Job ID = 14172851 SRX = SRX7434126 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: 00:05:28 21964160 reads; of these: 21964160 (100.00%) were unpaired; of these: 3293399 (14.99%) aligned 0 times 14330878 (65.25%) aligned exactly 1 time 4339883 (19.76%) aligned >1 times 85.01% overall alignment rate Time searching: 00:05:28 Overall time: 00:05:28 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] 3285345 / 18670761 = 0.1760 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 17:17:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.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 @ Sat, 11 Dec 2021 17:17:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 17:17:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 17:17:29: 1000000 INFO @ Sat, 11 Dec 2021 17:17:35: 2000000 INFO @ Sat, 11 Dec 2021 17:17:41: 3000000 INFO @ Sat, 11 Dec 2021 17:17:47: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 17:17:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.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 @ Sat, 11 Dec 2021 17:17:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 17:17:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 17:17:53: 5000000 INFO @ Sat, 11 Dec 2021 17:17:58: 1000000 INFO @ Sat, 11 Dec 2021 17:18:00: 6000000 INFO @ Sat, 11 Dec 2021 17:18:04: 2000000 INFO @ Sat, 11 Dec 2021 17:18:07: 7000000 INFO @ Sat, 11 Dec 2021 17:18:10: 3000000 INFO @ Sat, 11 Dec 2021 17:18:13: 8000000 INFO @ Sat, 11 Dec 2021 17:18:16: 4000000 INFO @ Sat, 11 Dec 2021 17:18:20: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 17:18:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.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 @ Sat, 11 Dec 2021 17:18:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 17:18:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 17:18:22: 5000000 INFO @ Sat, 11 Dec 2021 17:18:26: 10000000 INFO @ Sat, 11 Dec 2021 17:18:28: 6000000 INFO @ Sat, 11 Dec 2021 17:18:29: 1000000 INFO @ Sat, 11 Dec 2021 17:18:33: 11000000 INFO @ Sat, 11 Dec 2021 17:18:34: 7000000 INFO @ Sat, 11 Dec 2021 17:18:36: 2000000 INFO @ Sat, 11 Dec 2021 17:18:40: 12000000 INFO @ Sat, 11 Dec 2021 17:18:40: 8000000 INFO @ Sat, 11 Dec 2021 17:18:43: 3000000 INFO @ Sat, 11 Dec 2021 17:18:46: 9000000 INFO @ Sat, 11 Dec 2021 17:18:47: 13000000 INFO @ Sat, 11 Dec 2021 17:18:49: 4000000 INFO @ Sat, 11 Dec 2021 17:18:52: 10000000 INFO @ Sat, 11 Dec 2021 17:18:53: 14000000 INFO @ Sat, 11 Dec 2021 17:18:56: 5000000 INFO @ Sat, 11 Dec 2021 17:18:58: 11000000 INFO @ Sat, 11 Dec 2021 17:19:00: 15000000 INFO @ Sat, 11 Dec 2021 17:19:03: 6000000 INFO @ Sat, 11 Dec 2021 17:19:03: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 17:19:03: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 17:19:03: #1 total tags in treatment: 15385416 INFO @ Sat, 11 Dec 2021 17:19:03: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 17:19:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 17:19:03: #1 tags after filtering in treatment: 15385346 INFO @ Sat, 11 Dec 2021 17:19:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 17:19:03: #1 finished! INFO @ Sat, 11 Dec 2021 17:19:03: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 17:19:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 17:19:04: #2 number of paired peaks: 172 WARNING @ Sat, 11 Dec 2021 17:19:04: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 11 Dec 2021 17:19:04: start model_add_line... INFO @ Sat, 11 Dec 2021 17:19:04: start X-correlation... INFO @ Sat, 11 Dec 2021 17:19:04: end of X-cor INFO @ Sat, 11 Dec 2021 17:19:04: #2 finished! INFO @ Sat, 11 Dec 2021 17:19:04: #2 predicted fragment length is 71 bps INFO @ Sat, 11 Dec 2021 17:19:04: #2 alternative fragment length(s) may be 4,71 bps INFO @ Sat, 11 Dec 2021 17:19:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.05_model.r WARNING @ Sat, 11 Dec 2021 17:19:04: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 17:19:04: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Sat, 11 Dec 2021 17:19:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 17:19:04: #3 Call peaks... INFO @ Sat, 11 Dec 2021 17:19:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 17:19:04: 12000000 INFO @ Sat, 11 Dec 2021 17:19:09: 7000000 INFO @ Sat, 11 Dec 2021 17:19:11: 13000000 INFO @ Sat, 11 Dec 2021 17:19:16: 8000000 INFO @ Sat, 11 Dec 2021 17:19:17: 14000000 INFO @ Sat, 11 Dec 2021 17:19:22: 9000000 INFO @ Sat, 11 Dec 2021 17:19:23: 15000000 INFO @ Sat, 11 Dec 2021 17:19:25: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 17:19:25: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 17:19:25: #1 total tags in treatment: 15385416 INFO @ Sat, 