Job ID = 6529292 SRX = SRX1300696 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: 00:06:06 24483693 reads; of these: 24483693 (100.00%) were unpaired; of these: 1854789 (7.58%) aligned 0 times 16571039 (67.68%) aligned exactly 1 time 6057865 (24.74%) aligned >1 times 92.42% overall alignment rate Time searching: 00:06:06 Overall time: 00:06:06 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] 3359163 / 22628904 = 0.1484 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 02:35:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.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 02:35:17: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:35:17: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:35:24: 1000000 INFO @ Tue, 30 Jun 2020 02:35:30: 2000000 INFO @ Tue, 30 Jun 2020 02:35:36: 3000000 INFO @ Tue, 30 Jun 2020 02:35:42: 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 02:35:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.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 02:35:47: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:35:47: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:35:49: 5000000 INFO @ Tue, 30 Jun 2020 02:35:54: 1000000 INFO @ Tue, 30 Jun 2020 02:35:55: 6000000 INFO @ Tue, 30 Jun 2020 02:36:00: 2000000 INFO @ Tue, 30 Jun 2020 02:36:02: 7000000 INFO @ Tue, 30 Jun 2020 02:36:06: 3000000 INFO @ Tue, 30 Jun 2020 02:36:08: 8000000 INFO @ Tue, 30 Jun 2020 02:36:12: 4000000 INFO @ Tue, 30 Jun 2020 02:36:15: 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 02:36:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.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 02:36:17: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:36:17: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:36:18: 5000000 INFO @ Tue, 30 Jun 2020 02:36:22: 10000000 INFO @ Tue, 30 Jun 2020 02:36:24: 6000000 INFO @ Tue, 30 Jun 2020 02:36:24: 1000000 INFO @ Tue, 30 Jun 2020 02:36:28: 11000000 INFO @ Tue, 30 Jun 2020 02:36:30: 7000000 INFO @ Tue, 30 Jun 2020 02:36:31: 2000000 INFO @ Tue, 30 Jun 2020 02:36:35: 12000000 INFO @ Tue, 30 Jun 2020 02:36:36: 8000000 INFO @ Tue, 30 Jun 2020 02:36:38: 3000000 INFO @ Tue, 30 Jun 2020 02:36:42: 13000000 INFO @ Tue, 30 Jun 2020 02:36:42: 9000000 INFO @ Tue, 30 Jun 2020 02:36:45: 4000000 INFO @ Tue, 30 Jun 2020 02:36:48: 10000000 INFO @ Tue, 30 Jun 2020 02:36:49: 14000000 INFO @ Tue, 30 Jun 2020 02:36:52: 5000000 INFO @ Tue, 30 Jun 2020 02:36:54: 11000000 INFO @ Tue, 30 Jun 2020 02:36:55: 15000000 INFO @ Tue, 30 Jun 2020 02:36:58: 6000000 INFO @ Tue, 30 Jun 2020 02:37:00: 12000000 INFO @ Tue, 30 Jun 2020 02:37:03: 16000000 INFO @ Tue, 30 Jun 2020 02:37:05: 7000000 INFO @ Tue, 30 Jun 2020 02:37:06: 13000000 INFO @ Tue, 30 Jun 2020 02:37:10: 17000000 INFO @ Tue, 30 Jun 2020 02:37:12: 14000000 INFO @ Tue, 30 Jun 2020 02:37:12: 8000000 INFO @ Tue, 30 Jun 2020 02:37:16: 18000000 INFO @ Tue, 30 Jun 2020 02:37:18: 15000000 INFO @ Tue, 30 Jun 2020 02:37:19: 9000000 INFO @ Tue, 30 Jun 2020 02:37:23: 19000000 INFO @ Tue, 30 Jun 2020 02:37:24: 16000000 INFO @ Tue, 30 Jun 2020 02:37:25: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:37:25: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:37:25: #1 total tags in treatment: 19269741 INFO @ Tue, 30 Jun 2020 02:37:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:37:25: #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 02:37:26: 10000000 INFO @ Tue, 30 Jun 2020 02:37:26: #1 tags after filtering in treatment: 19269741 INFO @ Tue, 30 Jun 2020 02:37:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:37:26: #1 finished! INFO @ Tue, 30 Jun 2020 02:37:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:37:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:37:27: #2 number of paired peaks: 451 WARNING @ Tue, 30 Jun 2020 02:37:27: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Tue, 30 Jun 2020 02:37:27: start model_add_line... INFO @ Tue, 30 Jun 2020 02:37:27: start X-correlation... INFO @ Tue, 30 Jun 2020 02:37:27: end of X-cor INFO @ Tue, 30 Jun 2020 02:37:27: #2 finished! INFO @ Tue, 30 Jun 2020 02:37:27: #2 predicted fragment length is 31 bps INFO @ Tue, 30 Jun 2020 02:37:27: #2 alternative fragment length(s) may be 2,31,551,572 bps INFO @ Tue, 30 Jun 2020 02:37:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.05_model.r WARNING @ Tue, 30 Jun 2020 02:37:27: #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 02:37:27: #2 You may need to consider one of the other alternative d(s): 2,31,551,572 WARNING @ Tue, 30 Jun 2020 02:37:27: #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 02:37:27: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:37:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:37:31: 17000000 INFO @ Tue, 30 Jun 2020 02:37:32: 11000000 INFO @ Tue, 30 Jun 2020 02:37:37: 18000000 INFO @ Tue, 30 Jun 2020 02:37:39: 12000000 