Job ID = 10166634 SRX = SRX7723722 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:16 26142343 reads; of these: 26142343 (100.00%) were unpaired; of these: 5403608 (20.67%) aligned 0 times 17695597 (67.69%) aligned exactly 1 time 3043138 (11.64%) aligned >1 times 79.33% overall alignment rate Time searching: 00:07:17 Overall time: 00:07:17 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] 6185289 / 20738735 = 0.2982 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 @ Thu, 08 Oct 2020 22:12:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.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 @ Thu, 08 Oct 2020 22:12:55: #1 read tag files... INFO @ Thu, 08 Oct 2020 22:12:55: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 22:13:02: 1000000 INFO @ Thu, 08 Oct 2020 22:13:08: 2000000 INFO @ Thu, 08 Oct 2020 22:13:15: 3000000 INFO @ Thu, 08 Oct 2020 22:13:21: 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 @ Thu, 08 Oct 2020 22:13:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.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 @ Thu, 08 Oct 2020 22:13:25: #1 read tag files... INFO @ Thu, 08 Oct 2020 22:13:25: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 22:13:28: 5000000 INFO @ Thu, 08 Oct 2020 22:13:31: 1000000 INFO @ Thu, 08 Oct 2020 22:13:34: 6000000 INFO @ Thu, 08 Oct 2020 22:13:38: 2000000 INFO @ Thu, 08 Oct 2020 22:13:41: 7000000 INFO @ Thu, 08 Oct 2020 22:13:44: 3000000 INFO @ Thu, 08 Oct 2020 22:13:48: 8000000 INFO @ Thu, 08 Oct 2020 22:13:50: 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 @ Thu, 08 Oct 2020 22:13:55: 9000000 INFO @ Thu, 08 Oct 2020 22:13:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.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 @ Thu, 08 Oct 2020 22:13:55: #1 read tag files... INFO @ Thu, 08 Oct 2020 22:13:55: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 22:13:57: 5000000 INFO @ Thu, 08 Oct 2020 22:14:01: 10000000 INFO @ Thu, 08 Oct 2020 22:14:02: 1000000 INFO @ Thu, 08 Oct 2020 22:14:03: 6000000 INFO @ Thu, 08 Oct 2020 22:14:08: 11000000 INFO @ Thu, 08 Oct 2020 22:14:09: 7000000 INFO @ Thu, 08 Oct 2020 22:14:10: 2000000 INFO @ Thu, 08 Oct 2020 22:14:16: 8000000 INFO @ Thu, 08 Oct 2020 22:14:16: 12000000 INFO @ Thu, 08 Oct 2020 22:14:17: 3000000 INFO @ Thu, 08 Oct 2020 22:14:22: 9000000 INFO @ Thu, 08 Oct 2020 22:14:23: 13000000 INFO @ Thu, 08 Oct 2020 22:14:24: 4000000 INFO @ Thu, 08 Oct 2020 22:14:28: 10000000 INFO @ Thu, 08 Oct 2020 22:14:31: 14000000 INFO @ Thu, 08 Oct 2020 22:14:31: 5000000 INFO @ Thu, 08 Oct 2020 22:14:34: 11000000 INFO @ Thu, 08 Oct 2020 22:14:35: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 22:14:35: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 22:14:35: #1 total tags in treatment: 14553446 INFO @ Thu, 08 Oct 2020 22:14:35: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 22:14:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 22:14:35: #1 tags after filtering in treatment: 14553310 INFO @ Thu, 08 Oct 2020 22:14:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 22:14:35: #1 finished! INFO @ Thu, 08 Oct 2020 22:14:35: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 22:14:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 22:14:36: #2 number of paired peaks: 309 WARNING @ Thu, 08 Oct 2020 22:14:36: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Thu, 08 Oct 2020 22:14:36: start model_add_line... INFO @ Thu, 08 Oct 2020 22:14:36: start X-correlation... INFO @ Thu, 08 Oct 2020 22:14:36: end of X-cor INFO @ Thu, 08 Oct 2020 22:14:36: #2 finished! INFO @ Thu, 08 Oct 2020 22:14:36: #2 predicted fragment length is 73 bps INFO @ Thu, 08 Oct 2020 22:14:36: #2 alternative fragment length(s) may be 4,73,574 bps INFO @ Thu, 08 Oct 2020 22:14:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.05_model.r WARNING @ Thu, 08 Oct 2020 22:14:36: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 22:14:36: #2 You may need to consider one of the other alternative d(s): 4,73,574 WARNING @ Thu, 08 Oct 2020 22:14:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 22:14:36: #3 Call peaks... INFO @ Thu, 08 Oct 2020 22:14:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 22:14:38: 6000000 INFO @ Thu, 08 Oct 2020 22:14:41: 12000000 INFO @ Thu, 08 Oct 2020 22:14:45: 7000000 INFO @ Thu, 08 Oct 2020 22:14:47: 13000000 INFO @ Thu, 08 Oct 2020 22:14:51: 8000000 INFO @ Thu, 08 Oct 2020 22:14:54: 14000000 INFO @ Thu, 08 Oct 2020 22:14:58: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 22:14:58: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 22:14:58: #1 total tags in treatment: 14553446 INFO @ Thu, 08 Oct 2020 22:14:58: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 