Job ID = 6529172 SRX = SRX025482 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: 00:04:12 24057117 reads; of these: 24057117 (100.00%) were unpaired; of these: 1851683 (7.70%) aligned 0 times 17666430 (73.44%) aligned exactly 1 time 4539004 (18.87%) aligned >1 times 92.30% overall alignment rate Time searching: 00:04:13 Overall time: 00:04:13 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] 8854408 / 22205434 = 0.3987 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 01:56:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.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 01:56:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:56:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:56:07: 1000000 INFO @ Tue, 30 Jun 2020 01:56:12: 2000000 INFO @ Tue, 30 Jun 2020 01:56:17: 3000000 INFO @ Tue, 30 Jun 2020 01:56:22: 4000000 INFO @ Tue, 30 Jun 2020 01:56:27: 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 01:56:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.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 01:56:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:56:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:56:32: 6000000 INFO @ Tue, 30 Jun 2020 01:56:36: 1000000 INFO @ Tue, 30 Jun 2020 01:56:37: 7000000 INFO @ Tue, 30 Jun 2020 01:56:41: 2000000 INFO @ Tue, 30 Jun 2020 01:56:42: 8000000 INFO @ Tue, 30 Jun 2020 01:56:45: 3000000 INFO @ Tue, 30 Jun 2020 01:56:47: 9000000 INFO @ Tue, 30 Jun 2020 01:56:50: 4000000 INFO @ Tue, 30 Jun 2020 01:56:52: 10000000 INFO @ Tue, 30 Jun 2020 01:56:55: 5000000 INFO @ Tue, 30 Jun 2020 01:56:57: 11000000 INFO @ Tue, 30 Jun 2020 01:56:59: 6000000 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 01:57:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.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 01:57:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:57:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:57:03: 12000000 INFO @ Tue, 30 Jun 2020 01:57:04: 7000000 INFO @ Tue, 30 Jun 2020 01:57:07: 1000000 INFO @ Tue, 30 Jun 2020 01:57:08: 8000000 INFO @ Tue, 30 Jun 2020 01:57:08: 13000000 INFO @ Tue, 30 Jun 2020 01:57:10: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:57:10: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:57:10: #1 total tags in treatment: 13351026 INFO @ Tue, 30 Jun 2020 01:57:10: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:57:10: #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 01:57:11: #1 tags after filtering in treatment: 13351024 INFO @ Tue, 30 Jun 2020 01:57:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:57:11: #1 finished! INFO @ Tue, 30 Jun 2020 01:57:11: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:57:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:57:12: #2 number of paired peaks: 356 WARNING @ Tue, 30 Jun 2020 01:57:12: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Tue, 30 Jun 2020 01:57:12: start model_add_line... INFO @ Tue, 30 Jun 2020 01:57:12: start X-correlation... INFO @ Tue, 30 Jun 2020 01:57:12: end of X-cor INFO @ Tue, 30 Jun 2020 01:57:12: #2 finished! INFO @ Tue, 30 Jun 2020 01:57:12: #2 predicted fragment length is 31 bps INFO @ Tue, 30 Jun 2020 01:57:12: #2 alternative fragment length(s) may be 3,31,588 bps INFO @ Tue, 30 Jun 2020 01:57:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.05_model.r WARNING @ Tue, 30 Jun 2020 01:57:12: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:57:12: #2 You may need to consider one of the other alternative d(s): 3,31,588 WARNING @ Tue, 30 Jun 2020 01:57:12: #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 01:57:12: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:57:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:57:12: 2000000 INFO @ Tue, 30 Jun 2020 01:57:13: 9000000 INFO @ Tue, 30 Jun 2020 01:57:17: 10000000 INFO @ Tue, 30 Jun 2020 01:57:17: 3000000 INFO @ Tue, 30 Jun 2020 01:57:22: 11000000 INFO @ Tue, 30 Jun 2020 01:57:22: 4000000 INFO @ Tue, 30 Jun 2020 01:57:27: 12000000 INFO @ Tue, 30 Jun 2020 01:57:27: 5000000 INFO @ Tue, 30 Jun 2020 01:57:31: 13000000 INFO @ Tue, 30 Jun 2020 01:57:32: 6000000 INFO @ Tue, 30 Jun 2020 01:57:33: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:57:33: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:57:33: #1 total tags in treatment: 13351026 INFO @ Tue, 30 Jun 2020 01:57:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:57:33: #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 01:57:34: #1 tags after filtering in treatment: 13351024 INFO @ Tue, 30 Jun 2020 01:57:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:57:34: #1 finished! INFO @ Tue, 30 Jun 2020 01:57:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:57:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:57:35: #2 number of paired peaks: 356 WARNING @ Tue, 30 Jun 2020 01:57:35: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Tue, 30 Jun 2020 01:57:35: start model_add_line... INFO @ Tue, 30 Jun 2020 01:57:35: start X-correlation... INFO @ Tue, 30 Jun 2020 01:57:35: end of X-cor INFO @ Tue, 30 Jun 2020 01:57:35: #2 finished! INFO @ Tue, 30 Jun 2020 01:57:35: #2 predicted fragment length is 31 bps INFO @ Tue, 30 Jun 2020 01:57:35: #2 alternative fragment length(s) may be 3,31,588 bps INFO @ Tue, 30 Jun 2020 01:57:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.10_model.r WARNING @ Tue, 30 Jun 2020 01:57:35: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:57:35: #2 You may need to consider one of the other alternative d(s): 3,31,588 WARNING @ Tue, 30 Jun 2020 01:57:35: #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 01:57:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:57:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:57:36: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:57:37: 7000000 INFO @ Tue, 30 Jun 2020 01:57:42: 8000000 INFO @ Tue, 30 Jun 2020 01:57:47: 9000000 INFO @ Tue, 30 Jun 2020 01:57:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:57:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:57:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.05_summits.bed INFO @ Tue, 30 Jun 2020 01:57:49: Done! pass1 - making usageList (507 chroms): 2 millis pass2 - checking and writing primary data (2196 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:57:52: 10000000 INFO @ Tue, 30 Jun 2020 01:57:58: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:57:59: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:58:03: 12000000 INFO @ Tue, 30 Jun 2020 01:58:08: 13000000 INFO @ Tue, 30 Jun 2020 01:58:10: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:58:10: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:58:10: #1 total tags in treatment: 13351026 INFO @ Tue, 30 Jun 2020 01:58:10: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:58:10: #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 01:58:11: #1 tags after filtering in treatment: 13351024 INFO @ Tue, 30 Jun 2020 01:58:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:58:11: #1 finished! INFO @ Tue, 30 Jun 2020 01:58:11: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:58:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:58:11: #2 number of paired peaks: 356 WARNING @ Tue, 30 Jun 2020 01:58:11: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Tue, 30 Jun 2020 01:58:11: start model_add_line... INFO @ Tue, 30 Jun 2020 01:58:12: start X-correlation... INFO @ Tue, 30 Jun 2020 01:58:12: end of X-cor INFO @ Tue, 30 Jun 2020 01:58:12: #2 finished! INFO @ Tue, 30 Jun 2020 01:58:12: #2 predicted fragment length is 31 bps INFO @ Tue, 30 Jun 2020 01:58:12: #2 alternative fragment length(s) may be 3,31,588 bps INFO @ Tue, 30 Jun 2020 01:58:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.20_model.r WARNING @ Tue, 30 Jun 2020 01:58:12: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:58:12: #2 You may need to consider one of the other alternative d(s): 3,31,588 WARNING @ Tue, 30 Jun 2020 01:58:12: #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 01:58:12: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:58:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:58:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:58:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:58:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.10_summits.bed INFO @ Tue, 30 Jun 2020 01:58:12: Done! pass1 - making usageList (350 chroms): 1 millis pass2 - checking and writing primary data (1211 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:58:38: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:58:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:58:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:58:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025482/SRX025482.20_summits.bed INFO @ Tue, 30 Jun 2020 01:58:50: Done! pass1 - making usageList (115 chroms): 1 millis pass2 - checking and writing primary data (241 records, 4 fields): 5 millis CompletedMACS2peakCalling