Job ID = 6456345 SRX = SRX3380792 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:56:46 prefetch.2.10.7: 1) Downloading 'SRR6278155'... 2020-06-21T10:56:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:59:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:59:11 prefetch.2.10.7: 'SRR6278155' is valid 2020-06-21T10:59:11 prefetch.2.10.7: 1) 'SRR6278155' was downloaded successfully Read 15653947 spots for SRR6278155/SRR6278155.sra Written 15653947 spots for SRR6278155/SRR6278155.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: 00:04:27 15653947 reads; of these: 15653947 (100.00%) were unpaired; of these: 617859 (3.95%) aligned 0 times 11108726 (70.96%) aligned exactly 1 time 3927362 (25.09%) aligned >1 times 96.05% overall alignment rate Time searching: 00:04:27 Overall time: 00:04:27 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] 1746285 / 15036088 = 0.1161 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 20:09:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.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 20:09:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:09:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:09:50: 1000000 INFO @ Sun, 21 Jun 2020 20:09:57: 2000000 INFO @ Sun, 21 Jun 2020 20:10:04: 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 20:10:11: 4000000 INFO @ Sun, 21 Jun 2020 20:10:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.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 20:10:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:10:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:10:19: 5000000 INFO @ Sun, 21 Jun 2020 20:10:21: 1000000 INFO @ Sun, 21 Jun 2020 20:10:26: 6000000 INFO @ Sun, 21 Jun 2020 20:10:30: 2000000 INFO @ Sun, 21 Jun 2020 20:10:33: 7000000 INFO @ Sun, 21 Jun 2020 20:10:38: 3000000 INFO @ Sun, 21 Jun 2020 20:10:40: 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 20:10:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.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 20:10:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:10:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:10:46: 4000000 INFO @ Sun, 21 Jun 2020 20:10:47: 9000000 INFO @ Sun, 21 Jun 2020 20:10:51: 1000000 INFO @ Sun, 21 Jun 2020 20:10:54: 5000000 INFO @ Sun, 21 Jun 2020 20:10:55: 10000000 INFO @ Sun, 21 Jun 2020 20:10:59: 2000000 INFO @ Sun, 21 Jun 2020 20:11:02: 6000000 INFO @ Sun, 21 Jun 2020 20:11:03: 11000000 INFO @ Sun, 21 Jun 2020 20:11:06: 3000000 INFO @ Sun, 21 Jun 2020 20:11:10: 7000000 INFO @ Sun, 21 Jun 2020 20:11:11: 12000000 INFO @ Sun, 21 Jun 2020 20:11:13: 4000000 INFO @ Sun, 21 Jun 2020 20:11:17: 8000000 INFO @ Sun, 21 Jun 2020 20:11:19: 13000000 INFO @ Sun, 21 Jun 2020 20:11:21: 5000000 INFO @ Sun, 21 Jun 2020 20:11:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:11:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:11:22: #1 total tags in treatment: 13289803 INFO @ Sun, 21 Jun 2020 20:11:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:11:22: #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 20:11:23: #1 tags after filtering in treatment: 13289803 INFO @ Sun, 21 Jun 2020 20:11:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:11:23: #1 finished! INFO @ Sun, 21 Jun 2020 20:11:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:11:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:11:24: 9000000 INFO @ Sun, 21 Jun 2020 20:11:24: #2 number of paired peaks: 288 WARNING @ Sun, 21 Jun 2020 20:11:24: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Sun, 21 Jun 2020 20:11:24: start model_add_line... INFO @ Sun, 21 Jun 2020 20:11:24: start X-correlation... INFO @ Sun, 21 Jun 2020 20:11:24: end of X-cor INFO @ Sun, 21 Jun 2020 20:11:24: #2 finished! INFO @ Sun, 21 Jun 2020 20:11:24: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 20:11:24: #2 alternative fragment length(s) may be 4,48 bps INFO @ Sun, 21 Jun 2020 20:11:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.05_model.r WARNING @ Sun, 21 Jun 2020 20:11:24: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:11:24: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Sun, 21 Jun 2020 20:11:24: #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 20:11:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:11:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:11:28: 6000000 INFO @ Sun, 21 Jun 2020 20:11:30: 10000000 INFO @ Sun, 21 Jun 2020 20:11:36: 7000000 INFO @ Sun, 21 Jun 2020 20:11:38: 11000000 INFO @ Sun, 21 Jun 2020 20:11:43: 8000000 INFO @ Sun, 21 Jun 2020 20:11:45: 12000000 INFO @ Sun, 21 Jun 2020 20:11:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:11:50: 9000000 INFO @ Sun, 21 Jun 