Job ID = 6529541 SRX = SRX3049399 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: 00:08:52 32602709 reads; of these: 32602709 (100.00%) were unpaired; of these: 2369166 (7.27%) aligned 0 times 22773239 (69.85%) aligned exactly 1 time 7460304 (22.88%) aligned >1 times 92.73% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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] 5606383 / 30233543 = 0.1854 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 02:28:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.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 02:28:38: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:28:38: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:28:44: 1000000 INFO @ Tue, 30 Jun 2020 02:28:50: 2000000 INFO @ Tue, 30 Jun 2020 02:28:55: 3000000 INFO @ Tue, 30 Jun 2020 02:29:01: 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 02:29:07: 5000000 INFO @ Tue, 30 Jun 2020 02:29:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.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 02:29:08: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:29:08: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:29:14: 6000000 INFO @ Tue, 30 Jun 2020 02:29:16: 1000000 INFO @ Tue, 30 Jun 2020 02:29:21: 7000000 INFO @ Tue, 30 Jun 2020 02:29:25: 2000000 INFO @ Tue, 30 Jun 2020 02:29:28: 8000000 INFO @ Tue, 30 Jun 2020 02:29:33: 3000000 INFO @ Tue, 30 Jun 2020 02:29:35: 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 02:29:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.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 02:29:38: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:29:38: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:29:42: 10000000 INFO @ Tue, 30 Jun 2020 02:29:42: 4000000 INFO @ Tue, 30 Jun 2020 02:29:45: 1000000 INFO @ Tue, 30 Jun 2020 02:29:49: 11000000 INFO @ Tue, 30 Jun 2020 02:29:49: 5000000 INFO @ Tue, 30 Jun 2020 02:29:52: 2000000 INFO @ Tue, 30 Jun 2020 02:29:56: 12000000 INFO @ Tue, 30 Jun 2020 02:29:57: 6000000 INFO @ Tue, 30 Jun 2020 02:29:59: 3000000 INFO @ Tue, 30 Jun 2020 02:30:03: 13000000 INFO @ Tue, 30 Jun 2020 02:30:05: 7000000 INFO @ Tue, 30 Jun 2020 02:30:06: 4000000 INFO @ Tue, 30 Jun 2020 02:30:10: 14000000 INFO @ Tue, 30 Jun 2020 02:30:13: 8000000 INFO @ Tue, 30 Jun 2020 02:30:13: 5000000 INFO @ Tue, 30 Jun 2020 02:30:16: 15000000 INFO @ Tue, 30 Jun 2020 02:30:20: 6000000 INFO @ Tue, 30 Jun 2020 02:30:21: 9000000 INFO @ Tue, 30 Jun 2020 02:30:23: 16000000 INFO @ Tue, 30 Jun 2020 02:30:27: 7000000 INFO @ Tue, 30 Jun 2020 02:30:29: 10000000 INFO @ Tue, 30 Jun 2020 02:30:30: 17000000 INFO @ Tue, 30 Jun 2020 02:30:34: 8000000 INFO @ Tue, 30 Jun 2020 02:30:36: 11000000 INFO @ Tue, 30 Jun 2020 02:30:37: 18000000 INFO @ Tue, 30 Jun 2020 02:30:41: 9000000 INFO @ Tue, 30 Jun 2020 02:30:44: 12000000 INFO @ Tue, 30 Jun 2020 02:30:44: 19000000 INFO @ Tue, 30 Jun 2020 02:30:48: 10000000 INFO @ Tue, 30 Jun 2020 02:30:51: 13000000 INFO @ Tue, 30 Jun 2020 02:30:51: 20000000 INFO @ Tue, 30 Jun 2020 02:30:54: 11000000 INFO @ Tue, 30 Jun 2020 02:30:58: 21000000 INFO @ Tue, 30 Jun 2020 02:30:58: 14000000 INFO @ Tue, 30 Jun 2020 02:31:01: 12000000 INFO @ Tue, 30 Jun 2020 02:31:05: 22000000 INFO @ Tue, 30 Jun 2020 02:31:06: 15000000 INFO @ Tue, 30 Jun 2020 02:31:08: 13000000 INFO @ Tue, 30 Jun 2020 02:31:12: 23000000 INFO @ Tue, 30 Jun 2020 02:31:13: 16000000 INFO @ Tue, 30 Jun 2020 02:31:16: 14000000 INFO @ Tue, 30 Jun 2020 02:31:19: 24000000 INFO @ Tue, 30 Jun 2020 02:31:20: 17000000 INFO @ Tue, 30 Jun 2020 02:31:22: 15000000 INFO @ Tue, 30 Jun 2020 02:31:24: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:31:24: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:31:24: #1 total tags in treatment: 24627160 INFO @ Tue, 30 Jun 2020 02:31:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:31:24: #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 02:31:24: #1 tags after filtering in treatment: 24627160 INFO @ Tue, 30 Jun 2020 02:31:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:31:24: #1 finished! INFO @ Tue, 30 Jun 2020 02:31:24: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:31:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:31:26: #2 number of paired peaks: 196 WARNING @ Tue, 30 Jun 2020 02:31:26: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Tue, 30 Jun 2020 02:31:26: start model_add_line... INFO @ Tue, 30 Jun 2020 02:31:26: start X-correlation... INFO @ Tue, 30 Jun 2020 02:31:26: end of X-cor INFO @ Tue, 30 Jun 2020 02:31:26: #2 finished! INFO @ Tue, 30 Jun 2020 02:31:26: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:31:26: #2 alternative fragment length(s) may be 2,45 bps INFO @ Tue, 30 Jun 2020 02:31:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.05_model.r WARNING @ Tue, 30 Jun 2020 02:31:26: #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 02:31:26: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Tue, 30 Jun 2020 02:31:26: #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 02:31:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:31:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:31:27: 