Job ID = 6529335 SRX = SRX1840078 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:14:34 30646875 reads; of these: 30646875 (100.00%) were unpaired; of these: 844178 (2.75%) aligned 0 times 22949635 (74.88%) aligned exactly 1 time 6853062 (22.36%) aligned >1 times 97.25% overall alignment rate Time searching: 00:14:34 Overall time: 00:14:34 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 16 files... [bam_rmdupse_core] 3605549 / 29802697 = 0.1210 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 @ Tue, 30 Jun 2020 02:08:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.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 @ Tue, 30 Jun 2020 02:08:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:08:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:08:41: 1000000 INFO @ Tue, 30 Jun 2020 02:08:47: 2000000 INFO @ Tue, 30 Jun 2020 02:08:53: 3000000 INFO @ Tue, 30 Jun 2020 02:08:59: 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 @ Tue, 30 Jun 2020 02:09:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.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 @ Tue, 30 Jun 2020 02:09:05: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:09:05: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:09:05: 5000000 INFO @ Tue, 30 Jun 2020 02:09:12: 6000000 INFO @ Tue, 30 Jun 2020 02:09:12: 1000000 INFO @ Tue, 30 Jun 2020 02:09:18: 7000000 INFO @ Tue, 30 Jun 2020 02:09:20: 2000000 INFO @ Tue, 30 Jun 2020 02:09:25: 8000000 INFO @ Tue, 30 Jun 2020 02:09:27: 3000000 INFO @ Tue, 30 Jun 2020 02:09:32: 9000000 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 @ Tue, 30 Jun 2020 02:09:35: 4000000 INFO @ Tue, 30 Jun 2020 02:09:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.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 @ Tue, 30 Jun 2020 02:09:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:09:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:09:38: 10000000 INFO @ Tue, 30 Jun 2020 02:09:42: 1000000 INFO @ Tue, 30 Jun 2020 02:09:42: 5000000 INFO @ Tue, 30 Jun 2020 02:09:45: 11000000 INFO @ Tue, 30 Jun 2020 02:09:48: 2000000 INFO @ Tue, 30 Jun 2020 02:09:50: 6000000 INFO @ Tue, 30 Jun 2020 02:09:52: 12000000 INFO @ Tue, 30 Jun 2020 02:09:55: 3000000 INFO @ Tue, 30 Jun 2020 02:09:57: 7000000 INFO @ Tue, 30 Jun 2020 02:09:58: 13000000 INFO @ Tue, 30 Jun 2020 02:10:02: 4000000 INFO @ Tue, 30 Jun 2020 02:10:05: 8000000 INFO @ Tue, 30 Jun 2020 02:10:05: 14000000 INFO @ Tue, 30 Jun 2020 02:10:08: 5000000 INFO @ Tue, 30 Jun 2020 02:10:11: 15000000 INFO @ Tue, 30 Jun 2020 02:10:12: 9000000 INFO @ Tue, 30 Jun 2020 02:10:15: 6000000 INFO @ Tue, 30 Jun 2020 02:10:18: 16000000 INFO @ Tue, 30 Jun 2020 02:10:20: 10000000 INFO @ Tue, 30 Jun 2020 02:10:21: 7000000 INFO @ Tue, 30 Jun 2020 02:10:25: 17000000 INFO @ Tue, 30 Jun 2020 02:10:27: 11000000 INFO @ Tue, 30 Jun 2020 02:10:28: 8000000 INFO @ Tue, 30 Jun 2020 02:10:31: 18000000 INFO @ Tue, 30 Jun 2020 02:10:35: 9000000 INFO @ Tue, 30 Jun 2020 02:10:35: 12000000 INFO @ Tue, 30 Jun 2020 02:10:38: 19000000 INFO @ Tue, 30 Jun 2020 02:10:41: 10000000 INFO @ Tue, 30 Jun 2020 02:10:42: 13000000 INFO @ Tue, 30 Jun 2020 02:10:45: 20000000 INFO @ Tue, 30 Jun 2020 02:10:48: 11000000 INFO @ Tue, 30 Jun 2020 02:10:50: 14000000 INFO @ Tue, 30 Jun 2020 02:10:51: 21000000 INFO @ Tue, 30 Jun 2020 02:10:55: 12000000 INFO @ Tue, 30 Jun 2020 02:10:57: 15000000 INFO @ Tue, 30 Jun 2020 02:10:58: 22000000 INFO @ Tue, 30 Jun 2020 02:11:01: 13000000 INFO @ Tue, 30 Jun 2020 02:11:05: 16000000 INFO @ Tue, 30 Jun 2020 02:11:05: 23000000 INFO @ Tue, 30 Jun 2020 