Job ID = 6529873 SRX = SRX5343135 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: 00:09:23 26063129 reads; of these: 26063129 (100.00%) were unpaired; of these: 1004922 (3.86%) aligned 0 times 17655315 (67.74%) aligned exactly 1 time 7402892 (28.40%) aligned >1 times 96.14% overall alignment rate Time searching: 00:09:23 Overall time: 00:09:23 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] 3529827 / 25058207 = 0.1409 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 03:21:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.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 03:21:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:21:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:21:40: 1000000 INFO @ Tue, 30 Jun 2020 03:21:45: 2000000 INFO @ Tue, 30 Jun 2020 03:21:50: 3000000 INFO @ Tue, 30 Jun 2020 03:21:55: 4000000 INFO @ Tue, 30 Jun 2020 03:22:00: 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 @ Tue, 30 Jun 2020 03:22:05: 6000000 INFO @ Tue, 30 Jun 2020 03:22:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.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 03:22:05: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:22:05: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:22:10: 7000000 INFO @ Tue, 30 Jun 2020 03:22:10: 1000000 INFO @ Tue, 30 Jun 2020 03:22:15: 8000000 INFO @ Tue, 30 Jun 2020 03:22:16: 2000000 INFO @ Tue, 30 Jun 2020 03:22:20: 9000000 INFO @ Tue, 30 Jun 2020 03:22:21: 3000000 INFO @ Tue, 30 Jun 2020 03:22:26: 10000000 INFO @ Tue, 30 Jun 2020 03:22:26: 4000000 INFO @ Tue, 30 Jun 2020 03:22:31: 11000000 INFO @ Tue, 30 Jun 2020 03:22:31: 5000000 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 03:22:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.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 03:22:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:22:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:22:36: 12000000 INFO @ Tue, 30 Jun 2020 03:22:36: 6000000 INFO @ Tue, 30 Jun 2020 03:22:41: 1000000 INFO @ Tue, 30 Jun 2020 03:22:41: 13000000 INFO @ Tue, 30 Jun 2020 03:22:41: 7000000 INFO @ Tue, 30 Jun 2020 03:22:46: 2000000 INFO @ Tue, 30 Jun 2020 03:22:46: 14000000 INFO @ Tue, 30 Jun 2020 03:22:47: 8000000 INFO @ Tue, 30 Jun 2020 03:22:51: 15000000 INFO @ Tue, 30 Jun 2020 03:22:51: 3000000 INFO @ Tue, 30 Jun 2020 03:22:52: 9000000 INFO @ Tue, 30 Jun 2020 03:22:56: 16000000 INFO @ Tue, 30 Jun 2020 03:22:56: 4000000 INFO @ Tue, 30 Jun 2020 03:22:57: 10000000 INFO @ Tue, 30 Jun 2020 03:23:01: 17000000 INFO @ Tue, 30 Jun 2020 03:23:01: 5000000 INFO @ Tue, 30 Jun 2020 03:23:02: 11000000 INFO @ Tue, 30 Jun 2020 03:23:06: 18000000 INFO @ Tue, 30 Jun 2020 03:23:07: 6000000 INFO @ Tue, 30 Jun 2020 03:23:07: 12000000 INFO @ Tue, 30 Jun 2020 03:23:12: 7000000 INFO @ Tue, 30 Jun 2020 03:23:12: 19000000 INFO @ Tue, 30 Jun 2020 03:23:12: 13000000 INFO @ Tue, 30 Jun 2020 03:23:17: 8000000 INFO @ Tue, 30 Jun 2020 03:23:17: 20000000 INFO @ Tue, 30 Jun 2020 03:23:17: 14000000 INFO @ Tue, 30 Jun 2020 03:23:22: 9000000 INFO @ Tue, 30 Jun 2020 03:23:22: 15000000 INFO @ Tue, 30 Jun 2020 03:23:23: 21000000 INFO @ Tue, 30 Jun 2020 03:23:26: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:23:26: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:23:26: #1 total tags in treatment: 21528380 INFO @ Tue, 30 Jun 2020 03:23:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:23:26: #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 03:23:26: #1 tags after filtering in treatment: 21528380 INFO @ Tue, 30 Jun 2020 03:23:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:23:26: #1 finished! INFO @ Tue, 30 Jun 2020 03:23:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:23:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:23:27: 10000000 INFO @ Tue, 30 Jun 2020 03:23:27: 16000000 INFO @ Tue, 30 Jun 2020 03:23:28: #2 number of paired peaks: 227 WARNING @ Tue, 30 Jun 2020 03:23:28: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Tue, 30 Jun 2020 03:23:28: start model_add_line... INFO @ Tue, 30 Jun 2020 03:23:28: start X-correlation... INFO @ Tue, 30 Jun 2020 03:23:28: end of X-cor INFO @ Tue, 30 Jun 2020 03:23:28: #2 finished! INFO @ Tue, 30 Jun 2020 03:23:28: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 03:23:28: #2 alternative fragment length(s) may be 3,45 bps INFO @ Tue, 30 Jun 2020 03:23:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.05_model.r WARNING @ Tue, 30 Jun 2020 03:23:28: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:23:28: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Tue, 30 Jun 2020 03:23:28: #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 03:23:28: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:23:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:23:32: 11000000 INFO @ Tue, 30 Jun 2020 03:23:33: 17000000 INFO @ Tue, 30 Jun 2020 03:23:37: 12000000 INFO @ Tue, 30 Jun 2020 03:23:38: 18000000 INFO @ Tue, 