020 20:08:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:08:08: #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 20:08:09: #1 tags after filtering in treatment: 14255729 INFO @ Sun, 21 Jun 2020 20:08:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:08:09: #1 finished! INFO @ Sun, 21 Jun 2020 20:08:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:08:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:08:10: #2 number of paired peaks: 530 WARNING @ Sun, 21 Jun 2020 20:08:10: Fewer paired peaks (530) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 530 pairs to build model! INFO @ Sun, 21 Jun 2020 20:08:10: start model_add_line... INFO @ Sun, 21 Jun 2020 20:08:10: start X-correlation... INFO @ Sun, 21 Jun 2020 20:08:10: end of X-cor INFO @ Sun, 21 Jun 2020 20:08:10: #2 finished! INFO @ Sun, 21 Jun 2020 20:08:10: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 20:08:10: #2 alternative fragment length(s) may be 56 bps INFO @ Sun, 21 Jun 2020 20:08:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.10_model.r WARNING @ Sun, 21 Jun 2020 20:08:10: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:08:10: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sun, 21 Jun 2020 20:08:10: #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 20:08:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:08:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:08:10: 13000000 INFO @ Sun, 21 Jun 2020 20:08:16: 14000000 INFO @ Sun, 21 Jun 2020 20:08:17: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:08:17: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:08:17: #1 total tags in treatment: 14255798 INFO @ Sun, 21 Jun 2020 20:08:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:08:17: #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 20:08:18: #1 tags after filtering in treatment: 14255729 INFO @ Sun, 21 Jun 2020 20:08:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:08:18: #1 finished! INFO @ Sun, 21 Jun 2020 20:08:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:08:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:08:19: #2 number of paired peaks: 530 WARNING @ Sun, 21 Jun 2020 20:08:19: Fewer paired peaks (530) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 530 pairs to build model! INFO @ Sun, 21 Jun 2020 20:08:19: start model_add_line... INFO @ Sun, 21 Jun 2020 20:08:19: start X-correlation... INFO @ Sun, 21 Jun 2020 20:08:19: end of X-cor INFO @ Sun, 21 Jun 2020 20:08:19: #2 finished! INFO @ Sun, 21 Jun 2020 20:08:19: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 20:08:19: #2 alternative fragment length(s) may be 56 bps INFO @ Sun, 21 Jun 2020 20:08:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.20_model.r WARNING @ Sun, 21 Jun 2020 20:08:19: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:08:19: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sun, 21 Jun 2020 20:08:19: #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 20:08:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:08:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:08:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:08:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:08:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:08:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:08:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.10_summits.bed INFO @ Sun, 21 Jun 2020 20:08:54: Done! pass1 - making usageList (292 chroms): 2 millis pass2 - checking and writing primary data (3116 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:09:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:09:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:09:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX365704/SRX365704.20_summits.bed INFO @ Sun, 21 Jun 2020 20:09:01: Done! pass1 - making usageList (142 chroms): 1 millis pass2 - checking and writing primary data (1415 records, 4 fields): 11 millis CompletedMACS2peakCalling