Job ID = 6456451 SRX = SRX3404048 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:43:08 prefetch.2.10.7: 1) Downloading 'SRR6303525'... 2020-06-21T10:43:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:46:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:46:25 prefetch.2.10.7: 'SRR6303525' is valid 2020-06-21T10:46:25 prefetch.2.10.7: 1) 'SRR6303525' was downloaded successfully 2020-06-21T10:46:25 prefetch.2.10.7: 'SRR6303525' has 0 unresolved dependencies Read 22696988 spots for SRR6303525/SRR6303525.sra Written 22696988 spots for SRR6303525/SRR6303525.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: 00:05:38 22696988 reads; of these: 22696988 (100.00%) were unpaired; of these: 706047 (3.11%) aligned 0 times 16081603 (70.85%) aligned exactly 1 time 5909338 (26.04%) aligned >1 times 96.89% overall alignment rate Time searching: 00:05:38 Overall time: 00:05:38 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] 2144930 / 21990941 = 0.0975 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 19:58:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.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 19:58:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:58:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:58:10: 1000000 INFO @ Sun, 21 Jun 2020 19:58:16: 2000000 INFO @ Sun, 21 Jun 2020 19:58:21: 3000000 INFO @ Sun, 21 Jun 2020 19:58:26: 4000000 INFO @ Sun, 21 Jun 2020 19:58:32: 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 19:58:37: 6000000 INFO @ Sun, 21 Jun 2020 19:58:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.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 19:58:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:58:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:58:43: 7000000 INFO @ Sun, 21 Jun 2020 19:58:43: 1000000 INFO @ Sun, 21 Jun 2020 19:58:48: 8000000 INFO @ Sun, 21 Jun 2020 19:58:49: 2000000 INFO @ Sun, 21 Jun 2020 19:58:54: 3000000 INFO @ Sun, 21 Jun 2020 19:58:54: 9000000 INFO @ Sun, 21 Jun 2020 19:58:59: 4000000 INFO @ Sun, 21 Jun 2020 19:59:00: 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 19:59:05: 5000000 INFO @ Sun, 21 Jun 2020 19:59:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.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 19:59:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:59:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:59:05: 11000000 INFO @ Sun, 21 Jun 2020 19:59:10: 6000000 INFO @ Sun, 21 Jun 2020 19:59:10: 1000000 INFO @ Sun, 21 Jun 2020 19:59:11: 12000000 INFO @ Sun, 21 Jun 2020 19:59:16: 7000000 INFO @ Sun, 21 Jun 2020 19:59:16: 2000000 INFO @ Sun, 21 Jun 2020 19:59:16: 13000000 INFO @ Sun, 21 Jun 2020 19:59:21: 8000000 INFO @ Sun, 21 Jun 2020 19:59:22: 3000000 INFO @ Sun, 21 Jun 2020 19:59:22: 14000000 INFO @ Sun, 21 Jun 2020 19:59:26: 9000000 INFO @ Sun, 21 Jun 2020 19:59:27: 4000000 INFO @ Sun, 21 Jun 2020 19:59:27: 15000000 INFO @ Sun, 21 Jun 2020 19:59:32: 10000000 INFO @ Sun, 21 Jun 2020 19:59:33: 5000000 INFO @ Sun, 21 Jun 2020 19:59:33: 16000000 INFO @ Sun, 21 Jun 2020 19:59:37: 11000000 INFO @ Sun, 21 Jun 2020 19:59:38: 6000000 INFO @ Sun, 21 Jun 2020 19:59:39: 17000000 INFO @ Sun, 21 Jun 2020 19:59:43: 12000000 INFO @ Sun, 21 Jun 2020 19:59:44: 7000000 INFO @ Sun, 21 Jun 2020 19:59:44: 18000000 INFO @ Sun, 21 Jun 2020 19:59:48: 13000000 INFO @ Sun, 21 Jun 2020 19:59:49: 8000000 INFO @ Sun, 21 Jun 2020 19:59:50: 19000000 INFO @ Sun, 21 Jun 2020 19:59:54: 14000000 INFO @ Sun, 21 Jun 2020 19:59:55: 9000000 INFO @ Sun, 21 Jun 2020 19:59:55: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:59:55: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:59:55: #1 total tags in treatment: 19846011 INFO @ Sun, 21 Jun 2020 19:59:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:59:55: #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 19:59:56: #1 tags after filtering in treatment: 19845949 INFO @ Sun, 21 Jun 2020 19:59:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:59:56: #1 finished! INFO @ Sun, 21 Jun 2020 19:59:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:59:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:59:57: #2 number of paired peaks: 726 WARNING @ Sun, 21 Jun 2020 19:59:57: Fewer paired peaks (726) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 726 pairs to build model! INFO @ Sun, 21 Jun 2020 19:59:57: start model_add_line... INFO @ Sun, 21 Jun 2020 19:59:57: start X-correlation... INFO @ Sun, 21 Jun 2020 19:59:57: end of X-cor INFO @ Sun, 21 Jun 2020 19:59:57: #2 finished! INFO @ Sun, 21 Jun 2020 19:59:57: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 19:59:57: #2 alternative fragment length(s) may be 2,53,598 bps INFO @ Sun, 21 Jun 2020 19:59:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.05_model.r WARNING @ Sun, 21 Jun 2020 19:59:57: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:59:57: #2 You may need to consider one of the other alternative d(s): 2,53,598 WARNING @ Sun, 21 Jun 2020 19:59:57: #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 19:59:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:59:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:59:59: 15000000 INFO @ Sun, 21 