18000000 INFO @ Tue, 30 Jun 2020 02:31:29: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:31:35: 19000000 INFO @ Tue, 30 Jun 2020 02:31:36: 17000000 INFO @ Tue, 30 Jun 2020 02:31:42: 20000000 INFO @ Tue, 30 Jun 2020 02:31:43: 18000000 INFO @ Tue, 30 Jun 2020 02:31:49: 21000000 INFO @ Tue, 30 Jun 2020 02:31:50: 19000000 INFO @ Tue, 30 Jun 2020 02:31:57: 22000000 INFO @ Tue, 30 Jun 2020 02:31:57: 20000000 INFO @ Tue, 30 Jun 2020 02:32:04: 21000000 INFO @ Tue, 30 Jun 2020 02:32:04: 23000000 INFO @ Tue, 30 Jun 2020 02:32:10: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:32:11: 22000000 INFO @ Tue, 30 Jun 2020 02:32:12: 24000000 INFO @ Tue, 30 Jun 2020 02:32:17: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:32:17: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:32:17: #1 total tags in treatment: 24627160 INFO @ Tue, 30 Jun 2020 02:32:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:32:17: #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 02:32:18: 23000000 INFO @ Tue, 30 Jun 2020 02:32:18: #1 tags after filtering in treatment: 24627160 INFO @ Tue, 30 Jun 2020 02:32:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:32:18: #1 finished! INFO @ Tue, 30 Jun 2020 02:32:18: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:32:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:32:19: #2 number of paired peaks: 196 WARNING @ Tue, 30 Jun 2020 02:32:19: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Tue, 30 Jun 2020 02:32:19: start model_add_line... INFO @ Tue, 30 Jun 2020 02:32:19: start X-correlation... INFO @ Tue, 30 Jun 2020 02:32:19: end of X-cor INFO @ Tue, 30 Jun 2020 02:32:19: #2 finished! INFO @ Tue, 30 Jun 2020 02:32:19: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:32:19: #2 alternative fragment length(s) may be 2,45 bps INFO @ Tue, 30 Jun 2020 02:32:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.10_model.r WARNING @ Tue, 30 Jun 2020 02:32:19: #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 02:32:19: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Tue, 30 Jun 2020 02:32:19: #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 02:32:19: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:32:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:32:24: 24000000 INFO @ Tue, 30 Jun 2020 02:32:28: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:32:28: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:32:28: #1 total tags in treatment: 24627160 INFO @ Tue, 30 Jun 2020 02:32:28: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:32:28: #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 02:32:29: #1 tags after filtering in treatment: 24627160 INFO @ Tue, 30 Jun 2020 02:32:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:32:29: #1 finished! INFO @ Tue, 30 Jun 2020 02:32:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:32:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:32:30: #2 number of paired peaks: 196 WARNING @ Tue, 30 Jun 2020 02:32:30: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Tue, 30 Jun 2020 02:32:30: start model_add_line... INFO @ Tue, 30 Jun 2020 02:32:30: start X-correlation... INFO @ Tue, 30 Jun 2020 02:32:30: end of X-cor INFO @ Tue, 30 Jun 2020 02:32:30: #2 finished! INFO @ Tue, 30 Jun 2020 02:32:30: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:32:30: #2 alternative fragment length(s) may be 2,45 bps INFO @ Tue, 30 Jun 2020 02:32:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.20_model.r WARNING @ Tue, 30 Jun 2020 02:32:30: #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 02:32:30: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Tue, 30 Jun 2020 02:32:30: #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 02:32:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:32:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:32:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:32:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:32:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.05_summits.bed INFO @ Tue, 30 Jun 2020 02:32:33: Done! pass1 - making usageList (633 chroms): 3 millis pass2 - checking and writing primary data (2447 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:33:05: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:33:17: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:33:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:33:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:33:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.10_summits.bed INFO @ Tue, 30 Jun 2020 02:33:27: Done! pass1 - making usageList (508 chroms): 2 millis pass2 - checking and writing primary data (1850 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:33:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:33:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:33:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3049399/SRX3049399.20_summits.bed INFO @ Tue, 30 Jun 2020 02:33:39: Done! pass1 - making usageList (269 chroms): 1 millis pass2 - checking and writing primary data (576 records, 4 fields): 11 millis CompletedMACS2peakCalling