02:11:08: 14000000 INFO @ Tue, 30 Jun 2020 02:11:12: 24000000 INFO @ Tue, 30 Jun 2020 02:11:12: 17000000 INFO @ Tue, 30 Jun 2020 02:11:15: 15000000 INFO @ Tue, 30 Jun 2020 02:11:18: 25000000 INFO @ Tue, 30 Jun 2020 02:11:20: 18000000 INFO @ Tue, 30 Jun 2020 02:11:21: 16000000 INFO @ Tue, 30 Jun 2020 02:11:25: 26000000 INFO @ Tue, 30 Jun 2020 02:11:26: #1 tag size is determined as 101 bps INFO @ Tue, 30 Jun 2020 02:11:26: #1 tag size = 101 INFO @ Tue, 30 Jun 2020 02:11:26: #1 total tags in treatment: 26197148 INFO @ Tue, 30 Jun 2020 02:11:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:11:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:11:27: #1 tags after filtering in treatment: 26197146 INFO @ Tue, 30 Jun 2020 02:11:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:11:27: #1 finished! INFO @ Tue, 30 Jun 2020 02:11:27: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:11:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:11:27: 19000000 INFO @ Tue, 30 Jun 2020 02:11:28: 17000000 INFO @ Tue, 30 Jun 2020 02:11:29: #2 number of paired peaks: 168 WARNING @ Tue, 30 Jun 2020 02:11:29: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Tue, 30 Jun 2020 02:11:29: start model_add_line... INFO @ Tue, 30 Jun 2020 02:11:29: start X-correlation... INFO @ Tue, 30 Jun 2020 02:11:29: end of X-cor INFO @ Tue, 30 Jun 2020 02:11:29: #2 finished! INFO @ Tue, 30 Jun 2020 02:11:29: #2 predicted fragment length is 95 bps INFO @ Tue, 30 Jun 2020 02:11:29: #2 alternative fragment length(s) may be 4,95 bps INFO @ Tue, 30 Jun 2020 02:11:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.05_model.r WARNING @ Tue, 30 Jun 2020 02:11:29: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:11:29: #2 You may need to consider one of the other alternative d(s): 4,95 WARNING @ Tue, 30 Jun 2020 02:11:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:11:29: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:11:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:11:34: 18000000 INFO @ Tue, 30 Jun 2020 02:11:35: 20000000 INFO @ Tue, 30 Jun 2020 02:11:41: 19000000 INFO @ Tue, 30 Jun 2020 02:11:42: 21000000 INFO @ Tue, 30 Jun 2020 02:11:47: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:11:50: 22000000 INFO @ Tue, 30 Jun 2020 02:11:54: 21000000 INFO @ Tue, 30 Jun 2020 02:11:58: 23000000 INFO @ Tue, 30 Jun 2020 02:12:01: 22000000 INFO @ Tue, 30 Jun 2020 02:12:05: 24000000 INFO @ Tue, 30 Jun 2020 02:12:07: 23000000 INFO @ Tue, 30 Jun 2020 02:12:12: 25000000 INFO @ Tue, 30 Jun 2020 02:12:14: 24000000 INFO @ Tue, 30 Jun 2020 02:12:14: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:12:20: 26000000 INFO @ Tue, 30 Jun 2020 02:12:20: 25000000 INFO @ Tue, 30 Jun 2020 02:12:22: #1 tag size is determined as 101 bps INFO @ Tue, 30 Jun 2020 02:12:22: #1 tag size = 101 INFO @ Tue, 30 Jun 2020 02:12:22: #1 total tags in treatment: 26197148 INFO @ Tue, 30 Jun 2020 02:12:22: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:12:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:12:22: #1 tags after filtering in treatment: 26197146 INFO @ Tue, 30 Jun 2020 02:12:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:12:22: #1 finished! INFO @ Tue, 30 Jun 2020 02:12:22: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:12:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:12:24: #2 number of paired peaks: 168 WARNING @ Tue, 30 Jun 2020 02:12:24: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Tue, 30 Jun 2020 02:12:24: start model_add_line... INFO @ Tue, 30 Jun 2020 02:12:24: start X-correlation... INFO @ Tue, 30 Jun 2020 