Jun 2020 20:00:01: 10000000 INFO @ Sun, 21 Jun 2020 20:00:04: 16000000 INFO @ Sun, 21 Jun 2020 20:00:06: 11000000 INFO @ Sun, 21 Jun 2020 20:00:10: 17000000 INFO @ Sun, 21 Jun 2020 20:00:12: 12000000 INFO @ Sun, 21 Jun 2020 20:00:16: 18000000 INFO @ Sun, 21 Jun 2020 20:00:17: 13000000 INFO @ Sun, 21 Jun 2020 20:00:21: 19000000 INFO @ Sun, 21 Jun 2020 20:00:23: 14000000 INFO @ Sun, 21 Jun 2020 20:00:26: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:00:26: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:00:26: #1 total tags in treatment: 19846011 INFO @ Sun, 21 Jun 2020 20:00:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:00:26: #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 20:00:27: #1 tags after filtering in treatment: 19845949 INFO @ Sun, 21 Jun 2020 20:00:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:00:27: #1 finished! INFO @ Sun, 21 Jun 2020 20:00:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:00:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:00:28: #2 number of paired peaks: 726 WARNING @ Sun, 21 Jun 2020 20:00:28: Fewer paired peaks (726) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 726 pairs to build model! INFO @ Sun, 21 Jun 2020 20:00:28: start model_add_line... INFO @ Sun, 21 Jun 2020 20:00:28: 15000000 INFO @ Sun, 21 Jun 2020 20:00:28: start X-correlation... INFO @ Sun, 21 Jun 2020 20:00:28: end of X-cor INFO @ Sun, 21 Jun 2020 20:00:28: #2 finished! INFO @ Sun, 21 Jun 2020 20:00:28: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 20:00:28: #2 alternative fragment length(s) may be 2,53,598 bps INFO @ Sun, 21 Jun 2020 20:00:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.10_model.r WARNING @ Sun, 21 Jun 2020 20:00:28: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:00:28: #2 You may need to consider one of the other alternative d(s): 2,53,598 WARNING @ Sun, 21 Jun 2020 20:00:28: #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 20:00:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:00:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:00:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:00:34: 16000000 INFO @ Sun, 21 Jun 2020 20:00:39: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:00:45: 18000000 INFO @ Sun, 21 Jun 2020 20:00:51: 19000000 INFO @ Sun, 21 Jun 2020 20:00:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:00:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:00:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.05_summits.bed INFO @ Sun, 21 Jun 2020 20:00:52: Done! pass1 - making usageList (679 chroms): 1 millis pass2 - checking and writing primary data (3303 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:00:55: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:00:55: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:00:55: #1 total tags in treatment: 19846011 INFO @ Sun, 21 Jun 2020 20:00:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:00:55: #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 20:00:56: #1 tags after filtering in treatment: 19845949 INFO @ Sun, 21 Jun 2020 20:00:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:00:56: #1 finished! INFO @ Sun, 21 Jun 2020 20:00:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:00:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:00:57: #2 number of paired peaks: 726 WARNING @ Sun, 21 Jun 2020 20:00:57: Fewer paired peaks (726) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 726 pairs to build model! INFO @ Sun, 21 Jun 2020 20:00:57: start model_add_line... INFO @ Sun, 21 Jun 2020 20:00:57: start X-correlation... INFO @ Sun, 21 Jun 2020 20:00:57: end of X-cor INFO @ Sun, 21 Jun 2020 20:00:57: #2 finished! INFO @ Sun, 21 Jun 2020 20:00:57: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 20:00:57: #2 alternative fragment length(s) may be 2,53,598 bps INFO @ Sun, 21 Jun 2020 20:00:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.20_model.r WARNING @ Sun, 21 Jun 2020 20:00:57: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:00:57: #2 You may need to consider one of the other alternative d(s): 2,53,598 WARNING @ Sun, 21 Jun 2020 20:00:57: #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 20:00:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:00:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:01:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:01:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:01:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:01:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.10_summits.bed INFO @ Sun, 21 Jun 2020 20:01:22: Done! pass1 - making usageList (479 chroms): 1 millis pass2 - checking and writing primary data (1553 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:01:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:01:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:01:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:01:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404048/SRX3404048.20_summits.bed INFO @ Sun, 21 Jun 2020 20:01:51: Done! pass1 - making usageList (222 chroms): 1 millis pass2 - checking and writing primary data (567 records, 4 fields): 8 millis CompletedMACS2peakCalling