11 Dec 2021 17:19:25: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 17:19:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 17:19:26: #1 tags after filtering in treatment: 15385346 INFO @ Sat, 11 Dec 2021 17:19:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 17:19:26: #1 finished! INFO @ Sat, 11 Dec 2021 17:19:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 17:19:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 17:19:27: #2 number of paired peaks: 172 WARNING @ Sat, 11 Dec 2021 17:19:27: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 11 Dec 2021 17:19:27: start model_add_line... INFO @ Sat, 11 Dec 2021 17:19:27: start X-correlation... INFO @ Sat, 11 Dec 2021 17:19:27: end of X-cor INFO @ Sat, 11 Dec 2021 17:19:27: #2 finished! INFO @ Sat, 11 Dec 2021 17:19:27: #2 predicted fragment length is 71 bps INFO @ Sat, 11 Dec 2021 17:19:27: #2 alternative fragment length(s) may be 4,71 bps INFO @ Sat, 11 Dec 2021 17:19:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.10_model.r WARNING @ Sat, 11 Dec 2021 17:19:27: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 17:19:27: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Sat, 11 Dec 2021 17:19:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 17:19:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 17:19:27: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 17:19:29: 10000000 INFO @ Sat, 11 Dec 2021 17:19:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 17:19:35: 11000000 INFO @ Sat, 11 Dec 2021 17:19:42: 12000000 INFO @ Sat, 11 Dec 2021 17:19:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.05_peaks.xls INFO @ Sat, 11 Dec 2021 17:19:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 17:19:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.05_summits.bed INFO @ Sat, 11 Dec 2021 17:19:45: Done! pass1 - making usageList (669 chroms): 1 millis pass2 - checking and writing primary data (3101 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 17:19:48: 13000000 INFO @ Sat, 11 Dec 2021 17:19:55: 14000000 INFO @ Sat, 11 Dec 2021 17:19:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 17:20:01: 15000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 17:20:04: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 17:20:04: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 17:20:04: #1 total tags in treatment: 15385416 INFO @ Sat, 11 Dec 2021 17:20:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 17:20:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 17:20:04: #1 tags after filtering in treatment: 15385346 INFO @ Sat, 11 Dec 2021 17:20:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 17:20:04: #1 finished! INFO @ Sat, 11 Dec 2021 17:20:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 17:20:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 17:20:05: #2 number of paired peaks: 172 WARNING @ Sat, 11 Dec 2021 17:20:05: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 11 Dec 2021 17:20:05: start model_add_line... INFO @ Sat, 11 Dec 2021 17:20:05: start X-correlation... INFO @ Sat, 11 Dec 2021 17:20:05: end of X-cor INFO @ Sat, 11 Dec 2021 17:20:05: #2 finished! INFO @ Sat, 11 Dec 2021 17:20:05: #2 predicted fragment length is 71 bps INFO @ Sat, 11 Dec 2021 17:20:05: #2 alternative fragment length(s) may be 4,71 bps INFO @ Sat, 11 Dec 2021 17:20:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.20_model.r WARNING @ Sat, 11 Dec 2021 17:20:05: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 17:20:05: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Sat, 11 Dec 2021 17:20:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 17:20:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 17:20:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 17:20:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.10_peaks.xls INFO @ Sat, 11 Dec 2021 17:20:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 17:20:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.10_summits.bed INFO @ Sat, 11 Dec 2021 17:20:08: Done! pass1 - making usageList (515 chroms): 1 millis pass2 - checking and writing primary data (1653 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 17:20:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 17:20:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.20_peaks.xls INFO @ Sat, 11 Dec 2021 17:20:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 17:20:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7434126/SRX7434126.20_summits.bed INFO @ Sat, 11 Dec 2021 17:20:45: Done! pass1 - making usageList (231 chroms): 0 millis pass2 - checking and writing primary data (464 records, 4 fields): 8 millis CompletedMACS2peakCalling