30 Jun 2020 03:23:43: 13000000 INFO @ Tue, 30 Jun 2020 03:23:43: 19000000 INFO @ Tue, 30 Jun 2020 03:23:48: 14000000 INFO @ Tue, 30 Jun 2020 03:23:48: 20000000 INFO @ Tue, 30 Jun 2020 03:23:53: 15000000 INFO @ Tue, 30 Jun 2020 03:23:54: 21000000 INFO @ Tue, 30 Jun 2020 03:23:57: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:23:57: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:23:57: #1 total tags in treatment: 21528380 INFO @ Tue, 30 Jun 2020 03:23:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:23:57: #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 03:23:58: #1 tags after filtering in treatment: 21528380 INFO @ Tue, 30 Jun 2020 03:23:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:23:58: #1 finished! INFO @ Tue, 30 Jun 2020 03:23:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:23:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:23:58: 16000000 INFO @ Tue, 30 Jun 2020 03:23:59: #2 number of paired peaks: 227 WARNING @ Tue, 30 Jun 2020 03:23:59: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Tue, 30 Jun 2020 03:23:59: start model_add_line... INFO @ Tue, 30 Jun 2020 03:23:59: start X-correlation... INFO @ Tue, 30 Jun 2020 03:23:59: end of X-cor INFO @ Tue, 30 Jun 2020 03:23:59: #2 finished! INFO @ Tue, 30 Jun 2020 03:23:59: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 03:23:59: #2 alternative fragment length(s) may be 3,45 bps INFO @ Tue, 30 Jun 2020 03:23:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.10_model.r WARNING @ Tue, 30 Jun 2020 03:23:59: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:23:59: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Tue, 30 Jun 2020 03:23:59: #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 03:23:59: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:23:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:24:03: 17000000 INFO @ Tue, 30 Jun 2020 03:24:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:24:08: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:24:13: 19000000 INFO @ Tue, 30 Jun 2020 03:24:18: 20000000 INFO @ Tue, 30 Jun 2020 03:24:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:24:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:24:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.05_summits.bed INFO @ Tue, 30 Jun 2020 03:24:22: Done! pass1 - making usageList (718 chroms): 1 millis pass2 - checking and writing primary data (2525 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:24:24: 21000000 INFO @ Tue, 30 Jun 2020 03:24:26: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:24:26: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:24:26: #1 total tags in treatment: 21528380 INFO @ Tue, 30 Jun 2020 03:24:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:24:26: #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 03:24:27: #1 tags after filtering in treatment: 21528380 INFO @ Tue, 30 Jun 2020 03:24:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:24:27: #1 finished! INFO @ Tue, 30 Jun 2020 03:24:27: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:24:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:24:28: #2 number of paired peaks: 227 WARNING @ Tue, 30 Jun 2020 03:24:28: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Tue, 30 Jun 2020 03:24:28: start model_add_line... INFO @ Tue, 30 Jun 2020 03:24:28: start X-correlation... INFO @ Tue, 30 Jun 2020 03:24:28: end of X-cor INFO @ Tue, 30 Jun 2020 03:24:28: #2 finished! INFO @ Tue, 30 Jun 2020 03:24:28: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 03:24:28: #2 alternative fragment length(s) may be 3,45 bps INFO @ Tue, 30 Jun 2020 03:24:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.20_model.r WARNING @ Tue, 30 Jun 2020 03:24:28: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:24:28: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Tue, 30 Jun 2020 03:24:28: #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 03:24:28: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:24:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:24:35: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:24:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:24:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:24:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.10_summits.bed INFO @ Tue, 30 Jun 2020 03:24:52: Done! pass1 - making usageList (559 chroms): 1 millis pass2 - checking and writing primary data (1652 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:25:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:25:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:25:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:25:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343135/SRX5343135.20_summits.bed INFO @ Tue, 30 Jun 2020 03:25:21: Done! pass1 - making usageList (283 chroms): 1 millis pass2 - checking and writing primary data (550 records, 4 fields): 9 millis CompletedMACS2peakCalling