02:12:24: end of X-cor INFO @ Tue, 30 Jun 2020 02:12:24: #2 finished! INFO @ Tue, 30 Jun 2020 02:12:24: #2 predicted fragment length is 95 bps INFO @ Tue, 30 Jun 2020 02:12:24: #2 alternative fragment length(s) may be 4,95 bps INFO @ Tue, 30 Jun 2020 02:12:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.10_model.r WARNING @ Tue, 30 Jun 2020 02:12:24: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:12:24: #2 You may need to consider one of the other alternative d(s): 4,95 WARNING @ Tue, 30 Jun 2020 02:12:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:12:24: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:12:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:12:27: 26000000 INFO @ Tue, 30 Jun 2020 02:12:28: #1 tag size is determined as 101 bps INFO @ Tue, 30 Jun 2020 02:12:28: #1 tag size = 101 INFO @ Tue, 30 Jun 2020 02:12:28: #1 total tags in treatment: 26197148 INFO @ Tue, 30 Jun 2020 02:12:28: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:12:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:12:29: #1 tags after filtering in treatment: 26197146 INFO @ Tue, 30 Jun 2020 02:12:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:12:29: #1 finished! INFO @ Tue, 30 Jun 2020 02:12:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:12:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:12:31: #2 number of paired peaks: 168 WARNING @ Tue, 30 Jun 2020 02:12:31: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Tue, 30 Jun 2020 02:12:31: start model_add_line... INFO @ Tue, 30 Jun 2020 02:12:31: start X-correlation... INFO @ Tue, 30 Jun 2020 02:12:31: end of X-cor INFO @ Tue, 30 Jun 2020 02:12:31: #2 finished! INFO @ Tue, 30 Jun 2020 02:12:31: #2 predicted fragment length is 95 bps INFO @ Tue, 30 Jun 2020 02:12:31: #2 alternative fragment length(s) may be 4,95 bps INFO @ Tue, 30 Jun 2020 02:12:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.20_model.r WARNING @ Tue, 30 Jun 2020 02:12:31: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:12:31: #2 You may need to consider one of the other alternative d(s): 4,95 WARNING @ Tue, 30 Jun 2020 02:12:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:12:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:12:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:12:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:12:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:12:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.05_summits.bed INFO @ Tue, 30 Jun 2020 02:12:37: Done! pass1 - making usageList (778 chroms): 2 millis pass2 - checking and writing primary data (3262 records, 4 fields): 23 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:13:07: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:13:16: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:13:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:13:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:13:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.10_summits.bed INFO @ Tue, 30 Jun 2020 02:13:28: Done! pass1 - making usageList (650 chroms): 2 millis pass2 - checking and writing primary data (2022 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:13:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:13:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:13:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840078/SRX1840078.20_summits.bed INFO @ Tue, 30 Jun 2020 02:13:37: Done! pass1 - making usageList (492 chroms): 1 millis pass2 - checking and writing primary data (1049 records, 4 fields): 14 millis CompletedMACS2peakCalling