Job ID = 6529266 SRX = SRX1144604 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:55 52299212 reads; of these: 52299212 (100.00%) were unpaired; of these: 26520770 (50.71%) aligned 0 times 20642160 (39.47%) aligned exactly 1 time 5136282 (9.82%) aligned >1 times 49.29% overall alignment rate Time searching: 00:07:56 Overall time: 00:07:56 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] 6173120 / 25778442 = 0.2395 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 02:04:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.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 02:04:10: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:04:10: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:04:16: 1000000 INFO @ Tue, 30 Jun 2020 02:04:23: 2000000 INFO @ Tue, 30 Jun 2020 02:04:28: 3000000 INFO @ Tue, 30 Jun 2020 02:04:35: 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 02:04:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.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 02:04:40: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:04:40: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:04:41: 5000000 INFO @ Tue, 30 Jun 2020 02:04:47: 1000000 INFO @ Tue, 30 Jun 2020 02:04:47: 6000000 INFO @ Tue, 30 Jun 2020 02:04:53: 2000000 INFO @ Tue, 30 Jun 2020 02:04:53: 7000000 INFO @ Tue, 30 Jun 2020 02:05:00: 3000000 INFO @ Tue, 30 Jun 2020 02:05:00: 8000000 INFO @ Tue, 30 Jun 2020 02:05:06: 4000000 INFO @ Tue, 30 Jun 2020 02:05:06: 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 02:05:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.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 02:05:11: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:05:11: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:05:13: 5000000 INFO @ Tue, 30 Jun 2020 02:05:13: 10000000 INFO @ Tue, 30 Jun 2020 02:05:18: 1000000 INFO @ Tue, 30 Jun 2020 02:05:20: 11000000 INFO @ Tue, 30 Jun 2020 02:05:20: 6000000 INFO @ Tue, 30 Jun 2020 02:05:25: 2000000 INFO @ Tue, 30 Jun 2020 02:05:26: 12000000 INFO @ Tue, 30 Jun 2020 02:05:27: 7000000 INFO @ Tue, 30 Jun 2020 02:05:33: 3000000 INFO @ Tue, 30 Jun 2020 02:05:33: 13000000 INFO @ Tue, 30 Jun 2020 02:05:34: 8000000 INFO @ Tue, 30 Jun 2020 02:05:40: 14000000 INFO @ Tue, 30 Jun 2020 02:05:40: 4000000 INFO @ Tue, 30 Jun 2020 02:05:41: 9000000 INFO @ Tue, 30 Jun 2020 02:05:46: 15000000 INFO @ Tue, 30 Jun 2020 02:05:47: 5000000 INFO @ Tue, 30 Jun 2020 02:05:48: 10000000 INFO @ Tue, 30 Jun 2020 02:05:53: 6000000 INFO @ Tue, 30 Jun 2020 02:05:53: 16000000 INFO @ Tue, 30 Jun 2020 02:05:54: 11000000 INFO @ Tue, 30 Jun 2020 02:06:00: 17000000 INFO @ Tue, 30 Jun 2020 02:06:00: 7000000 INFO @ Tue, 30 Jun 2020 02:06:01: 12000000 INFO @ Tue, 30 Jun 2020 02:06:06: 18000000 INFO @ Tue, 30 Jun 2020 02:06:07: 8000000 INFO @ Tue, 30 Jun 2020 02:06:08: 13000000 INFO @ Tue, 30 Jun 2020 02:06:13: 19000000 INFO @ Tue, 30 Jun 2020 02:06:14: 9000000 INFO @ Tue, 30 Jun 2020 02:06:15: 14000000 INFO @ Tue, 30 Jun 2020 02:06:18: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:06:18: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:06:18: #1 total tags in treatment: 19605322 INFO @ Tue, 30 Jun 2020 02:06:18: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:06:18: #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 02:06:18: #1 tags after filtering in treatment: 19605245 INFO @ Tue, 30 Jun 2020 02:06:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:06:18: #1 finished! INFO @ Tue, 30 Jun 2020 02:06:18: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:06:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:06:20: #2 number of paired peaks: 248 WARNING @ Tue, 30 Jun 2020 02:06:20: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 30 Jun 2020 02:06:20: start model_add_line... INFO @ Tue, 30 Jun 2020 02:06:20: start X-correlation... INFO @ Tue, 30 Jun 2020 02:06:20: end of X-cor INFO @ Tue, 30 Jun 2020 02:06:20: #2 finished! INFO @ Tue, 30 Jun 2020 02:06:20: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 02:06:20: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 30 Jun 2020 02:06:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.05_model.r WARNING @ Tue, 30 Jun 2020 02:06:20: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:06:20: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 30 Jun 2020 02:06:20: #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 02:06:20: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:06:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:06:21: 10000000 INFO @ Tue, 30 Jun 2020 02:06:22: 15000000 INFO @ Tue, 30 Jun 2020 02:06:27: 11000000 INFO @ Tue, 30 Jun 2020 02:06:29: 16000000 INFO @ Tue, 30 Jun 2020 02:06:34: 12000000 INFO @ Tue, 30 Jun 2020 02:06:35: 17000000 INFO @ Tue, 