22:14:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 22:14:58: 9000000 INFO @ Thu, 08 Oct 2020 22:14:58: #1 tags after filtering in treatment: 14553310 INFO @ Thu, 08 Oct 2020 22:14:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 22:14:58: #1 finished! INFO @ Thu, 08 Oct 2020 22:14:58: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 22:14:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 22:14:59: #2 number of paired peaks: 309 WARNING @ Thu, 08 Oct 2020 22:14:59: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Thu, 08 Oct 2020 22:14:59: start model_add_line... INFO @ Thu, 08 Oct 2020 22:14:59: start X-correlation... INFO @ Thu, 08 Oct 2020 22:14:59: end of X-cor INFO @ Thu, 08 Oct 2020 22:14:59: #2 finished! INFO @ Thu, 08 Oct 2020 22:14:59: #2 predicted fragment length is 73 bps INFO @ Thu, 08 Oct 2020 22:14:59: #2 alternative fragment length(s) may be 4,73,574 bps INFO @ Thu, 08 Oct 2020 22:14:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.10_model.r WARNING @ Thu, 08 Oct 2020 22:14:59: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 22:14:59: #2 You may need to consider one of the other alternative d(s): 4,73,574 WARNING @ Thu, 08 Oct 2020 22:14:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 22:14:59: #3 Call peaks... INFO @ Thu, 08 Oct 2020 22:14:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 22:15:04: 10000000 INFO @ Thu, 08 Oct 2020 22:15:06: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 22:15:11: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 22:15:18: 12000000 INFO @ Thu, 08 Oct 2020 22:15:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.05_peaks.xls INFO @ Thu, 08 Oct 2020 22:15:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 22:15:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.05_summits.bed INFO @ Thu, 08 Oct 2020 22:15:21: Done! pass1 - making usageList (441 chroms): 1 millis pass2 - checking and writing primary data (1552 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 22:15:24: 13000000 INFO @ Thu, 08 Oct 2020 22:15:29: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 22:15:30: 14000000 INFO @ Thu, 08 Oct 2020 22:15:34: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 22:15:34: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 22:15:34: #1 total tags in treatment: 14553446 INFO @ Thu, 08 Oct 2020 22:15:34: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 22:15:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 22:15:35: #1 tags after filtering in treatment: 14553310 INFO @ Thu, 08 Oct 2020 22:15:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 22:15:35: #1 finished! INFO @ Thu, 08 Oct 2020 22:15:35: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 22:15:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 22:15:36: #2 number of paired peaks: 309 WARNING @ Thu, 08 Oct 2020 22:15:36: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Thu, 08 Oct 2020 22:15:36: start model_add_line... INFO @ Thu, 08 Oct 2020 22:15:36: start X-correlation... INFO @ Thu, 08 Oct 2020 22:15:36: end of X-cor INFO @ Thu, 08 Oct 2020 22:15:36: #2 finished! INFO @ Thu, 08 Oct 2020 22:15:36: #2 predicted fragment length is 73 bps INFO @ Thu, 08 Oct 2020 22:15:36: #2 alternative fragment length(s) may be 4,73,574 bps INFO @ Thu, 08 Oct 2020 22:15:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.20_model.r WARNING @ Thu, 08 Oct 2020 22:15:36: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 22:15:36: #2 You may need to consider one of the other alternative d(s): 4,73,574 WARNING @ Thu, 08 Oct 2020 22:15:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 22:15:36: #3 Call peaks... INFO @ Thu, 08 Oct 2020 22:15:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 22:15:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.10_peaks.xls INFO @ Thu, 08 Oct 2020 22:15:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 22:15:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.10_summits.bed INFO @ Thu, 08 Oct 2020 22:15:44: Done! pass1 - making usageList (307 chroms): 1 millis pass2 - checking and writing primary data (806 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 22:16:05: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 22:16:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.20_peaks.xls INFO @ Thu, 08 Oct 2020 22:16:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 22:16:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723722/SRX7723722.20_summits.bed INFO @ Thu, 08 Oct 2020 22:16:19: Done! pass1 - making usageList (128 chroms): 1 millis pass2 - checking and writing primary data (286 records, 4 fields): 6 millis CompletedMACS2peakCalling