Job ID = 6530096 SRX = SRX815532 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: 00:05:27 19002887 reads; of these: 19002887 (100.00%) were unpaired; of these: 528882 (2.78%) aligned 0 times 13803763 (72.64%) aligned exactly 1 time 4670242 (24.58%) aligned >1 times 97.22% overall alignment rate Time searching: 00:05:27 Overall time: 00:05:27 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 8 files... [bam_rmdupse_core] 1561324 / 18474005 = 0.0845 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 03:23:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.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 03:23:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:23:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:23:41: 1000000 INFO @ Tue, 30 Jun 2020 03:23:47: 2000000 INFO @ Tue, 30 Jun 2020 03:23:53: 3000000 INFO @ Tue, 30 Jun 2020 03:23:59: 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 03:24:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.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 03:24:05: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:24:05: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:24:05: 5000000 INFO @ Tue, 30 Jun 2020 03:24:11: 1000000 INFO @ Tue, 30 Jun 2020 03:24:12: 6000000 INFO @ Tue, 30 Jun 2020 03:24:17: 2000000 INFO @ Tue, 30 Jun 2020 03:24:18: 7000000 INFO @ Tue, 30 Jun 2020 03:24:23: 3000000 INFO @ Tue, 30 Jun 2020 03:24:25: 8000000 INFO @ Tue, 30 Jun 2020 03:24:29: 4000000 INFO @ Tue, 30 Jun 2020 03:24:31: 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 03:24:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.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 03:24:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:24:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:24:35: 5000000 INFO @ Tue, 30 Jun 2020 03:24:37: 10000000 INFO @ Tue, 30 Jun 2020 03:24:41: 6000000 INFO @ Tue, 30 Jun 2020 03:24:42: 1000000 INFO @ Tue, 30 Jun 2020 03:24:44: 11000000 INFO @ Tue, 30 Jun 2020 03:24:47: 7000000 INFO @ Tue, 30 Jun 2020 03:24:49: 2000000 INFO @ Tue, 30 Jun 2020 03:24:51: 12000000 INFO @ Tue, 30 Jun 2020 03:24:53: 8000000 INFO @ Tue, 30 Jun 2020 03:24:56: 3000000 INFO @ Tue, 30 Jun 2020 03:24:58: 13000000 INFO @ Tue, 30 Jun 2020 03:24:59: 9000000 INFO @ Tue, 30 Jun 2020 03:25:03: 4000000 INFO @ Tue, 30 Jun 2020 03:25:05: 10000000 INFO @ Tue, 30 Jun 2020 03:25:05: 14000000 INFO @ Tue, 30 Jun 2020 03:25:10: 5000000 INFO @ Tue, 30 Jun 2020 03:25:11: 11000000 INFO @ Tue, 30 Jun 2020 03:25:13: 15000000 INFO @ Tue, 30 Jun 2020 03:25:17: 12000000 INFO @ Tue, 30 Jun 2020 03:25:18: 6000000 INFO @ Tue, 30 Jun 2020 03:25:20: 16000000 INFO @ Tue, 30 Jun 2020 03:25:23: 13000000 INFO @ Tue, 30 Jun 2020 03:25:25: 7000000 INFO @ Tue, 30 Jun 2020 03:25:26: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:25:26: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:25:26: #1 total tags in treatment: 16912681 INFO @ Tue, 30 Jun 2020 03:25:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:25:26: #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 03:25:28: #1 tags after filtering in treatment: 16912680 INFO @ Tue, 30 Jun 2020 03:25:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:25:28: #1 finished! INFO @ Tue, 30 Jun 2020 03:25:28: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:25:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:25:29: #2 number of paired peaks: 308 WARNING @ Tue, 30 Jun 2020 03:25:29: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Tue, 30 Jun 2020 03:25:29: start model_add_line... INFO @ Tue, 30 Jun 2020 03:25:29: start X-correlation... INFO @ Tue, 30 Jun 2020 03:25:29: end of X-cor INFO @ Tue, 30 Jun 2020 03:25:29: #2 finished! INFO @ Tue, 30 Jun 2020 03:25:29: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 03:25:29: #2 alternative fragment length(s) may be 3,51,572 bps INFO @ Tue, 30 Jun 2020 03:25:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.05_model.r WARNING @ Tue, 30 Jun 2020 03:25:29: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:25:29: #2 You may need to consider one of the other alternative d(s): 3,51,572 WARNING @ Tue, 30 Jun 2020 03:25:29: #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 03:25:29: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:25:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:25:30: 14000000 INFO @ Tue, 30 Jun 2020 03:25:31: 8000000 INFO @ Tue, 30 Jun 2020 03:25:36: 15000000 INFO @ Tue, 30 Jun 2020 03:25:38: 9000000 INFO @ Tue, 30 Jun 2020 03:25:42: 16000000 INFO @ Tue, 30 Jun 2020 03:25:45: 10000000 INFO @ Tue, 30 Jun 2020 03:25:48: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:25:48: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:25:48: #1 total tags in treatment: 16912681 INFO @ Tue, 30 Jun 2020 03:25:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:25:48: #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 03:25:49: #1 tags after filtering in treatment: 16912680 INFO @ Tue, 30 Jun 2020 03:25:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:25:49: #1 finished! INFO @ Tue, 30 Jun 2020 03:25:49: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:25:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:25:50: #2 number of paired peaks: 308 WARNING @ Tue, 30 Jun 2020 03:25:50: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Tue, 30 Jun 2020 03:25:50: start model_add_line... INFO @ Tue, 30 Jun 2020 03:25:50: start X-correlation... INFO @ Tue, 30 Jun 2020 03:25:50: end of X-cor INFO @ Tue, 30 Jun 2020 03:25:50: #2 finished! INFO @ Tue, 30 Jun 2020 03:25:50: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 03:25:50: #2 alternative fragment length(s) may be 3,51,572 bps INFO @ Tue, 30 Jun 2020 03:25:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.10_model.r WARNING @ Tue, 30 Jun 2020 03:25:50: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:25:50: #2 You may need to consider one of the other alternative d(s): 3,51,572 WARNING @ Tue, 30 Jun 2020 03:25:50: #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 03:25:50: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:25:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:25:51: 11000000 INFO @ Tue, 30 Jun 2020 03:25:57: 12000000 INFO @ Tue, 30 Jun 2020 03:25:59: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:26:03: 13000000 INFO @ Tue, 30 Jun 2020 03:26:10: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:26:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:26:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:26:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.05_summits.bed INFO @ Tue, 30 Jun 2020 03:26:14: Done! pass1 - making usageList (649 chroms): 1 millis pass2 - checking and writing primary data (2717 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:26:16: 15000000 INFO @ Tue, 30 Jun 2020 03:26:19: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:26:23: 16000000 INFO @ Tue, 30 Jun 2020 03:26:29: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:26:29: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:26:29: #1 total tags in treatment: 16912681 INFO @ Tue, 30 Jun 2020 03:26:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:26:29: #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 03:26:30: #1 tags after filtering in treatment: 16912680 INFO @ Tue, 30 Jun 2020 03:26:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:26:30: #1 finished! INFO @ Tue, 30 Jun 2020 03:26:30: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:26:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:26:31: #2 number of paired peaks: 308 WARNING @ Tue, 30 Jun 2020 03:26:31: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Tue, 30 Jun 2020 03:26:31: start model_add_line... INFO @ Tue, 30 Jun 2020 03:26:31: start X-correlation... INFO @ Tue, 30 Jun 2020 03:26:31: end of X-cor INFO @ Tue, 30 Jun 2020 03:26:31: #2 finished! INFO @ Tue, 30 Jun 2020 03:26:31: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 03:26:31: #2 alternative fragment length(s) may be 3,51,572 bps INFO @ Tue, 30 Jun 2020 03:26:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.20_model.r WARNING @ Tue, 30 Jun 2020 03:26:31: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:26:31: #2 You may need to consider one of the other alternative d(s): 3,51,572 WARNING @ Tue, 30 Jun 2020 03:26:31: #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 03:26:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:26:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:26:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:26:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:26:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.10_summits.bed INFO @ Tue, 30 Jun 2020 03:26:34: Done! pass1 - making usageList (537 chroms): 1 millis pass2 - checking and writing primary data (1816 records, 4 fields): 31 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:27:02: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:27:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:27:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:27:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX815532/SRX815532.20_summits.bed INFO @ Tue, 30 Jun 2020 03:27:16: Done! pass1 - making usageList (239 chroms): 1 millis pass2 - checking and writing primary data (445 records, 4 fields): 14 millis CompletedMACS2peakCalling