Job ID = 6529331 SRX = SRX183888 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: 00:10:03 35738149 reads; of these: 35738149 (100.00%) were unpaired; of these: 1144680 (3.20%) aligned 0 times 24579057 (68.78%) aligned exactly 1 time 10014412 (28.02%) aligned >1 times 96.80% overall alignment rate Time searching: 00:10:03 Overall time: 00:10:03 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] 7996659 / 34593469 = 0.2312 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 02:12:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.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 02:12:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:12:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:12:31: 1000000 INFO @ Tue, 30 Jun 2020 02:12:36: 2000000 INFO @ Tue, 30 Jun 2020 02:12:42: 3000000 INFO @ Tue, 30 Jun 2020 02:12:48: 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 02:12:53: 5000000 INFO @ Tue, 30 Jun 2020 02:12:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.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 02:12:57: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:12:57: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:12:59: 6000000 INFO @ Tue, 30 Jun 2020 02:13:02: 1000000 INFO @ Tue, 30 Jun 2020 02:13:05: 7000000 INFO @ Tue, 30 Jun 2020 02:13:08: 2000000 INFO @ Tue, 30 Jun 2020 02:13:11: 8000000 INFO @ Tue, 30 Jun 2020 02:13:14: 3000000 INFO @ Tue, 30 Jun 2020 02:13:17: 9000000 INFO @ Tue, 30 Jun 2020 02:13:20: 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 @ Tue, 30 Jun 2020 02:13:23: 10000000 INFO @ Tue, 30 Jun 2020 02:13:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.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 02:13:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:13:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:13:27: 5000000 INFO @ Tue, 30 Jun 2020 02:13:29: 11000000 INFO @ Tue, 30 Jun 2020 02:13:32: 1000000 INFO @ Tue, 30 Jun 2020 02:13:33: 6000000 INFO @ Tue, 30 Jun 2020 02:13:36: 12000000 INFO @ Tue, 30 Jun 2020 02:13:39: 2000000 INFO @ Tue, 30 Jun 2020 02:13:40: 7000000 INFO @ Tue, 30 Jun 2020 02:13:42: 13000000 INFO @ Tue, 30 Jun 2020 02:13:46: 8000000 INFO @ Tue, 30 Jun 2020 02:13:46: 3000000 INFO @ Tue, 30 Jun 2020 02:13:49: 14000000 INFO @ Tue, 30 Jun 2020 02:13:52: 9000000 INFO @ Tue, 30 Jun 2020 02:13:53: 4000000 INFO @ Tue, 30 Jun 2020 02:13:55: 15000000 INFO @ Tue, 30 Jun 2020 02:13:59: 10000000 INFO @ Tue, 30 Jun 2020 02:14:00: 5000000 INFO @ Tue, 30 Jun 2020 02:14:02: 16000000 INFO @ Tue, 30 Jun 2020 02:14:05: 11000000 INFO @ Tue, 30 Jun 2020 02:14:07: 6000000 INFO @ Tue, 30 Jun 2020 02:14:08: 17000000 INFO @ Tue, 30 Jun 2020 02:14:11: 12000000 INFO @ Tue, 30 Jun 2020 02:14:14: 7000000 INFO @ Tue, 30 Jun 2020 02:14:14: 18000000 INFO @ Tue, 30 Jun 2020 02:14:18: 13000000 INFO @ Tue, 30 Jun 2020 02:14:21: 19000000 INFO @ Tue, 30 Jun 2020 02:14:21: 8000000 INFO @ Tue, 30 Jun 2020 02:14:24: 14000000 INFO @ Tue, 30 Jun 2020 02:14:27: 20000000 INFO @ Tue, 30 Jun 2020 02:14:28: 9000000 INFO @ Tue, 30 Jun 2020 02:14:30: 15000000 INFO @ Tue, 30 Jun 2020 02:14:33: 21000000 INFO @ Tue, 30 Jun 2020 02:14:35: 10000000 INFO @ Tue, 30 Jun 2020 02:14:37: 16000000 INFO @ Tue, 30 Jun 2020 02:14:40: 22000000 INFO @ Tue, 30 Jun 2020 02:14:42: 11000000 INFO @ Tue, 30 Jun 2020 02:14:43: 17000000 INFO @ Tue, 30 Jun 2020 02:14:46: 23000000 INFO @ Tue, 30 Jun 2020 02:14:49: 12000000 INFO @ Tue, 30 Jun 2020 02:14:49: 18000000 INFO @ Tue, 30 Jun 2020 02:14:52: 24000000 INFO @ Tue, 30 Jun 2020 02:14:56: 19000000 INFO @ Tue, 30 Jun 2020 02:14:56: 13000000 INFO @ Tue, 30 Jun 2020 02:14:59: 25000000 INFO @ Tue, 30 Jun 2020 02:15:02: 20000000 INFO @ Tue, 30 Jun 2020 02:15:03: 14000000 INFO @ Tue, 30 Jun 2020 02:15:05: 26000000 INFO @ Tue, 30 Jun 2020 02:15:08: 21000000 INFO @ Tue, 30 Jun 2020 02:15:10: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 02:15:10: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 02:15:10: #1 total tags in treatment: 26596810 INFO @ Tue, 30 Jun 2020 02:15:10: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:15:10: #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 02:15:10: 15000000 INFO @ Tue, 30 Jun 2020 02:15:10: #1 tags after filtering in treatment: 26596809 INFO @ Tue, 30 Jun 2020 02:15:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:15:10: #1 finished! INFO @ Tue, 30 Jun 2020 02:15:10: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:15:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:15:12: #2 number of paired peaks: 197 WARNING @ Tue, 30 Jun 2020 02:15:12: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Tue, 30 Jun 2020 02:15:12: start model_add_line... INFO @ Tue, 30 Jun 2020 02:15:12: start X-correlation... INFO @ Tue, 30 Jun 2020 02:15:12: end of X-cor INFO @ Tue, 30 Jun 2020 02:15:12: #2 finished! INFO @ Tue, 30 Jun 2020 02:15:12: #2 predicted fragment length is 41 bps INFO @ Tue, 30 Jun 2020 02:15:12: #2 alternative fragment length(s) may be 2,41,598 bps INFO @ Tue, 30 Jun 2020 02:15:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.05_model.r WARNING @ Tue, 30 Jun 2020 02:15:12: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:15:12: #2 You may need to consider one of the other alternative d(s): 2,41,598 WARNING @ Tue, 30 Jun 2020 02:15:12: #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 