Job ID = 6529389 SRX = SRX2325649 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: 00:11:58 53329806 reads; of these: 53329806 (100.00%) were unpaired; of these: 40498676 (75.94%) aligned 0 times 9987988 (18.73%) aligned exactly 1 time 2843142 (5.33%) aligned >1 times 24.06% overall alignment rate Time searching: 00:11:58 Overall time: 00:11:58 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] 5817312 / 12831130 = 0.4534 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 02:17:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.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 02:17:06: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:17:06: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:17:13: 1000000 INFO @ Tue, 30 Jun 2020 02:17:20: 2000000 INFO @ Tue, 30 Jun 2020 02:17:27: 3000000 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 02:17:34: 4000000 INFO @ Tue, 30 Jun 2020 02:17:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.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 02:17:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:17:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:17:41: 5000000 INFO @ Tue, 30 Jun 2020 02:17:42: 1000000 INFO @ Tue, 30 Jun 2020 02:17:48: 2000000 INFO @ Tue, 30 Jun 2020 02:17:49: 6000000 INFO @ Tue, 30 Jun 2020 02:17:54: 3000000 INFO @ Tue, 30 Jun 2020 02:17:57: 7000000 INFO @ Tue, 30 Jun 2020 02:17:57: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 02:17:57: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 02:17:57: #1 total tags in treatment: 7013818 INFO @ Tue, 30 Jun 2020 02:17:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:17:57: #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 02:17:58: #1 tags after filtering in treatment: 7013808 INFO @ Tue, 30 Jun 2020 02:17:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:17:58: #1 finished! INFO @ Tue, 30 Jun 2020 02:17:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:17:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:17:58: #2 number of paired peaks: 491 WARNING @ Tue, 30 Jun 2020 02:17:58: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Tue, 30 Jun 2020 02:17:58: start model_add_line... INFO @ Tue, 30 Jun 2020 02:17:58: start X-correlation... INFO @ Tue, 30 Jun 2020 02:17:58: end of X-cor INFO @ Tue, 30 Jun 2020 02:17:58: #2 finished! INFO @ Tue, 30 Jun 2020 02:17:58: #2 predicted fragment length is 89 bps INFO @ Tue, 30 Jun 2020 02:17:58: #2 alternative fragment length(s) may be 89 bps INFO @ Tue, 30 Jun 2020 02:17:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.05_model.r WARNING @ Tue, 30 Jun 2020 02:17:58: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:17:58: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Tue, 30 Jun 2020 02:17:58: #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 02:17:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:17:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:18:00: 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 @ Tue, 30 Jun 2020 02:18:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.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 02:18:06: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:18:06: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:18:06: 5000000 INFO @ Tue, 30 Jun 2020 02:18:12: 1000000 INFO @ Tue, 30 Jun 2020 02:18:13: 6000000 INFO @ Tue, 30 Jun 2020 02:18:15: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:18:18: 2000000 INFO @ Tue, 30 Jun 2020 02:18:19: 7000000 INFO @ Tue, 30 Jun 2020 02:18:20: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 02:18:20: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 02:18:20: #1 total tags in treatment: 7013818 INFO @ Tue, 30 Jun 2020 02:18:20: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:18:20: #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 02:18:20: #1 tags after filtering in treatment: 7013808 INFO @ Tue, 30 Jun 2020 02:18:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:18:20: #1 finished! INFO @ Tue, 30 Jun 2020 02:18:20: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:18:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:18:21: #2 number of paired peaks: 491 WARNING @ Tue, 30 Jun 2020 02:18:21: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Tue, 30 Jun 2020 02:18:21: start model_add_line... INFO @ Tue, 30 Jun 2020 02:18:21: start X-correlation... INFO @ Tue, 30 Jun 2020 02:18:21: end of X-cor INFO @ Tue, 30 Jun 2020 02:18:21: #2 finished! INFO @ Tue, 30 Jun 2020 02:18:21: #2 predicted fragment length is 89 bps INFO @ Tue, 30 Jun 2020 02:18:21: #2 alternative fragment length(s) may be 89 bps INFO @ Tue, 30 Jun 2020 02:18:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.10_model.r WARNING @ Tue, 30 Jun 2020 02:18:21: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:18:21: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Tue, 30 Jun 2020 02:18:21: #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 02:18:21: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:18:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:18:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:18:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:18:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.05_summits.bed INFO @ Tue, 30 Jun 2020 02:18:23: Done! INFO @ Tue, 30 Jun 2020 02:18:24: 3000000 pass1 - making usageList (585 chroms): 2 millis pass2 - checking and writing primary data (1536 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:18:30: 4000000 INFO @ Tue, 30 Jun 2020 02:18:36: 5000000 INFO @ Tue, 30 Jun 2020 02:18:37: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:18:42: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:18:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:18:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:18:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.10_summits.bed INFO @ Tue, 30 Jun 2020 02:18:46: Done! pass1 - making usageList (352 chroms): 1 millis pass2 - checking and writing primary data (688 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:18:49: 7000000 INFO @ Tue, 30 Jun 2020 02:18:49: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 02:18:49: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 02:18:49: #1 total tags in treatment: 7013818 INFO @ Tue, 30 Jun 2020 02:18:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:18:49: #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 02:18:49: #1 tags after filtering in treatment: 7013808 INFO @ Tue, 30 Jun 2020 02:18:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:18:49: #1 finished! INFO @ Tue, 30 Jun 2020 02:18:49: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:18:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:18:50: #2 number of paired peaks: 491 WARNING @ Tue, 30 Jun 2020 02:18:50: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Tue, 30 Jun 2020 02:18:50: start model_add_line... INFO @ Tue, 30 Jun 2020 02:18:50: start X-correlation... INFO @ Tue, 30 Jun 2020 02:18:50: end of X-cor INFO @ Tue, 30 Jun 2020 02:18:50: #2 finished! INFO @ Tue, 30 Jun 2020 02:18:50: #2 predicted fragment length is 89 bps INFO @ Tue, 30 Jun 2020 02:18:50: #2 alternative fragment length(s) may be 89 bps INFO @ Tue, 30 Jun 2020 02:18:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.20_model.r WARNING @ Tue, 30 Jun 2020 02:18:50: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:18:50: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Tue, 30 Jun 2020 02:18:50: #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 02:18:50: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:18:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:19:07: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:19:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:19:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:19:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325649/SRX2325649.20_summits.bed INFO @ Tue, 30 Jun 2020 02:19:15: Done! pass1 - making usageList (145 chroms): 1 millis pass2 - checking and writing primary data (284 records, 4 fields): 6 millis CompletedMACS2peakCalling