Job ID = 6529350 SRX = SRX2011088 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: 00:07:12 15423880 reads; of these: 15423880 (100.00%) were unpaired; of these: 590701 (3.83%) aligned 0 times 12088229 (78.37%) aligned exactly 1 time 2744950 (17.80%) aligned >1 times 96.17% overall alignment rate Time searching: 00:07:12 Overall time: 00:07:12 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] 963417 / 14833179 = 0.0650 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 01:59:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.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 01:59:18: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:59:18: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:59:24: 1000000 INFO @ Tue, 30 Jun 2020 01:59:29: 2000000 INFO @ Tue, 30 Jun 2020 01:59:35: 3000000 INFO @ Tue, 30 Jun 2020 01:59:40: 4000000 INFO @ Tue, 30 Jun 2020 01:59:46: 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 01:59:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.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 01:59:48: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:59:48: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:59:51: 6000000 INFO @ Tue, 30 Jun 2020 01:59:54: 1000000 INFO @ Tue, 30 Jun 2020 01:59:57: 7000000 INFO @ Tue, 30 Jun 2020 01:59:59: 2000000 INFO @ Tue, 30 Jun 2020 02:00:02: 8000000 INFO @ Tue, 30 Jun 2020 02:00:05: 3000000 INFO @ Tue, 30 Jun 2020 02:00:08: 9000000 INFO @ Tue, 30 Jun 2020 02:00:10: 4000000 INFO @ Tue, 30 Jun 2020 02:00:14: 10000000 INFO @ Tue, 30 Jun 2020 02:00:16: 5000000 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 02:00:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.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 02:00:18: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:00:18: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:00:19: 11000000 INFO @ Tue, 30 Jun 2020 02:00:21: 6000000 INFO @ Tue, 30 Jun 2020 02:00:25: 1000000 INFO @ Tue, 30 Jun 2020 02:00:25: 12000000 INFO @ Tue, 30 Jun 2020 02:00:27: 7000000 INFO @ Tue, 30 Jun 2020 02:00:31: 13000000 INFO @ Tue, 30 Jun 2020 02:00:31: 2000000 INFO @ Tue, 30 Jun 2020 02:00:32: 8000000 INFO @ Tue, 30 Jun 2020 02:00:36: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:00:36: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:00:36: #1 total tags in treatment: 13869762 INFO @ Tue, 30 Jun 2020 02:00:36: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:00:36: #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 02:00:37: #1 tags after filtering in treatment: 13869733 INFO @ Tue, 30 Jun 2020 02:00:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:00:37: #1 finished! INFO @ Tue, 30 Jun 2020 02:00:37: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:00:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:00:37: 3000000 INFO @ Tue, 30 Jun 2020 02:00:38: #2 number of paired peaks: 191 WARNING @ Tue, 30 Jun 2020 02:00:38: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Tue, 30 Jun 2020 02:00:38: start model_add_line... INFO @ Tue, 30 Jun 2020 02:00:38: start X-correlation... INFO @ Tue, 30 Jun 2020 02:00:38: end of X-cor INFO @ Tue, 30 Jun 2020 02:00:38: #2 finished! INFO @ Tue, 30 Jun 2020 02:00:38: #2 predicted fragment length is 99 bps INFO @ Tue, 30 Jun 2020 02:00:38: #2 alternative fragment length(s) may be 4,99 bps INFO @ Tue, 30 Jun 2020 02:00:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.05_model.r WARNING @ Tue, 30 Jun 2020 02:00:38: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:00:38: #2 You may need to consider one of the other alternative d(s): 4,99 WARNING @ Tue, 30 Jun 2020 02:00:38: #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 02:00:38: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:00:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:00:38: 9000000 INFO @ Tue, 30 Jun 2020 02:00:44: 4000000 INFO @ Tue, 30 Jun 2020 02:00:44: 10000000 INFO @ Tue, 30 Jun 2020 02:00:49: 11000000 INFO @ Tue, 30 Jun 2020 02:00:50: 5000000 INFO @ Tue, 30 Jun 2020 02:00:56: 12000000 INFO @ Tue, 30 Jun 2020 02:00:57: 6000000 INFO @ Tue, 30 Jun 2020 02:01:01: 13000000 INFO @ Tue, 30 Jun 2020 02:01:03: 7000000 INFO @ Tue, 30 Jun 2020 02:01:05: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:01:06: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:01:06: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:01:06: #1 total tags in treatment: 13869762 INFO @ Tue, 30 Jun 2020 