02:15:12: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:15:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:15:15: 22000000 INFO @ Tue, 30 Jun 2020 02:15:16: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:15:21: 23000000 INFO @ Tue, 30 Jun 2020 02:15:23: 17000000 INFO @ Tue, 30 Jun 2020 02:15:27: 24000000 INFO @ Tue, 30 Jun 2020 02:15:30: 18000000 INFO @ Tue, 30 Jun 2020 02:15:34: 25000000 INFO @ Tue, 30 Jun 2020 02:15:36: 19000000 INFO @ Tue, 30 Jun 2020 02:15:40: 26000000 INFO @ Tue, 30 Jun 2020 02:15:43: 20000000 INFO @ Tue, 30 Jun 2020 02:15:44: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 02:15:44: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 02:15:44: #1 total tags in treatment: 26596810 INFO @ Tue, 30 Jun 2020 02:15:44: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:15:44: #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 02:15:45: #1 tags after filtering in treatment: 26596809 INFO @ Tue, 30 Jun 2020 02:15:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:15:45: #1 finished! INFO @ Tue, 30 Jun 2020 02:15:45: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:15:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:15:47: #2 number of paired peaks: 197 WARNING @ Tue, 30 Jun 2020 02:15:47: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Tue, 30 Jun 2020 02:15:47: start model_add_line... INFO @ Tue, 30 Jun 2020 02:15:47: start X-correlation... INFO @ Tue, 30 Jun 2020 02:15:47: end of X-cor INFO @ Tue, 30 Jun 2020 02:15:47: #2 finished! INFO @ Tue, 30 Jun 2020 02:15:47: #2 predicted fragment length is 41 bps INFO @ Tue, 30 Jun 2020 02:15:47: #2 alternative fragment length(s) may be 2,41,598 bps INFO @ Tue, 30 Jun 2020 02:15:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.10_model.r WARNING @ Tue, 30 Jun 2020 02:15:47: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:15:47: #2 You may need to consider one of the other alternative d(s): 2,41,598 WARNING @ Tue, 30 Jun 2020 02:15:47: #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 02:15:47: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:15:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:15:49: 21000000 INFO @ Tue, 30 Jun 2020 02:15:56: 22000000 INFO @ Tue, 30 Jun 2020 02:16:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:16:02: 23000000 INFO @ Tue, 30 Jun 2020 02:16:09: 24000000 INFO @ Tue, 30 Jun 2020 02:16:15: 25000000 INFO @ Tue, 30 Jun 2020 02:16:21: 26000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:16:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:16:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:16:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.05_summits.bed INFO @ Tue, 30 Jun 2020 02:16:24: Done! pass1 - making usageList (721 chroms): 2 millis pass2 - checking and writing primary data (3833 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:16:25: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 02:16:25: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 02:16:25: #1 total tags in treatment: 26596810 INFO @ Tue, 30 Jun 2020 02:16:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:16:25: #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 02:16:26: #1 tags after filtering in treatment: 26596809 INFO @ Tue, 30 Jun 2020 02:16:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:16:26: #1 finished! INFO @ Tue, 30 Jun 2020 02:16:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:16:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:16:28: #2 number of paired peaks: 197 WARNING @ Tue, 30 Jun 2020 02:16:28: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Tue, 30 Jun 2020 02:16:28: start model_add_line... INFO @ Tue, 30 Jun 2020 02:16:28: start X-correlation... INFO @ Tue, 30 Jun 2020 02:16:28: end of X-cor INFO @ Tue, 30 Jun 2020 02:16:28: #2 finished! INFO @ Tue, 30 Jun 2020 02:16:28: #2 predicted fragment length is 41 bps INFO @ Tue, 30 Jun 2020 02:16:28: #2 alternative fragment length(s) may be 2,41,598 bps INFO @ Tue, 30 Jun 2020 02:16:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.20_model.r WARNING @ Tue, 30 Jun 2020 02:16:28: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:16:28: #2 You may need to consider one of the other alternative d(s): 2,41,598 WARNING @ Tue, 30 Jun 2020 02:16:28: #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 02:16:28: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:16:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:16:36: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:17:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:17:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:17:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.10_summits.bed INFO @ Tue, 30 Jun 2020 02:17:01: Done! pass1 - making usageList (578 chroms): 1 millis pass2 - checking and writing primary data (2639 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:17:16: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:17:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:17:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:17:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX183888/SRX183888.20_summits.bed INFO @ Tue, 30 Jun 2020 02:17:39: Done! pass1 - making usageList (274 chroms): 1 millis pass2 - checking and writing primary data (554 records, 4 fields): 9 millis CompletedMACS2peakCalling