30 Jun 2020 02:06:40: 13000000 INFO @ Tue, 30 Jun 2020 02:06:42: 18000000 INFO @ Tue, 30 Jun 2020 02:06:47: 14000000 INFO @ Tue, 30 Jun 2020 02:06:48: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:06:53: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:06:53: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:06:53: #1 total tags in treatment: 19605322 INFO @ Tue, 30 Jun 2020 02:06:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:06:53: #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 02:06:53: 15000000 INFO @ Tue, 30 Jun 2020 02:06:54: #1 tags after filtering in treatment: 19605245 INFO @ Tue, 30 Jun 2020 02:06:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:06:54: #1 finished! INFO @ Tue, 30 Jun 2020 02:06:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:06:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:06:55: #2 number of paired peaks: 248 WARNING @ Tue, 30 Jun 2020 02:06:55: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 30 Jun 2020 02:06:55: start model_add_line... INFO @ Tue, 30 Jun 2020 02:06:55: start X-correlation... INFO @ Tue, 30 Jun 2020 02:06:55: end of X-cor INFO @ Tue, 30 Jun 2020 02:06:55: #2 finished! INFO @ Tue, 30 Jun 2020 02:06:55: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 02:06:55: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 30 Jun 2020 02:06:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.10_model.r WARNING @ Tue, 30 Jun 2020 02:06:55: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:06:55: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 30 Jun 2020 02:06:55: #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 02:06:55: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:06:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:07:00: 16000000 INFO @ Tue, 30 Jun 2020 02:07:02: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:07:06: 17000000 INFO @ Tue, 30 Jun 2020 02:07:12: 18000000 INFO @ Tue, 30 Jun 2020 02:07:18: 19000000 INFO @ Tue, 30 Jun 2020 02:07:23: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:07:23: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:07:23: #1 total tags in treatment: 19605322 INFO @ Tue, 30 Jun 2020 02:07:23: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:07:23: #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 02:07:23: #1 tags after filtering in treatment: 19605245 INFO @ Tue, 30 Jun 2020 02:07:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:07:23: #1 finished! INFO @ Tue, 30 Jun 2020 02:07:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:07:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:07:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:07:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:07:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.05_summits.bed INFO @ Tue, 30 Jun 2020 02:07:24: Done! pass1 - making usageList (549 chroms): 2 millis pass2 - checking and writing primary data (2343 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:07:25: #2 number of paired peaks: 248 WARNING @ Tue, 30 Jun 2020 02:07:25: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 30 Jun 2020 02:07:25: start model_add_line... INFO @ Tue, 30 Jun 2020 02:07:25: start X-correlation... INFO @ Tue, 30 Jun 2020 02:07:25: end of X-cor INFO @ Tue, 30 Jun 2020 02:07:25: #2 finished! INFO @ Tue, 30 Jun 2020 02:07:25: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 02:07:25: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 30 Jun 2020 02:07:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.20_model.r WARNING @ Tue, 30 Jun 2020 02:07:25: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:07:25: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 30 Jun 2020 02:07:25: #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 02:07:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:07:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:07:37: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:07:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:07:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:07:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.10_summits.bed INFO @ Tue, 30 Jun 2020 02:07:59: Done! pass1 - making usageList (404 chroms): 1 millis pass2 - checking and writing primary data (1082 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:08:05: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:08:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:08:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:08:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1144604/SRX1144604.20_summits.bed INFO @ Tue, 30 Jun 2020 02:08:26: Done! pass1 - making usageList (137 chroms): 1 millis pass2 - checking and writing primary data (310 records, 4 fields): 5 millis CompletedMACS2peakCalling