02:01:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:01:06: #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 02:01:07: #1 tags after filtering in treatment: 13869733 INFO @ Tue, 30 Jun 2020 02:01:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:01:07: #1 finished! INFO @ Tue, 30 Jun 2020 02:01:07: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:01:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:01:08: #2 number of paired peaks: 191 WARNING @ Tue, 30 Jun 2020 02:01:08: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Tue, 30 Jun 2020 02:01:08: start model_add_line... INFO @ Tue, 30 Jun 2020 02:01:08: start X-correlation... INFO @ Tue, 30 Jun 2020 02:01:08: end of X-cor INFO @ Tue, 30 Jun 2020 02:01:08: #2 finished! INFO @ Tue, 30 Jun 2020 02:01:08: #2 predicted fragment length is 99 bps INFO @ Tue, 30 Jun 2020 02:01:08: #2 alternative fragment length(s) may be 4,99 bps INFO @ Tue, 30 Jun 2020 02:01:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.10_model.r WARNING @ Tue, 30 Jun 2020 02:01:08: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:01:08: #2 You may need to consider one of the other alternative d(s): 4,99 WARNING @ Tue, 30 Jun 2020 02:01:08: #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 02:01:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:01:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:01:09: 8000000 INFO @ Tue, 30 Jun 2020 02:01:15: 9000000 INFO @ Tue, 30 Jun 2020 02:01:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:01:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:01:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.05_summits.bed INFO @ Tue, 30 Jun 2020 02:01:18: Done! pass1 - making usageList (491 chroms): 1 millis pass2 - checking and writing primary data (1293 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:01:21: 10000000 INFO @ Tue, 30 Jun 2020 02:01:28: 11000000 INFO @ Tue, 30 Jun 2020 02:01:34: 12000000 INFO @ Tue, 30 Jun 2020 02:01:35: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:01:40: 13000000 INFO @ Tue, 30 Jun 2020 02:01:46: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:01:46: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:01:46: #1 total tags in treatment: 13869762 INFO @ Tue, 30 Jun 2020 02:01:46: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:01:46: #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 02:01:47: #1 tags after filtering in treatment: 13869733 INFO @ Tue, 30 Jun 2020 02:01:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:01:47: #1 finished! INFO @ Tue, 30 Jun 2020 02:01:47: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:01:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:01:48: #2 number of paired peaks: 191 WARNING @ Tue, 30 Jun 2020 02:01:48: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Tue, 30 Jun 2020 02:01:48: start model_add_line... INFO @ Tue, 30 Jun 2020 02:01:48: start X-correlation... INFO @ Tue, 30 Jun 2020 02:01:48: end of X-cor INFO @ Tue, 30 Jun 2020 02:01:48: #2 finished! INFO @ Tue, 30 Jun 2020 02:01:48: #2 predicted fragment length is 99 bps INFO @ Tue, 30 Jun 2020 02:01:48: #2 alternative fragment length(s) may be 4,99 bps INFO @ Tue, 30 Jun 2020 02:01:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.20_model.r WARNING @ Tue, 30 Jun 2020 02:01:48: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:01:48: #2 You may need to consider one of the other alternative d(s): 4,99 WARNING @ Tue, 30 Jun 2020 02:01:48: #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 02:01:48: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:01:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:01:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:01:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:01:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.10_summits.bed INFO @ Tue, 30 Jun 2020 02:01:48: Done! pass1 - making usageList (325 chroms): 1 millis pass2 - checking and writing primary data (660 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:02:15: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:02:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:02:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:02:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2011088/SRX2011088.20_summits.bed INFO @ Tue, 30 Jun 2020 02:02:28: Done! pass1 - making usageList (161 chroms): 1 millis pass2 - checking and writing primary data (283 records, 4 fields): 6 millis CompletedMACS2peakCalling