INFO @ Tue, 30 Jun 2020 02:37:43: 19000000 INFO @ Tue, 30 Jun 2020 02:37:45: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:37:45: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:37:45: #1 total tags in treatment: 19269741 INFO @ Tue, 30 Jun 2020 02:37:45: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:37:45: #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 02:37:45: #1 tags after filtering in treatment: 19269741 INFO @ Tue, 30 Jun 2020 02:37:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:37:45: #1 finished! INFO @ Tue, 30 Jun 2020 02:37:45: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:37:45: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:37:46: 13000000 INFO @ Tue, 30 Jun 2020 02:37:47: #2 number of paired peaks: 451 WARNING @ Tue, 30 Jun 2020 02:37:47: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Tue, 30 Jun 2020 02:37:47: start model_add_line... INFO @ Tue, 30 Jun 2020 02:37:47: start X-correlation... INFO @ Tue, 30 Jun 2020 02:37:47: end of X-cor INFO @ Tue, 30 Jun 2020 02:37:47: #2 finished! INFO @ Tue, 30 Jun 2020 02:37:47: #2 predicted fragment length is 31 bps INFO @ Tue, 30 Jun 2020 02:37:47: #2 alternative fragment length(s) may be 2,31,551,572 bps INFO @ Tue, 30 Jun 2020 02:37:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.10_model.r WARNING @ Tue, 30 Jun 2020 02:37:47: #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 02:37:47: #2 You may need to consider one of the other alternative d(s): 2,31,551,572 WARNING @ Tue, 30 Jun 2020 02:37:47: #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 02:37:47: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:37:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:37:52: 14000000 INFO @ Tue, 30 Jun 2020 02:37:59: 15000000 INFO @ Tue, 30 Jun 2020 02:38:02: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:38:05: 16000000 INFO @ Tue, 30 Jun 2020 02:38:11: 17000000 INFO @ Tue, 30 Jun 2020 02:38:17: 18000000 INFO @ Tue, 30 Jun 2020 02:38:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:38:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:38:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.05_summits.bed INFO @ Tue, 30 Jun 2020 02:38:18: Done! pass1 - making usageList (631 chroms): 1 millis pass2 - checking and writing primary data (2641 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:38:20: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:38:22: 19000000 INFO @ Tue, 30 Jun 2020 02:38:24: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:38:24: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:38:24: #1 total tags in treatment: 19269741 INFO @ Tue, 30 Jun 2020 02:38:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:38:24: #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 02:38:24: #1 tags after filtering in treatment: 19269741 INFO @ Tue, 30 Jun 2020 02:38:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:38:24: #1 finished! INFO @ Tue, 30 Jun 2020 02:38:24: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:38:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:38:26: #2 number of paired peaks: 451 WARNING @ Tue, 30 Jun 2020 02:38:26: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Tue, 30 Jun 2020 02:38:26: start model_add_line... INFO @ Tue, 30 Jun 2020 02:38:26: start X-correlation... INFO @ Tue, 30 Jun 2020 02:38:26: end of X-cor INFO @ Tue, 30 Jun 2020 02:38:26: #2 finished! INFO @ Tue, 30 Jun 2020 02:38:26: #2 predicted fragment length is 31 bps INFO @ Tue, 30 Jun 2020 02:38:26: #2 alternative fragment length(s) may be 2,31,551,572 bps INFO @ Tue, 30 Jun 2020 02:38:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.20_model.r WARNING @ Tue, 30 Jun 2020 02:38:26: #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 02:38:26: #2 You may need to consider one of the other alternative d(s): 2,31,551,572 WARNING @ Tue, 30 Jun 2020 02:38:26: #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 02:38:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:38:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:38:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:38:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:38:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.10_summits.bed INFO @ Tue, 30 Jun 2020 02:38:36: Done! pass1 - making usageList (490 chroms): 1 millis pass2 - checking and writing primary data (1929 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:39:00: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:39:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:39:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:39:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1300696/SRX1300696.20_summits.bed INFO @ Tue, 30 Jun 2020 02:39:16: Done! pass1 - making usageList (240 chroms): 1 millis pass2 - checking and writing primary data (471 records, 4 fields): 8 millis CompletedMACS2peakCalling