2020 20:11:53: 13000000 INFO @ Sun, 21 Jun 2020 20:11:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:11:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:11:55: #1 total tags in treatment: 13289803 INFO @ Sun, 21 Jun 2020 20:11:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:11:55: #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 20:11:56: #1 tags after filtering in treatment: 13289803 INFO @ Sun, 21 Jun 2020 20:11:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:11:56: #1 finished! INFO @ Sun, 21 Jun 2020 20:11:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:11:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:11:57: #2 number of paired peaks: 288 WARNING @ Sun, 21 Jun 2020 20:11:57: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Sun, 21 Jun 2020 20:11:57: start model_add_line... INFO @ Sun, 21 Jun 2020 20:11:57: start X-correlation... INFO @ Sun, 21 Jun 2020 20:11:57: end of X-cor INFO @ Sun, 21 Jun 2020 20:11:57: #2 finished! INFO @ Sun, 21 Jun 2020 20:11:57: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 20:11:57: #2 alternative fragment length(s) may be 4,48 bps INFO @ Sun, 21 Jun 2020 20:11:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.10_model.r WARNING @ Sun, 21 Jun 2020 20:11:57: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:11:57: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Sun, 21 Jun 2020 20:11:57: #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 20:11:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:11:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:11:57: 10000000 INFO @ Sun, 21 Jun 2020 20:12:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.05_peaks.xls BedGraph に変換しました。 INFO @ Sun, 21 Jun 2020 20:12:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.05_peaks.narrowPeak BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:12:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.05_summits.bed INFO @ Sun, 21 Jun 2020 20:12:00: Done! pass1 - making usageList (529 chroms): 2 millis pass2 - checking and writing primary data (1981 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:12:05: 11000000 INFO @ Sun, 21 Jun 2020 20:12:11: 12000000 INFO @ Sun, 21 Jun 2020 20:12:17: 13000000 INFO @ Sun, 21 Jun 2020 20:12:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:12:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:12:19: #1 total tags in treatment: 13289803 INFO @ Sun, 21 Jun 2020 20:12:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:12:19: #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 20:12:20: #1 tags after filtering in treatment: 13289803 INFO @ Sun, 21 Jun 2020 20:12:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:12:20: #1 finished! INFO @ Sun, 21 Jun 2020 20:12:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:12:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:12:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:12:21: #2 number of paired peaks: 288 WARNING @ Sun, 21 Jun 2020 20:12:21: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Sun, 21 Jun 2020 20:12:21: start model_add_line... INFO @ Sun, 21 Jun 2020 20:12:21: start X-correlation... INFO @ Sun, 21 Jun 2020 20:12:21: end of X-cor INFO @ Sun, 21 Jun 2020 20:12:21: #2 finished! INFO @ Sun, 21 Jun 2020 20:12:21: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 20:12:21: #2 alternative fragment length(s) may be 4,48 bps INFO @ Sun, 21 Jun 2020 20:12:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.20_model.r WARNING @ Sun, 21 Jun 2020 20:12:21: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:12:21: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Sun, 21 Jun 2020 20:12:21: #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 20:12:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:12:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:12:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:12:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:12:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.10_summits.bed INFO @ Sun, 21 Jun 2020 20:12:32: Done! pass1 - making usageList (418 chroms): 2 millis pass2 - checking and writing primary data (1391 records, 4 fields): 26 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:12:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:12:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:12:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:12:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380792/SRX3380792.20_summits.bed INFO @ Sun, 21 Jun 2020 20:12:56: Done! pass1 - making usageList (188 chroms): 1 millis pass2 - checking and writing primary data (362 records, 4 fields): 12 millis CompletedMACS2peakCalling